@article {pmid38785034,
year = {2024},
author = {McEachran, MC and Harvey, JA and Mummah, RO and Bletz, MC and Teitelbaum, CS and Rosenblatt, E and Rudolph, FJ and Arce, F and Yin, S and Prosser, DJ and Mosher, BA and Mullinax, JM and DiRenzo, GV and Couret, J and Runge, MC and Grant, EHC and Cook, JD},
title = {Reframing wildlife disease management problems with decision analysis.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {38},
number = {4},
pages = {e14284},
doi = {10.1111/cobi.14284},
pmid = {38785034},
issn = {1523-1739},
support = {//National Science Foundation/ ; 2200310//PIPP Phase 1: International Center for Avian Influenza Pandemic Prediction and Prevention/ ; P.L. 116-136//Coronavirus Aid, Relief, and Economic Security Act/ ; },
mesh = {Animals ; *Animals, Wild ; *Decision Support Techniques ; *Conservation of Natural Resources/methods ; *Decision Making ; COVID-19/epidemiology ; SARS-CoV-2 ; Uncertainty ; },
abstract = {Contemporary wildlife disease management is complex because managers need to respond to a wide range of stakeholders, multiple uncertainties, and difficult trade-offs that characterize the interconnected challenges of today. Despite general acknowledgment of these complexities, managing wildlife disease tends to be framed as a scientific problem, in which the major challenge is lack of knowledge. The complex and multifactorial process of decision-making is collapsed into a scientific endeavor to reduce uncertainty. As a result, contemporary decision-making may be oversimplified, rely on simple heuristics, and fail to account for the broader legal, social, and economic context in which the decisions are made. Concurrently, scientific research on wildlife disease may be distant from this decision context, resulting in information that may not be directly relevant to the pertinent management questions. We propose reframing wildlife disease management challenges as decision problems and addressing them with decision analytical tools to divide the complex problems into more cognitively manageable elements. In particular, structured decision-making has the potential to improve the quality, rigor, and transparency of decisions about wildlife disease in a variety of systems. Examples of management of severe acute respiratory syndrome coronavirus 2, white-nose syndrome, avian influenza, and chytridiomycosis illustrate the most common impediments to decision-making, including competing objectives, risks, prediction uncertainty, and limited resources.},
}

Animals
*Animals, Wild
*Decision Support Techniques
*Conservation of Natural Resources/methods
*Decision Making
COVID-19/epidemiology
SARS-CoV-2
Uncertainty

@article {pmid38708866,
year = {2024},
author = {Villarreal-Rosas, J and Brown, CJ and Andradi-Brown, DA and Domínguez, R and Jacobo, P and Martínez, A and Mascote, C and Najera, E and Paiz, Y and Vázquez Moran, VH and Villarreal, J and Adame, MF},
title = {Integrating socioeconomic and ecological data into restoration practice.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {38},
number = {4},
pages = {e14286},
doi = {10.1111/cobi.14286},
pmid = {38708866},
issn = {1523-1739},
support = {//Advance Queensland Industry Research Fellowship/ ; //Jeremy and Hannelore Grantham Environmental Trust/ ; FT210100792//Australian Research Council/ ; },
mesh = {*Conservation of Natural Resources/methods/economics ; Mexico ; *Socioeconomic Factors ; Environmental Restoration and Remediation/economics ; Ecosystem ; Decision Support Techniques ; },
abstract = {Driven by the United Nations Decade on Restoration and international funding initiatives, such as the Mangrove Breakthrough, investment in mangrove restoration is expected to increase. Yet, mangrove restoration efforts frequently fail, usually because of ad hoc site-selection processes that do not consider mangrove ecology and the socioeconomic context. Using decision analysis, we developed an approach that accounts for socioeconomic and ecological data to identify sites with the highest likelihood of mangrove restoration success. We applied our approach in the Biosphere Reserve Marismas Nacionales Nayarit, Mexico, an area that recently received funding for implementing mangrove restoration actions. We identified 468 potential restoration sites, assessed their restorability potential based on socioeconomic and ecological metrics, and ranked sites for implementation with spatial optimization. The metrics we used included favorable conditions for propagules to establish and survive under sea-level rise, provision of ecosystem services, and community dynamics. Sites that were selected based on socioeconomic or ecological metrics alone had lower likelihood of mangrove restoration success than sites that were selected based on integrated socioeconomic and ecological metrics. For example, selecting sites based on only socioeconomic metrics captured 16% of the maximum attainable value of functioning mangroves able to provide propagules to potential restoration sites, whereas selecting sites based on ecological and socioeconomic metrics captured 46% of functioning mangroves. Our approach was developed as part of a collaboration between nongovernmental organizations, local government, and academics under rapid delivery time lines given preexisting mangrove restoration implementation commitments. The systematic decision process we used integrated socioeconomic and ecological considerations even under short delivery deadlines, and our approach can be adapted to help mangrove restoration site-selection decisions elsewhere.},
}

*Conservation of Natural Resources/methods/economics
Mexico
*Socioeconomic Factors
Environmental Restoration and Remediation/economics
Ecosystem
Decision Support Techniques

@article {pmid39032150,
year = {2024},
author = {Kim, J and Foo, JC and Murata, T and Togo, F},
title = {Reduced heart rate variability is related to fluctuations in psychological stress levels in daily life.},
journal = {Stress and health : journal of the International Society for the Investigation of Stress},
volume = {},
number = {},
pages = {e3447},
doi = {10.1002/smi.3447},
pmid = {39032150},
issn = {1532-2998},
support = {19K24283//Japan Society for the Promotion of Science/ ; 21K17681//Japan Society for the Promotion of Science/ ; 031L0190A//Bundesministerium für Bildung und Forschung/ ; },
abstract = {Laboratory-based studies have shown that psychological stress caused by response to various stressors triggers acute changes in the cardiovascular system. A better understanding is needed of the emerging evidence on temporal associations between psychological stress and cardiovascular responses in natural settings. This study examined the association of psychological stress and heart rate variability (HRV) in daily life, at high resolution over 2 weeks, taking the effect of physical activity into account. Participants (n = 34) completed ecological momentary assessments (EMA) 6 times per day, reporting levels of perceived stress, low-arousal negative affect (LNA), and high-arousal negative affect. Chest-mounted heart-rate monitors were worn to assess HRV. Multilevel models were used to examine the association between psychological stress levels and preceding/subsequent HRV. Reduced time domain HRV measures (mean and standard deviation of R-wave to R-wave intervals) during the prior hour predicted higher levels of perceived stress. Frequency domain HRV measures higher low to high frequency (LF/HF) and lower HF to total power (HF nu) ratios during the preceding 10 min predicted higher perceived stress levels, suggesting the dominance of sympathetic nervous system activity. EMA reports of higher perceived stress levels were associated with reduced time domain HRV measures during the following 10 min. On the other hand, higher LNA were related to increased HRV measures, such as lower LF/HF and higher HF nu during the following hour. The dynamic associations observed may have therapeutic implications for 'just-in-time' interventions in the management of daily stress and cardiovascular health.},
}

@article {pmid39031697,
year = {2024},
author = {Zembere, K and Jones, CM and Mthawanji, R and Nkolokosa, C and Kamwezi, R and Kalonde, PK and Stanton, MC},
title = {Small dams drive Anopheles abundance during the dry season in a high malaria burden area of Malawi.},
journal = {Medical and veterinary entomology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mve.12733},
pmid = {39031697},
issn = {1365-2915},
support = {215184/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; },
abstract = {This study explores the influence of small dams on the exposure to malaria vectors during the dry season in Kasungu district, Malawi, an area recently identified as high priority for malaria interventions by the National Malaria Control Programme. Small dam impoundments provide communities with a continuous supply of water for domestic and agricultural activities across sub-Saharan Africa and are considered vital to food security and climate change resilience. However, these permanent water bodies also create ideal breeding sites for mosquitoes in typically arid landscapes. The study focuses on a specific dam impoundment and its vicinity, aiming to assess its spatial and temporal influence on indoor vector densities. From May to August 2021, CDC light traps were used to measure indoor mosquito densities for two consecutive nights per month in three communities located at increasing distances from the dam (0, ~1 and ~2 km). Simultaneously, drone imagery was captured for each community, enabling the identification of additional standing water within approximately 400 m of selected households. Larval sampling was carried out within the impoundment periphery and in additional water bodies identified in the drone imagery. Generalised linear mixed models (GLMMs) were employed to analyse the indoor Anopheles abundance data, estimating the effects of household structure (open/closed eaves), month, temperature and water proximity on malaria vector exposure. Throughout 685 trapping nights, a total of 1256 mosquitoes were captured, with 33% (412) being female Anopheles. Among these, 91% were morphologically identified as Anopheles funestus s.l., and 5% as Anopheles gambiae s.l. Catches progressively decline in each consecutive trapping month as the environment became drier. This decline was much slower in Malangano, the community next to the dam, with abundance being notably higher in June and July. Further, the majority of An. gambiae s.l. were caught in May, with none identified in July and August. Anopheles larvae were found both in the impoundment and other smaller water bodies such as irrigation wells in each survey month; however, the presence of these smaller water bodies did not have a significant impact on adult female mosquito catches in the GLMM. The study concludes that proximity to the dam impoundment was the primary driver of differences between survey communities with the abundance in Chikhombwe (~1 km away) and Chiponde (~2 km away) being 0.35 (95% confidence interval [CI], 0.19-0.66) and 0.28 (95% CI, 0.16-0.47) lower than Malangano, respectively, after adjusting for other factors. These findings underscore the importance of targeted interventions, such as larval source management or housing improvements, near small dams to mitigate malaria transmission risks during the dry season. Further research is needed to develop cost-effective strategies for vector control within and around these impoundments.},
}

@article {pmid39027808,
year = {2024},
author = {Falk, S and Poole, O and , and , and , and , and , and , and , },
title = {The genome sequence of a hoverfly, Cheilosia impressa (Loew, 1840).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {74},
pmid = {39027808},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Cheilosia impressa (hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 395.0 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.87 kilobases in length.},
}

@article {pmid39026607,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Brindled Beauty, Lycia hirtaria (Clerck, 1759).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {303},
pmid = {39026607},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Lycia hirtaria (the Brindled Beauty; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 552.0 megabases in span. Most of the assembly is scaffolded into 14 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.58 kilobases in length.},
}

@article {pmid39026606,
year = {2023},
author = {Boyes, D and Crowley, LM and Boyes, C and , and , and , and , and , and , },
title = {The genome sequence of the Little Grey, Eudonia lacustrata (Panzer, 1804).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {302},
pmid = {39026606},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Eudonia lacustrata (the Little Grey; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 699.5 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.29 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,652 protein coding genes.},
}

@article {pmid39026203,
year = {2024},
author = {Piacenza, F and Di Rosa, M and Soraci, L and Montesanto, A and Corsonello, A and Cherubini, A and Fabbietti, P and Provinciali, M and Lisa, R and Bonfigli, AR and Filicetti, E and Greco, GI and Muglia, L and Lattanzio, F and Volpentesta, M and Biscetti, L},
title = {Interactions between patterns of multimorbidity and functional status among hospitalized older patients: a novel approach using cluster analysis and association rule mining.},
journal = {Journal of translational medicine},
volume = {22},
number = {1},
pages = {669},
pmid = {39026203},
issn = {1479-5876},
support = {RF-2013-02358848//Ministero della Salute/ ; },
mesh = {Humans ; Male ; Female ; *Multimorbidity ; Aged ; Cluster Analysis ; *Hospitalization ; Aged, 80 and over ; *Activities of Daily Living ; Functional Status ; Data Mining ; Retrospective Studies ; },
abstract = {BACKGROUND: Multimorbidity (MM) is generally defined as the presence of 2 or more chronic diseases in the same patient and seems to be frequently associated with frailty and poor quality of life. However, the complex interplay between MM and functional status in hospitalized older patients has not been fully elucidated so far. Here, we implemented a 2-step approach, combining cluster analysis and association rule mining to explore how patterns of MM and disease associations change as a function of disability.

METHODS: This retrospective cohort study included 3366 hospitalized older patients discharged from acute care units of Ancona and Cosenza sites of Italian National Institute on Aging (INRCA-IRCCS) between 2011 and 2017. Cluster analysis and association rule mining (ARM) were used to explore patterns of MM and disease associations in the whole population and after stratifying by dependency in activities of daily living (ADL) at discharge. Sensitivity analyses in men and women were conducted to test for robustness of study findings.

RESULTS: Out of 3366 included patients, 78% were multimorbid. According to functional status, 22.2% of patients had no disability in ADL (functionally independent group), 22.7% had 1 ADL dependency (mildly dependent group), and 57.4% 2 or more ADL impaired (moderately-severely dependent group). Two main MM clusters were identified in the whole general population and in single ADL groups. ARM revealed interesting within-cluster disease associations, characterized by high lift and confidence. Specifically, in the functionally independent group, the most significant ones involved atrial fibrillation (AF)-anemia and chronic kidney disease (CKD) (lift = 2.32), followed by coronary artery disease (CAD)-AF and heart failure (HF) (lift = 2.29); in patients with moderate-severe ADL disability, the most significant ARM involved CAD-HF and AF (lift = 1.97), thyroid dysfunction and AF (lift = 1.75), cerebrovascular disease (CVD)-CAD and AF (lift = 1.55), and hypertension-anemia and CKD (lift = 1.43).

CONCLUSIONS: Hospitalized older patients have high rates of MM and functional impairment. Combining cluster analysis to ARM may assist physicians in discovering unexpected disease associations in patients with different ADL status. This could be relevant in the view of individuating personalized diagnostic and therapeutic approaches, according to the modern principles of precision medicine.},
}

Humans
Male
Female
*Multimorbidity
Aged
Cluster Analysis
*Hospitalization
Aged, 80 and over
*Activities of Daily Living
Functional Status
Data Mining
Retrospective Studies

@article {pmid39024004,
year = {2024},
author = {Hernandez, R and Hoogendoorn, C and Gonzalez, JS and Pyatak, EA and Crespo-Ramos, G and Schneider, S},
title = {Reliability and Validity of Ecological Momentary Assessment Response Time-Based Measures of Emotional Clarity: Secondary Data Analysis.},
journal = {JMIR mental health},
volume = {11},
number = {},
pages = {e58352},
doi = {10.2196/58352},
pmid = {39024004},
issn = {2368-7959},
mesh = {Humans ; *Ecological Momentary Assessment ; Female ; Male ; Reproducibility of Results ; Adult ; *Emotions ; Middle Aged ; Diabetes Mellitus, Type 1/psychology ; Reaction Time/physiology ; Emotional Regulation/physiology ; Data Analysis ; Personal Satisfaction ; Surveys and Questionnaires ; Secondary Data Analysis ; },
abstract = {BACKGROUND: Emotional clarity has often been assessed with self-report measures, but efforts have also been made to measure it passively, which has advantages such as avoiding potential inaccuracy in responses stemming from social desirability bias or poor insight into emotional clarity. Response times (RTs) to emotion items administered in ecological momentary assessments (EMAs) may be an indirect indicator of emotional clarity. Another proposed indicator is the drift rate parameter, which assumes that, aside from how fast a person responds to emotion items, the measurement of emotional clarity also requires the consideration of how careful participants were in providing responses.

OBJECTIVE: This paper aims to examine the reliability and validity of RTs and drift rate parameters from EMA emotion items as indicators of individual differences in emotional clarity.

METHODS: Secondary data analysis was conducted on data from 196 adults with type 1 diabetes who completed a 2-week EMA study involving the completion of 5 to 6 surveys daily. If lower RTs and higher drift rates (from EMA emotion items) were indicators of emotional clarity, we hypothesized that greater levels (ie, higher clarity) should be associated with greater life satisfaction; lower levels of neuroticism, depression, anxiety, and diabetes distress; and fewer difficulties with emotion regulation. Because prior literature suggested emotional clarity could be valence specific, EMA items for negative affect (NA) and positive affect were examined separately.

RESULTS: Reliability of the proposed indicators of emotional clarity was acceptable with a small number of EMA prompts (ie, 4 to 7 prompts in total or 1 to 2 days of EMA surveys). Consistent with expectations, the average drift rate of NA items across multiple EMAs had expected associations with other measures, such as correlations of r=-0.27 (P<.001) with depression symptoms, r=-0.27 (P=.001) with anxiety symptoms, r=-0.15 (P=.03) with emotion regulation difficulties, and r=0.63 (P<.001) with RTs to NA items. People with a higher NA drift rate responded faster to NA emotion items, had greater subjective well-being (eg, fewer depression symptoms), and had fewer difficulties with overall emotion regulation, which are all aligned with the expectation for an emotional clarity measure. Contrary to expectations, the validities of average RTs to NA items, the drift rate of positive affect items, and RTs to positive affect items were not strongly supported by our results.

CONCLUSIONS: Study findings provided initial support for the validity of NA drift rate as an indicator of emotional clarity but not for that of other RT-based clarity measures. Evidence was preliminary because the sample size was not sufficient to detect small but potentially meaningful correlations, as the sample size of the diabetes EMA study was chosen for other more primary research questions. Further research on passive emotional clarity measures is needed.},
}

Humans
*Ecological Momentary Assessment
Female
Male
Reproducibility of Results
Adult
*Emotions
Middle Aged
Diabetes Mellitus, Type 1/psychology
Reaction Time/physiology
Emotional Regulation/physiology
Data Analysis
Personal Satisfaction
Surveys and Questionnaires
Secondary Data Analysis

@article {pmid39023004,
year = {2024},
author = {Rillig, MC and Li, C and Rodríguez Del Río, Á and Zhu, YG and Jin, L},
title = {Elevated levels of antibiotic resistance genes as a factor of human-caused global environmental change.},
journal = {Global change biology},
volume = {30},
number = {7},
pages = {e17419},
doi = {10.1111/gcb.17419},
pmid = {39023004},
issn = {1365-2486},
support = {C5063-22G//Research Grants Council of Hong Kong/ ; 2021-DST-004//Ningbo S&T/ ; P0044024//Hong Kong Polytechnic University/ ; P0040336//Hong Kong Polytechnic University/ ; //Alexander-von-Humboldt Foundation/ ; },
mesh = {Humans ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Climate Change ; Ecosystem ; Human Activities ; },
abstract = {Antibiotic resistance genes (ARGs) have moved into focus as a critically important response variable in global change biology, given the increasing environmental and human health threat posed by these genes. However, we propose that elevated levels of ARGs should also be considered a factor of global change, not just a response. We provide evidence that elevated levels of ARGs are a global change factor, since this phenomenon is linked to human activity, occurs globally, and affects biota. We explain why ARGs could be considered the global change factor, rather than the organisms containing them; and we highlight the difference between ARGs and the presence of antibiotics, which are not necessarily linked since elevated levels of ARGs are caused by multiple factors. Importantly, shifting the perspective to elevated levels of ARGs as a factor of global change opens new avenues of research, where ARGs can be the experimental treatment. This includes asking questions about how elevated ARG levels interact with other global change factors, or how ARGs influence ecosystem processes, biodiversity or trophic relationships. Global change biology stands to profit from this new framing in terms of capturing more completely the real extent of human impacts on this planet.},
}

Humans
*Drug Resistance, Microbial/genetics
Anti-Bacterial Agents/pharmacology
Climate Change
Ecosystem
Human Activities

@article {pmid39018100,
year = {2024},
author = {Corponi, F and Li, BM and Anmella, G and Valenzuela-Pascual, C and Mas, A and Pacchiarotti, I and Valentí, M and Grande, I and Benabarre, A and Garriga, M and Vieta, E and Young, AH and Lawrie, SM and Whalley, HC and Hidalgo-Mazzei, D and Vergari, A},
title = {Wearable Data From Subjects Playing Super Mario, Taking University Exams, or Performing Physical Exercise Help Detect Acute Mood Disorder Episodes via Self-Supervised Learning: Prospective, Exploratory, Observational Study.},
journal = {JMIR mHealth and uHealth},
volume = {12},
number = {},
pages = {e55094},
doi = {10.2196/55094},
pmid = {39018100},
issn = {2291-5222},
mesh = {Humans ; *Supervised Machine Learning ; Prospective Studies ; *Wearable Electronic Devices/statistics & numerical data/standards ; Male ; Female ; *Mood Disorders/diagnosis/psychology ; Adult ; Exercise/psychology/physiology ; Universities/statistics & numerical data/organization & administration ; },
abstract = {BACKGROUND: Personal sensing, leveraging data passively and near-continuously collected with wearables from patients in their ecological environment, is a promising paradigm to monitor mood disorders (MDs), a major determinant of the worldwide disease burden. However, collecting and annotating wearable data is resource intensive. Studies of this kind can thus typically afford to recruit only a few dozen patients. This constitutes one of the major obstacles to applying modern supervised machine learning techniques to MD detection.

OBJECTIVE: In this paper, we overcame this data bottleneck and advanced the detection of acute MD episodes from wearables' data on the back of recent advances in self-supervised learning (SSL). This approach leverages unlabeled data to learn representations during pretraining, subsequently exploited for a supervised task.

METHODS: We collected open access data sets recording with the Empatica E4 wristband spanning different, unrelated to MD monitoring, personal sensing tasks-from emotion recognition in Super Mario players to stress detection in undergraduates-and devised a preprocessing pipeline performing on-/off-body detection, sleep/wake detection, segmentation, and (optionally) feature extraction. With 161 E4-recorded subjects, we introduced E4SelfLearning, the largest-to-date open access collection, and its preprocessing pipeline. We developed a novel E4-tailored transformer (E4mer) architecture, serving as the blueprint for both SSL and fully supervised learning; we assessed whether and under which conditions self-supervised pretraining led to an improvement over fully supervised baselines (ie, the fully supervised E4mer and pre-deep learning algorithms) in detecting acute MD episodes from recording segments taken in 64 (n=32, 50%, acute, n=32, 50%, stable) patients.

RESULTS: SSL significantly outperformed fully supervised pipelines using either our novel E4mer or extreme gradient boosting (XGBoost): n=3353 (81.23%) against n=3110 (75.35%; E4mer) and n=2973 (72.02%; XGBoost) correctly classified recording segments from a total of 4128 segments. SSL performance was strongly associated with the specific surrogate task used for pretraining, as well as with unlabeled data availability.

CONCLUSIONS: We showed that SSL, a paradigm where a model is pretrained on unlabeled data with no need for human annotations before deployment on the supervised target task of interest, helps overcome the annotation bottleneck; the choice of the pretraining surrogate task and the size of unlabeled data for pretraining are key determinants of SSL success. We introduced E4mer, which can be used for SSL, and shared the E4SelfLearning collection, along with its preprocessing pipeline, which can foster and expedite future research into SSL for personal sensing.},
}

Humans
*Supervised Machine Learning
Prospective Studies
*Wearable Electronic Devices/statistics & numerical data/standards
Male
Female
*Mood Disorders/diagnosis/psychology
Adult
Exercise/psychology/physiology
Universities/statistics & numerical data/organization & administration

@article {pmid39015757,
year = {2023},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , },
title = {The genome sequence of the Wainscot Smudge, Ypsolopha scabrella (Linnaeus, 1761).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {341},
pmid = {39015757},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Ypsolopha scabrella (the Wainscot Smudge; Arthropoda; Insecta; Lepidoptera; Ypsolophidae). The genome sequence is 853.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.7 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,594 protein coding genes.},
}

@article {pmid39015615,
year = {2024},
author = {Boyes, D and Lewis, OT and , and , and , and , and , and , and , },
title = {The genome sequence of the Mottled Pug, Eupithecia exiguata (Hübner, 1813).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {65},
pmid = {39015615},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Eupithecia exiguata (the Mottled Pug; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 372.9 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.39 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,194 protein coding genes.},
}

@article {pmid39015613,
year = {2024},
author = {Obbard, DJ and , and , and , and , and , and , },
title = {The genome sequence of a drosophilid fruit fly, Drosophila histrio (Meigen, 1830).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {56},
pmid = {39015613},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Drosophila histrio (the drosophilid fruit fly; Arthropoda; Insecta; Diptera; Drosophilidae). The genome sequence is 189.2 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.02 kilobases in length.},
}

@article {pmid39015611,
year = {2024},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Dotted Grey Groundling, Athrips mouffetella (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {42},
pmid = {39015611},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Athrips mouffetella (the Dotted Grey Groundling; Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence is 869.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.23 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,889 protein coding genes.},
}

@article {pmid39014019,
year = {2024},
author = {Cavaliere, M and Yang, G and De Dreu, CKW and Gross, J},
title = {Cooperation and social organization depend on weighing private and public reputations.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {16443},
pmid = {39014019},
issn = {2045-2322},
mesh = {Humans ; *Cooperative Behavior ; Social Networking ; Game Theory ; Interpersonal Relations ; },
abstract = {To avoid exploitation by defectors, people can use past experiences with others when deciding to cooperate or not ('private information'). Alternatively, people can derive others' reputation from 'public' information provided by individuals within the social network. However, public information may be aligned or misaligned with one's own private experiences and different individuals, such as 'friends' and 'enemies', may have different opinions about the reputation of others. Using evolutionary agent-based simulations, we examine how cooperation and social organization is shaped when agents (1) prioritize private or public information about others' reputation, and (2) integrate others' opinions using a friend-focused or a friend-and-enemy focused heuristic (relying on reputation information from only friends or also enemies, respectively). When agents prioritize public information and rely on friend-and-enemy heuristics, we observe polarization cycles marked by high cooperation, invasion by defectors, and subsequent population fragmentation. Prioritizing private information diminishes polarization and defector invasions, but also results in limited cooperation. Only when using friend-focused heuristics and following past experiences or the recommendation of friends create prosperous and stable populations based on cooperation. These results show how combining one's own experiences and the opinions of friends can lead to stable and large-scale cooperation and highlight the important role of following the advice of friends in the evolution of group cooperation.},
}

Humans
*Cooperative Behavior
Social Networking
Game Theory
Interpersonal Relations

@article {pmid39008135,
year = {2024},
author = {Urbano, F and Viterbi, R and Pedrotti, L and Vettorazzo, E and Movalli, C and Corlatti, L},
title = {Correction to: Enhancing biodiversity conservation and monitoring in protected areas through efficient data management.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {8},
pages = {733},
doi = {10.1007/s10661-024-12886-7},
pmid = {39008135},
issn = {1573-2959},
}

@article {pmid39007251,
year = {2024},
author = {Pili, AN and Leroy, B and Measey, JG and Farquhar, JE and Toomes, A and Cassey, P and Chekunov, S and Grenié, M and van Winkel, D and Maria, L and Diesmos, MLL and Diesmos, AC and Zurell, D and Courchamp, F and Chapple, DG},
title = {Forecasting potential invaders to prevent future biological invasions worldwide.},
journal = {Global change biology},
volume = {30},
number = {7},
pages = {e17399},
doi = {10.1111/gcb.17399},
pmid = {39007251},
issn = {1365-2486},
support = {DP210103050//Australian Research Council/ ; FT200100108//Australian Research Council/ ; IL230100175//Australian Research Council/ ; //Monash University Faculty of Science's Dean's Postgraduate Research Scholarship and Dean's International Postgraduate Research Scholarship, and by Monash University Graduate Research Office's Graduate Research Completion Award and Post-Graduate Publication Award/ ; BIFA3_026//the Philippine Department of Environment and Natural Resources FORIS project and the Global Biodiversity Information Facility Biodiversity Fund for Asia Project/ ; },
mesh = {*Introduced Species ; Animals ; *Forecasting ; *Reptiles/physiology ; *Amphibians/physiology ; Risk Assessment/methods ; Models, Theoretical ; Models, Biological ; },
abstract = {The ever-increasing and expanding globalisation of trade and transport underpins the escalating global problem of biological invasions. Developing biosecurity infrastructures is crucial to anticipate and prevent the transport and introduction of invasive alien species. Still, robust and defensible forecasts of potential invaders are rare, especially for species without known invasion history. Here, we aim to support decision-making by developing a quantitative invasion risk assessment tool based on invasion syndromes (i.e., generalising typical attributes of invasive alien species). We implemented a workflow based on 'Multiple Imputation with Chain Equation' to estimate invasion syndromes from imputed datasets of species' life-history and ecological traits and macroecological patterns. Importantly, our models disentangle the factors explaining (i) transport and introduction and (ii) establishment. We showcase our tool by modelling the invasion syndromes of 466 amphibians and reptile species with invasion history. Then, we project these models to amphibians and reptiles worldwide (16,236 species [c.76% global coverage]) to identify species with a risk of being unintentionally transported and introduced, and risk of establishing alien populations. Our invasion syndrome models showed high predictive accuracy with a good balance between specificity and generality. Unintentionally transported and introduced species tend to be common and thrive well in human-disturbed habitats. In contrast, those with established alien populations tend to be large-sized, are habitat generalists, thrive well in human-disturbed habitats, and have large native geographic ranges. We forecast that 160 amphibians and reptiles without known invasion history could be unintentionally transported and introduced in the future. Among them, 57 species have a high risk of establishing alien populations. Our reliable, reproducible, transferable, statistically robust and scientifically defensible quantitative invasion risk assessment tool is a significant new addition to the suite of decision-support tools needed for developing a future-proof preventative biosecurity globally.},
}

*Introduced Species
Animals
*Forecasting
*Reptiles/physiology
*Amphibians/physiology
Risk Assessment/methods
Models, Theoretical
Models, Biological

@article {pmid39004875,
year = {2024},
author = {Taylor, A and Sigona, A and Kelly, M},
title = {Centering Amah Mutsun voices in the analysis of a culturally important, fire-managed coastal grassland.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {},
number = {},
pages = {e3014},
doi = {10.1002/eap.3014},
pmid = {39004875},
issn = {1051-0761},
support = {//Critical Mission Studies Grant program of the University of California/ ; //Joseph A. Myers Center for Research on Native American Issues, UC Berkeley/ ; //California Native Plant Society (both statewide and from the Santa Clara Valley chapter)/ ; //UC Berkeley Chapter of Sigma Xi/ ; //California Native Grasslands Association/ ; //Department of Environmental Science, Policy, and Management at UC Berkeley/ ; //University of California Graduate Division Fellowship/ ; //Phi Beta Kappa Fellowship, UC Berkeley/ ; //Inter-institutional Network for Food, Agriculture and Sustainability and Intertribal Agriculture Council Tribal Fellowship/ ; //UC Berkeley Graduate Fellowship in Climate Equity/ ; //Ford Foundation Predoctoral Fellowship Program/ ; //Wilderness Society Scholarship/ ; //UC Berkeley Chancellor's Fellowship/ ; },
abstract = {Indigenous communities throughout California, USA, are increasingly advocating for and practicing cultural fire stewardship, leading to a host of social, cultural, and ecological benefits. Simultaneously, state agencies are recognizing the importance of controlled burning and cultural fire as a means of reducing the risk of severe wildfire while benefiting fire-adapted ecosystems. However, much of the current research on the impacts of controlled burning ignores the cultural importance of these ecosystems, and risks further marginalizing Indigenous knowledge systems. Our work adds a critical Indigenous perspective to the study of controlled burning in California's unique coastal grasslands, one of the most biodiverse and endangered ecosystems in the country. In this study, we partnered with the Amah Mutsun Tribal Band to investigate how the abundance and occurrence of shrubs, cultural plants, and invasive plants differed among three adjacent coastal grasslands with varying fire histories. These three sites are emblematic of the state's diverging approaches to grassland management: fire suppression, fire suppression followed by wildfire, and an exceedingly rare example of a grassland that has been repeatedly burned approximately every 2 years for more than 30 years. We found that Danthonia californica was significantly more abundant on the burned sites, whereas all included shrub species (Baccharis pilularis, Frangula californica, and Rubus ursinus) were significantly more abundant on the site with no recorded fire, results that have important implications for future cultural revitalization efforts and the loss of coastal grasslands to shrub encroachment. In addition to conducting a culturally relevant vegetation survey, we used Sentinel-2 satellite imagery to compare the relative severities of the two most recent fire events within the study area. Critically, we used interviews with Amah Mutsun tribal members to contextualize the results of our vegetation survey and remote sensing analysis, and to investigate how cultural burning contrasts from typical Western fire management approaches in this region. Our study is a novel example of how interviews, field data, and satellite imagery can be combined to gain a deeper ecological and cultural understanding of fire in California's endangered coastal grasslands.},
}

@article {pmid39004058,
year = {2024},
author = {Guo, J and Jin, Y and Liu, S and Li, T and Ji, D and Hou, C and Tang, H},
title = {Investigation of the causes and mechanisms of hypoxia in the central Bohai Sea in the summer of 2022.},
journal = {Marine pollution bulletin},
volume = {206},
number = {},
pages = {116710},
doi = {10.1016/j.marpolbul.2024.116710},
pmid = {39004058},
issn = {1879-3363},
abstract = {The deep-water area in the central Bohai Sea (BS) serves as a spawning ground and nursery for fish, shrimp, and crabs. Frequent hypoxia will affect the ecological environment in the central BS. Data from an on-site investigation of the central BS in the spring and summer of 2022 were used to analyze the relevant factors generating the occurrence of hypoxia in the central BS through the eutrophication index E, apparent oxygen consumption (AOU), and Spearman correlation. The hypoxia area was largely distributed in the study area's deep water section, and stratification was the main cause of hypoxia at the bottom. Organic matter mineralization, degradation, and biological respiration further exacerbated the hypoxia. In the summer of 2022, temperature stratification was the dominant factor influencing hypoxia.},
}

@article {pmid39001963,
year = {2024},
author = {Lu, Y and Xiao, X and Liang, Y and Li, J and Guo, C and Xu, L and Liu, Q and Xiao, Y and Zhou, S},
title = {Distribution and transformation of potentially toxic elements in cracks under coal mining disturbance in farmland.},
journal = {Environmental geochemistry and health},
volume = {46},
number = {9},
pages = {312},
pmid = {39001963},
issn = {1573-2983},
support = {52130402//State Key Program of National Natural Science Foundation of China/ ; },
mesh = {*Soil Pollutants/analysis/toxicity ; *Coal Mining ; *Environmental Monitoring ; *Metals, Heavy/analysis/toxicity ; Soil/chemistry ; Farms ; Risk Assessment ; },
abstract = {The ground cracks resulting from coal mining activities induce alterations in the physical and chemical characteristics of soil. However, limited knowledge exists regarding the impact of subsidence caused by coal mining on the distribution of potentially toxic elements (PTEs) fractions in farmland soil. In this study, we collected 19 soil profiles at varying depths from the soil surface and at horizontal distances of 0, 1, 2, and 5 m from the vertical crack. Using BCR extraction fractionation, we determined the geochemical fractions and total concentrations of Chromium (Cr), nickel (Ni), copper (Cu), zinc (Zn), arsenic (As), cadmium (Cd) and lead (Pb) to investigate their ecological risk, spatial fraction distribution, and main influencing factors. Results showed that the E r i values of Cd appearing in 68.7% of the samples were higher than 40 and less than 80, presented a moderate ecological risk. Chromium (Cr), nickel (Ni), copper (Cu), zinc (Zn), arsenic (As), and lead (Pb) were mainly bound to residual fractions (> 60%) with lower mobility and Cd was dominated by F1 (acid-soluble fractions, 50%) and F2 (reducible fractions, 29%) in surface soil (0-20 cm). The geochemical fractionation revealed that the mobile fractions (F1-acid-soluble and F2-reducible) of PTEs were primarily located near the crack, influenced by available potassium. In contrast, the less mobile fractions (F3-oxidizable and F4-residual) exhibited higher concentrations at distances of 2 and 5 m from the crack, except for arsenic, influenced by the presence of clay particles and available phosphorus.},
}

*Soil Pollutants/analysis/toxicity
*Coal Mining
*Environmental Monitoring
*Metals, Heavy/analysis/toxicity
Soil/chemistry
Farms
Risk Assessment

@article {pmid39001714,
year = {2024},
author = {Williams, TA and Davin, AA and Szánthó, LL and Stamatakis, A and Wahl, NA and Woodcroft, BJ and Soo, RM and Eme, L and Sheridan, PO and Gubry-Rangin, C and Spang, A and Hugenholtz, P and Szöllősi, GJ},
title = {Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae129},
pmid = {39001714},
issn = {1751-7370},
abstract = {In recent years, phylogenetic reconciliation has emerged as a promising approach for studying microbial ecology and evolution. The core idea is to model how gene trees evolve along a species tree, and to explain differences between them via evolutionary events including gene duplications, transfers, and losses. Here, we describe how phylogenetic reconciliation provides a natural framework for studying genome evolution, and highlight recent applications including ancestral gene content inference, the rooting of species trees, and the insights into metabolic evolution and ecological transitions they yield. Reconciliation analyses have elucidated the evolution of diverse microbial lineages, from Chlamydiae to Asgard archaea, shedding light on ecological adaptation, host-microbe interactions, and symbiotic relationships. However, there are many opportunities for broader application of the approach in microbiology. Continuing improvements to make reconciliation models more realistic and scalable, and integration of ecological metadata such as habitat, pH, temperature and oxygen use, offer enormous potential for understanding the rich tapestry of microbial life.},
}

@article {pmid39000743,
year = {2024},
author = {Macchia, A and Marinelli, L and Barbaccia, FI and de Caro, T and Hansen, A and Schuberthan, LM and Izzo, FC and Pintus, V and Testa Chiari, K and La Russa, MF},
title = {Mattel's ©Barbie: Preventing Plasticizers Leakage in PVC Artworks and Design Objects through Film-Forming Solutions.},
journal = {Polymers},
volume = {16},
number = {13},
pages = {},
pmid = {39000743},
issn = {2073-4360},
abstract = {The main conservation problem of p-PVC artworks is phthalate-based plasticizer migration. Phthalate migration from the bulk to the surface of the materials leads to the formation of a glossy and oily film on the outer layers, ultimately reducing the flexibility of the material. This study aimed to develop a removable coating for the preservation of contemporary artworks and design objects made of plasticized polyvinyl chloride (p-PVC). Several coatings incorporating chitosan, collagen, and cellulose ethers were assessed as potential barriers to inhibiting plasticizer migration. Analytical techniques including optical microscopy (OM), ultraviolet/visible/near-infrared spectroscopy (UV/Vis/NIR), Fourier transform infrared spectroscopy with attenuated total reflection (FTIR-ATR), and scanning electron microscopy (SEM) were utilized to evaluate the optical and chemical stability of selected coating formulations applied to laboratory p-PVC sheet specimens. Subsequently, formulations were tested on a real tangible example of a design object, ©Barbie doll, characterized by the prevalent issue of plasticizer migration. Furthermore, the results obtained with the tested formulations were evaluated by a group of conservators using a tailored survey. Finally, a suitable coating formulation capable of safeguarding plastic substrates was suggested.},
}

@article {pmid39000053,
year = {2024},
author = {Wang, XY and Ren, CX and Fan, QW and Xu, YP and Wang, LW and Mao, ZL and Cai, XZ},
title = {Integrated Assays of Genome-Wide Association Study, Multi-Omics Co-Localization, and Machine Learning Associated Calcium Signaling Genes with Oilseed Rape Resistance to Sclerotinia sclerotiorum.},
journal = {International journal of molecular sciences},
volume = {25},
number = {13},
pages = {},
pmid = {39000053},
issn = {1422-0067},
support = {2021C02064//Zhejiang Science and Technology Major Program on Agricultural New Variety Breeding/ ; LZ18C140002//Zhejiang Provincial Natural Science Foundation of China/ ; 324CXTD430//Hainan Provincial Natural Science Foundation of China/ ; },
mesh = {*Ascomycota/pathogenicity ; *Machine Learning ; *Disease Resistance/genetics ; *Genome-Wide Association Study ; *Plant Diseases/microbiology/genetics ; *Brassica napus/genetics/microbiology/immunology ; *Calcium Signaling/genetics ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; Genomics/methods ; Multiomics ; },
abstract = {Sclerotinia sclerotiorum (Ss) is one of the most devastating fungal pathogens, causing huge yield loss in multiple economically important crops including oilseed rape. Plant resistance to Ss pertains to quantitative disease resistance (QDR) controlled by multiple minor genes. Genome-wide identification of genes involved in QDR to Ss is yet to be conducted. In this study, we integrated several assays including genome-wide association study (GWAS), multi-omics co-localization, and machine learning prediction to identify, on a genome-wide scale, genes involved in the oilseed rape QDR to Ss. Employing GWAS and multi-omics co-localization, we identified seven resistance-associated loci (RALs) associated with oilseed rape resistance to Ss. Furthermore, we developed a machine learning algorithm and named it Integrative Multi-Omics Analysis and Machine Learning for Target Gene Prediction (iMAP), which integrates multi-omics data to rapidly predict disease resistance-related genes within a broad chromosomal region. Through iMAP based on the identified RALs, we revealed multiple calcium signaling genes related to the QDR to Ss. Population-level analysis of selective sweeps and haplotypes of variants confirmed the positive selection of the predicted calcium signaling genes during evolution. Overall, this study has developed an algorithm that integrates multi-omics data and machine learning methods, providing a powerful tool for predicting target genes associated with specific traits. Furthermore, it makes a basis for further understanding the role and mechanisms of calcium signaling genes in the QDR to Ss.},
}

*Ascomycota/pathogenicity
*Machine Learning
*Disease Resistance/genetics
*Genome-Wide Association Study
*Plant Diseases/microbiology/genetics
*Brassica napus/genetics/microbiology/immunology
*Calcium Signaling/genetics
Polymorphism, Single Nucleotide
Quantitative Trait Loci
Genomics/methods
Multiomics

@article {pmid38997687,
year = {2024},
author = {Prakofjewa, J and Sartori, M and Šarka, P and Kalle, R and Pieroni, A and Sõukand, R},
title = {Knowledge in motion: temporal dynamics of wild food plant use in the Polish-Lithuanian-Belarusian border region.},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {20},
number = {1},
pages = {65},
pmid = {38997687},
issn = {1746-4269},
support = {grant agreement No 714874//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme/ ; grant agreement No 714874//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme/ ; grant agreement No 714874//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme/ ; grant agreement No 714874//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme/ ; grant agreement No 714874//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme/ ; grant agreement No 714874//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme/ ; },
mesh = {Lithuania ; Poland ; *Plants, Edible/classification ; Republic of Belarus ; Humans ; Knowledge ; Ethnobotany ; },
abstract = {BACKGROUND: Understanding how Local Ecological Knowledge (LEK) evolves over time is crucial for fostering social and environmental responsibility. This study aims to develop a conceptual model of plant knowledge circulation, providing insights into the temporal dynamics of LEK in the Polish-Lithuanian-Belarusian border region. It explores the key patterns and driving forces behind changes in the use of wild plants for food.

METHODS: Field research was conducted in 60 rural settlements across Podlasie Voivodeship (Poland), Vilnius Region (Lithuania), and Hrodna Region (Belarus). This included 200 semi-structured interviews and participant observation among two local communities, Lithuanians and Poles. To assess the temporal dynamics of wild food use, we performed a cross-ethnic, cross-border analysis over time, dividing the data into three major temporal dimensions: past, continuous, and recently acquired uses.

RESULTS: Of the 72 wild plant taxa reported by Poles or Lithuanians in the Polish-Lithuanian-Belarusian borderland, 47 were continuously used for food, 58 were utilised in the past, and 41 were recently acquired. Cross-country trends were similar, with Poland showing more past uses. Diachronic comparisons between Poles and Lithuanians in each studied country revealed no significant differences. Recently acquired taxa overlapped considerably with those used continuously and in the past. The most diversely utilised taxa showed the greatest overlaps. By observing the movement of specific plant taxa within various time dimensions, we distinguished overlapping flow variations: retention (3 taxa), decay (11), invention (8), stagnation (17), revitalisation (6), re-invention (3), and knowledge in motion (24). Shifts in the use of wild food plants were influenced by changes in environmental conditions, governmental policies, cultural practices, and economic factors.

CONCLUSION: The findings of this study have important implications for improving methods of tracking changes in LEK and enhancing our understanding of the relationship between people and nature. Our results underscore the importance of considering knowledge circulation over time in different directions. Recognising the various stages of knowledge circulation might help in pursuing sustainable solutions that balance the needs of human communities with environmental protection.},
}

Lithuania
Poland
*Plants, Edible/classification
Republic of Belarus
Humans
Knowledge
Ethnobotany

@article {pmid38994633,
year = {2024},
author = {Gómez-García, A and Prinz, AK and Jiménez, DAA and Zamora, WJ and Barazorda-Ccahuana, HL and Chávez-Fumagalli, MÁ and Valli, M and Andricopulo, AD and da S Bolzani, V and Olmedo, DA and Solís, PN and Núñez, MJ and Rodríguez Pérez, JR and Sánchez, HAV and Cortés Hernández, HF and Mosquera Martinez, OM and Koch, O and Medina-Franco, JL},
title = {Updating and profiling the natural product-likeness of Latin American compound libraries.},
journal = {Molecular informatics},
volume = {43},
number = {7},
pages = {e202400052},
doi = {10.1002/minf.202400052},
pmid = {38994633},
issn = {1868-1751},
mesh = {*Biological Products/chemistry/pharmacology ; Latin America ; Small Molecule Libraries/pharmacology/chemistry ; Drug Discovery ; Cheminformatics ; Databases, Chemical ; },
abstract = {Compound databases of natural products play a crucial role in drug discovery and development projects and have implications in other areas, such as food chemical research, ecology and metabolomics. Recently, we put together the first version of the Latin American Natural Product database (LANaPDB) as a collective effort of researchers from six countries to ensemble a public and representative library of natural products in a geographical region with a large biodiversity. The present work aims to conduct a comparative and extensive profiling of the natural product-likeness of an updated version of LANaPDB and the individual ten compound databases that form part of LANaPDB. The natural product-likeness profile of the Latin American compound databases is contrasted with the profile of other major natural product databases in the public domain and a set of small-molecule drugs approved for clinical use. As part of the extensive characterization, we employed several chemoinformatics metrics of natural product likeness. The results of this study will capture the attention of the global community engaged in natural product databases, not only in Latin America but across the world.},
}

*Biological Products/chemistry/pharmacology
Latin America
Small Molecule Libraries/pharmacology/chemistry
Drug Discovery
Cheminformatics
Databases, Chemical

@article {pmid38992177,
year = {2024},
author = {Alvarez-Mora, I and Arturi, K and Béen, F and Buchinger, S and El Mais, AER and Gallampois, C and Hahn, M and Hollender, J and Houtman, C and Johann, S and Krauss, M and Lamoree, M and Margalef, M and Massei, R and Brack, W and Muz, M},
title = {Progress, applications, and challenges in high-throughput effect-directed analysis for toxicity driver identification - is it time for HT-EDA?.},
journal = {Analytical and bioanalytical chemistry},
volume = {},
number = {},
pages = {},
pmid = {38992177},
issn = {1618-2650},
abstract = {The rapid increase in the production and global use of chemicals and their mixtures has raised concerns about their potential impact on human and environmental health. With advances in analytical techniques, in particular, high-resolution mass spectrometry (HRMS), thousands of compounds and transformation products with potential adverse effects can now be detected in environmental samples. However, identifying and prioritizing the toxicity drivers among these compounds remain a significant challenge. Effect-directed analysis (EDA) emerged as an important tool to address this challenge, combining biotesting, sample fractionation, and chemical analysis to unravel toxicity drivers in complex mixtures. Traditional EDA workflows are labor-intensive and time-consuming, hindering large-scale applications. The concept of high-throughput (HT) EDA has recently gained traction as a means of accelerating these workflows. Key features of HT-EDA include the combination of microfractionation and downscaled bioassays, automation of sample preparation and biotesting, and efficient data processing workflows supported by novel computational tools. In addition to microplate-based fractionation, high-performance thin-layer chromatography (HPTLC) offers an interesting alternative to HPLC in HT-EDA. This review provides an updated perspective on the state-of-the-art in HT-EDA, and novel methods/tools that can be incorporated into HT-EDA workflows. It also discusses recent studies on HT-EDA, HT bioassays, and computational prioritization tools, along with considerations regarding HPTLC. By identifying current gaps in HT-EDA and proposing new approaches to overcome them, this review aims to bring HT-EDA a step closer to monitoring applications.},
}

@article {pmid38989474,
year = {2024},
author = {Li, R and Li, J and Lemer, S and Lopez, JV and Oatley, G and Clayton-Lucey, IA and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The genome sequence of a heart cockle, Fragum fragum (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {129},
pmid = {38989474},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual specimen of Fragum fragum (a heart cockle; Mollusca; Bivalvia; Veneroida; Cardiidae). The genome sequence is 1,153.1 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 22.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,262 protein coding genes.},
}

@article {pmid38986397,
year = {2024},
author = {Hung, CC and Hsieh, HH and Chou, WC and Liu, EC and Chow, CH and Chang, Y and Lee, TM and Santschi, PH and Ranatunga, RRMKP and Bacosa, HP and Shih, YY},
title = {Assessing CO2 sources and sinks in and around Taiwan: Implication for achieving regional carbon neutrality by 2050.},
journal = {Marine pollution bulletin},
volume = {206},
number = {},
pages = {116664},
doi = {10.1016/j.marpolbul.2024.116664},
pmid = {38986397},
issn = {1879-3363},
abstract = {Taiwan has pledged to achieve net-zero carbon emissions by 2050, but the current extent of carbon sinks in Taiwan remains unclear. Therefore, this study aims to first review the existing nature-based carbon sinks on land and in the oceans around Taiwan. Subsequently, we suggest potential strategies to reduce CO2 emissions and propose carbon dioxide removal methods (CDRs). The natural carbon sinks by forests, sediments, and oceans in and around Taiwan are approximately 21.5, 42.1, and 96.8 Mt-CO2 y[-1], respectively, which is significantly less than Taiwan's CO2 emissions (280 Mt-CO2 y[-1]). Taiwan must consider decarbonization strategies like using electric vehicles, renewable energy, and hydrogen energy by formulating enabling policies. Besides more precisely assessing both terrestrial and marine carbon sinks, Taiwan should develop novel CDRs such as bioenergy with carbon capture and storage, afforestation, reforestation, biochar, seaweed cultivation, and ocean alkalinity enhancement, to reach carbon neutrality by 2050.},
}

@article {pmid38985613,
year = {2024},
author = {Filice, M and Crocco, MC and Agostino, RG and Barberi, RC and Amelio, D and Imbrogno, S and Formoso, V and Cerra, MC},
title = {An X-ray computed μ-tomography analysis for the characterization of 3D-heart shape in a model of cardiac plasticity.},
journal = {Vascular pharmacology},
volume = {155},
number = {},
pages = {107310},
doi = {10.1016/j.vph.2024.107310},
pmid = {38985613},
issn = {1879-3649},
mesh = {Animals ; *Imaging, Three-Dimensional ; *X-Ray Microtomography ; Heart/diagnostic imaging ; Radiographic Image Interpretation, Computer-Assisted ; },
}

Animals
*Imaging, Three-Dimensional
*X-Ray Microtomography
Heart/diagnostic imaging
Radiographic Image Interpretation, Computer-Assisted

@article {pmid38982382,
year = {2024},
author = {Blazanin, M},
title = {gcplyr: an R package for microbial growth curve data analysis.},
journal = {BMC bioinformatics},
volume = {25},
number = {1},
pages = {232},
pmid = {38982382},
issn = {1471-2105},
mesh = {*Software ; Computational Biology/methods ; Data Analysis ; },
abstract = {BACKGROUND: Characterization of microbial growth is of both fundamental and applied interest. Modern platforms can automate collection of high-throughput microbial growth curves, necessitating the development of computational tools to handle and analyze these data to produce insights.

RESULTS: To address this need, here I present a newly-developed R package: gcplyr. gcplyr can flexibly import growth curve data in common tabular formats, and reshapes it under a tidy framework that is flexible and extendable, enabling users to design custom analyses or plot data with popular visualization packages. gcplyr can also incorporate metadata and generate or import experimental designs to merge with data. Finally, gcplyr carries out model-free (non-parametric) analyses. These analyses do not require mathematical assumptions about microbial growth dynamics, and gcplyr is able to extract a broad range of important traits, including growth rate, doubling time, lag time, maximum density and carrying capacity, diauxie, area under the curve, extinction time, and more.

CONCLUSIONS: gcplyr makes scripted analyses of growth curve data in R straightforward, streamlines common data wrangling and analysis steps, and easily integrates with common visualization and statistical analyses.},
}

*Software
Computational Biology/methods
Data Analysis

@article {pmid38979368,
year = {2024},
author = {Xiao, Y and Elmasry, M and Bai, JDK and Chen, A and Chen, Y and Jackson, B and Johnson, JO and Gillies, RJ and Prasanna, P and Chen, C and Damaghi, M},
title = {Eco-evolutionary Guided Pathomic Analysis to Predict DCIS Upstaging.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38979368},
issn = {2692-8205},
support = {P30 CA076292/CA/NCI NIH HHS/United States ; R01 CA249016/CA/NCI NIH HHS/United States ; R01 CA272601/CA/NCI NIH HHS/United States ; U01 CA261841/CA/NCI NIH HHS/United States ; },
abstract = {Cancers evolve in a dynamic ecosystem. Thus, characterizing cancer's ecological dynamics is crucial to understanding cancer evolution and can lead to discovering novel biomarkers to predict disease progression. Ductal carcinoma in situ (DCIS) is an early-stage breast cancer characterized by abnormal epithelial cell growth confined within the milk ducts. Although there has been extensive research on genetic and epigenetic causes of breast carcinogenesis, none of these studies have successfully identified a biomarker for the progression and/or upstaging of DCIS. In this study, we show that ecological habitat analysis of hypoxia and acidosis biomarkers can significantly improve prediction of DCIS upstaging. First, we developed a novel eco-evolutionary designed approach to define habitats in the tumor intra-ductal microenvironment based on oxygen diffusion distance in our DCIS cohort of 84 patients. Then, we identify cancer cells with metabolic phenotypes attributed to their habitat conditions, such as the expression of CA9 indicating hypoxia responding phenotype, and LAMP2b indicating a hypoxia-induced acid adaptation. Traditionally these markers have shown limited predictive capabilities for DCIS upstaging, if any. However, when analyzed from an ecological perspective, their power to differentiate between indolent and upstaged DCIS increased significantly. Second, using eco-evolutionary guided computational and digital pathology techniques, we discovered distinct spatial patterns of these biomarkers and used the distribution of such patterns to predict patient upstaging. The patterns were characterized by both cellular features and spatial features. With a 5-fold validation on the biopsy cohort, we trained a random forest classifier to achieve the area under curve(AUC) of 0.74. Our results affirm the importance of using eco-evolutionary-designed approaches in biomarkers discovery studies in the era of digital pathology by demonstrating the role of eco-evolution dynamics in predicting cancer progression.},
}

@article {pmid38976642,
year = {2024},
author = {Pisarenco, VA and Vizueta, J and Rozas, J},
title = {GALEON: a comprehensive bioinformatic tool to analyse and visualize gene clusters in complete genomes.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {7},
pages = {},
pmid = {38976642},
issn = {1367-4811},
support = {MCIN/AEI/10.13039/501100011033//Ministerio de Ciencia e Innovación of Spain/ ; },
mesh = {*Multigene Family ; *Software ; *Computational Biology/methods ; Genome ; Genomics/methods ; Evolution, Molecular ; Humans ; },
abstract = {MOTIVATION: Gene clusters, defined as a set of genes encoding functionally related proteins, are abundant in eukaryotic genomes. Despite the increasing availability of chromosome-level genomes, the comprehensive analysis of gene family evolution remains largely unexplored, particularly for large and highly dynamic gene families or those including very recent family members. These challenges stem from limitations in genome assembly contiguity, particularly in repetitive regions such as large gene clusters. Recent advancements in sequencing technology, such as long reads and chromatin contact mapping, hold promise in addressing these challenges.

RESULTS: To facilitate the identification, analysis, and visualization of physically clustered gene family members within chromosome-level genomes, we introduce GALEON, a user-friendly bioinformatic tool. GALEON identifies gene clusters by studying the spatial distribution of pairwise physical distances among gene family members along with the genome-wide gene density. The pipeline also enables the simultaneous analysis and comparison of two gene families and allows the exploration of the relationship between physical and evolutionary distances. This tool offers a novel approach for studying the origin and evolution of gene families.

GALEON is freely available from https://www.ub.edu/softevol/galeon and https://github.com/molevol-ub/galeon.},
}

*Multigene Family
*Software
*Computational Biology/methods
Genome
Genomics/methods
Evolution, Molecular
Humans

@article {pmid38974014,
year = {2024},
author = {Cassee, FR and Bleeker, EAJ and Durand, C and Exner, T and Falk, A and Friedrichs, S and Heunisch, E and Himly, M and Hofer, S and Hofstätter, N and Hristozov, D and Nymark, P and Pohl, A and Soeteman-Hernández, LG and Suarez-Merino, B and Valsami-Jones, E and Groenewold, M},
title = {Roadmap towards safe and sustainable advanced and innovative materials. (Outlook for 2024-2030).},
journal = {Computational and structural biotechnology journal},
volume = {25},
number = {},
pages = {105-126},
pmid = {38974014},
issn = {2001-0370},
abstract = {The adoption of innovative advanced materials holds vast potential, contingent upon addressing safety and sustainability concerns. The European Commission advocates the integration of Safe and Sustainable by Design (SSbD) principles early in the innovation process to streamline market introduction and mitigate costs. Within this framework, encompassing ecological, social, and economic factors is paramount. The NanoSafety Cluster (NSC) delineates key safety and sustainability areas, pinpointing unresolved issues and research gaps to steer the development of safe(r) materials. Leveraging FAIR data management and integration, alongside the alignment of regulatory aspects, fosters informed decision-making and innovation. Integrating circularity and sustainability mandates clear guidance, ensuring responsible innovation at every stage. Collaboration among stakeholders, anticipation of regulatory demands, and a commitment to sustainability are pivotal for translating SSbD into tangible advancements. Harmonizing standards and test guidelines, along with regulatory preparedness through an exchange platform, is imperative for governance and market readiness. By adhering to these principles, the effective and sustainable deployment of innovative materials can be realized, propelling positive transformation and societal acceptance.},
}

@article {pmid38973368,
year = {2024},
author = {Martínez, L and Zattara, EE and Arbetman, MP and Morales, CL and Masonbrink, RE and Severin, AJ and Aizen, MA and Toth, AL},
title = {Chromosome-Level Assembly and Annotation of the Genome of the Endangered Giant Patagonian Bumble Bee Bombus dahlbomii.},
journal = {Genome biology and evolution},
volume = {16},
number = {7},
pages = {},
doi = {10.1093/gbe/evae146},
pmid = {38973368},
issn = {1759-6653},
support = {//Fulbright Science and Technology Award, Argentina Commission/ ; //Iowa State University Faculty Professional Development Leave/ ; NGS-57001R-19//National Geographic Society/ ; },
mesh = {Animals ; Bees/genetics ; *Endangered Species ; *Molecular Sequence Annotation ; *Genome, Insect ; Male ; Chromosomes, Insect/genetics ; },
abstract = {This article describes a genome assembly and annotation for Bombus dahlbomii, the giant Patagonian bumble bee. DNA from a single, haploid male collected in Argentina was used for PacBio (HiFi) sequencing, and Hi-C technology was then used to map chromatin contacts. Using Juicer and manual curation, the genome was scaffolded into 18 main pseudomolecules, representing a high-quality, near chromosome-level assembly. The sequenced genome size is estimated at 265 Mb. The genome was annotated based on RNA sequencing data of another male from Argentina, and BRAKER3 produced 15,767 annotated genes. The genome and annotation show high completeness, with >95% BUSCO scores for both the genome and annotated genes (based on conserved genes from Hymenoptera). This genome provides a valuable resource for studying the biology of this iconic and endangered species, as well as for understanding the impacts of its decline and designing strategies for its preservation.},
}

Animals
Bees/genetics
*Endangered Species
*Molecular Sequence Annotation
*Genome, Insect
Male
Chromosomes, Insect/genetics

@article {pmid38972117,
year = {2024},
author = {Hyman, S and Zhang, J and Lim, YH and Jovanovic Andersen, Z and Cole-Hunter, T and Li, Y and Møller, P and Daras, K and Williams, R and Thomas, ML and Labib, SM and Topping, D},
title = {Residential greenspace and COVID-19 Severity: A cohort study of 313,657 individuals in Greater Manchester, United Kingdom.},
journal = {Environment international},
volume = {190},
number = {},
pages = {108843},
doi = {10.1016/j.envint.2024.108843},
pmid = {38972117},
issn = {1873-6750},
abstract = {BACKGROUND: Greenspaces contribute positively to mental and physical well-being, promote social cohesion, and alleviate environmental stressors, such as air pollution. Ecological studies suggest that greenspace may affect incidence and severity of Coronavirus Disease 2019 (COVID-19).

OBJECTIVE: This study examines the association between residential greenspace and COVID-19 related hospitalization and death.

METHOD: In this retrospective cohort based on patient records from the Greater Manchester Care Records, all first COVID-19 cases diagnosed between March 1, 2020, and May 31, 2022 were followed until COVID-19 related hospitalization or death within 28 days. Residential greenspace availability was assessed using the Normalized Difference Vegetation Index per lower super output area in Greater Manchester. The association of greenspace with COVID-19 hospitalization and mortality were estimated using multivariate logistic regression models after adjusting for potential individual, temporal, and spatial confounders. We explored potential effect modifications of the associations with greenspace and COVID-19 severity by age, sex, body mass index, smoking, deprivation, and certain comorbidities. Combined effects of greenspace and air pollution (NO2 and PM2.5) were investigated by mutually adjusting pairs with correlation coefficients ≤ 0·7.

RESULTS: Significant negative associations were observed between greenspace availability and COVID-19 hospitalization and mortality with odds ratios [OR] (95 % Confidence Intervals [CI]) of 0·96 (0·94-0·97) and 0·84 (0·80-0·88) (per interquartile range [IQR]), respectively. These were significantly modified by deprivation (P-value for interaction < 0.05), showing that those most deprived obtained largest benefits from greenspace. Inclusion of NO2 and PM2.5 diminished associations to null for COVID-19 hospitalization, but only reduced them slightly for mortality, where inverse associations remained.

CONCLUSION: In the Greater Manchester area, residential greenspace is associated with reduced risk of hospitalization or death in individuals with COVID-19, with deprived groups obtaining the greatest benefits. Associations were strongest for COVID-19 mortality, which were robust to inclusion of air pollutants in the models.},
}

@article {pmid38968897,
year = {2024},
author = {Zhu, Y and Chen, F and Jiang, F and Hua, Z and Luo, Z and Ma, J},
title = {Enhanced remediation of PFAS-metal co-contaminated soil by ceramsite supported Fe3O4-MoS2 heterojunction as a high-performance piezocatalyst.},
journal = {Journal of environmental management},
volume = {365},
number = {},
pages = {121716},
doi = {10.1016/j.jenvman.2024.121716},
pmid = {38968897},
issn = {1095-8630},
mesh = {*Soil Pollutants/chemistry/metabolism ; *Soil/chemistry ; *Metals, Heavy/chemistry ; Environmental Restoration and Remediation/methods ; Biodegradation, Environmental ; },
abstract = {In this study, a novel piezoremediation system was developed to remediate an actual soil co-polluted by high contents of per- and polyfluoroalkyl substances (PFAS, 5725 μg/kg soil) and heavy metals (6455 mg/kg soil). Two piezocatalysts, MoS2/ceramsite (MC) and Fe3O4-MoS2/ceramsite (FMC), were synthesized using a facile hydrothermal-coprecipitation method. These two materials were employed to treat the co-contaminated soil in soil slurry environment under sonication. FMC exhibited significantly higher piezoremediation performance than MC, wherein 91.6% of PFAS, 97.8% of Cr[6+] ions and 81% of total metals (Cr, Cu, Zn and Ni) were removed from the soil after 50 min of the FMC piezoremediation process. FMC also exhibited the advantages of easy separation from the slurry phase and excellent reusability. In comparison with MC, the Fe3O4-MoS2 heterojunction in FMC can stabilize MoS2 particles on the surface of ceramsite granules, promote the separation of electron/hole pairs, accelerate charge transfer, therefore enhancing piezocatalytic performance. The electron spin resonance analysis and free radical quenching tests show that [•]OH was the dominant oxidative radical responsible for PFAS degradation. The count of bacteria and the bacterial community structure in the treated soil can be basically restored to the initial states after 30 days of incubation under nutrient stimulation. Overall, this study not only provides a deep insight on soil remediation process, but also offers an efficient and reliable technique for simultaneous decontamination of organic and metal pollutants in soil.},
}

*Soil Pollutants/chemistry/metabolism
*Soil/chemistry
*Metals, Heavy/chemistry
Environmental Restoration and Remediation/methods
Biodegradation, Environmental

@article {pmid38968305,
year = {2024},
author = {Fu, X and Withers, J and Miyamae, JA and Moore, TY},
title = {ArborSim: Articulated, branching, OpenSim routing for constructing models of multi-jointed appendages with complex muscle-tendon architecture.},
journal = {PLoS computational biology},
volume = {20},
number = {7},
pages = {e1012243},
pmid = {38968305},
issn = {1553-7358},
mesh = {*Tendons/physiology/anatomy & histology ; Humans ; Biomechanical Phenomena ; *Software ; *Joints/physiology/anatomy & histology ; *Muscle, Skeletal/physiology/anatomy & histology ; Models, Biological ; Computational Biology ; Computer Simulation ; Animals ; },
abstract = {Computational models of musculoskeletal systems are essential tools for understanding how muscles, tendons, bones, and actuation signals generate motion. In particular, the OpenSim family of models has facilitated a wide range of studies on diverse human motions, clinical studies of gait, and even non-human locomotion. However, biological structures with many joints, such as fingers, necks, tails, and spines, have been a longstanding challenge to the OpenSim modeling community, especially because these structures comprise numerous bones and are frequently actuated by extrinsic muscles that span multiple joints-often more than three-and act through a complex network of branching tendons. Existing model building software, typically optimized for limb structures, makes it difficult to build OpenSim models that accurately reflect these intricacies. Here, we introduce ArborSim, customized software that efficiently creates musculoskeletal models of highly jointed structures and can build branched muscle-tendon architectures. We used ArborSim to construct toy models of articulated structures to determine which morphological features make a structure most sensitive to branching. By comparing the joint kinematics of models constructed with branched and parallel muscle-tendon units, we found that among various parameters-the number of tendon branches, the number of joints between branches, and the ratio of muscle fiber length to muscle tendon unit length-the number of tendon branches and the number of joints between branches are most sensitive to branching modeling method. Notably, the differences between these models showed no predictable pattern with increased complexity. As the proportion of muscle increased, the kinematic differences between branched and parallel models units also increased. Our findings suggest that stress and strain interactions between distal tendon branches and proximal tendon and muscle greatly affect the overall kinematics of a musculoskeletal system. By incorporating complex muscle-tendon branching into OpenSim models using ArborSim, we can gain deeper insight into the interactions between the axial and appendicular skeleton, model the evolution and function of diverse animal tails, and understand the mechanics of more complex motions and tasks.},
}

*Tendons/physiology/anatomy & histology
Humans
Biomechanical Phenomena
*Software
*Joints/physiology/anatomy & histology
*Muscle, Skeletal/physiology/anatomy & histology
Models, Biological
Computational Biology
Computer Simulation
Animals

@article {pmid38968199,
year = {2024},
author = {Stratton, CA and Thompson, Y and Zio, K and Morrison, WR and Murrell, EG},
title = {uafR: An R package that automates mass spectrometry data processing.},
journal = {PloS one},
volume = {19},
number = {7},
pages = {e0306202},
pmid = {38968199},
issn = {1932-6203},
mesh = {*Gas Chromatography-Mass Spectrometry/methods ; *Algorithms ; *Software ; Cheminformatics/methods ; },
abstract = {Chemical information has become increasingly ubiquitous and has outstripped the pace of analysis and interpretation. We have developed an R package, uafR, that automates a grueling retrieval process for gas -chromatography coupled mass spectrometry (GC -MS) data and allows anyone interested in chemical comparisons to quickly perform advanced structural similarity matches. Our streamlined cheminformatics workflows allow anyone with basic experience in R to pull out component areas for tentative compound identifications using the best published understanding of molecules across samples (pubchem.gov). Interpretations can now be done at a fraction of the time, cost, and effort it would typically take using a standard chemical ecology data analysis pipeline. The package was tested in two experimental contexts: (1) A dataset of purified internal standards, which showed our algorithms correctly identified the known compounds with R2 values ranging from 0.827-0.999 along concentrations ranging from 1 × 10-5 to 1 × 103 ng/μl, (2) A large, previously published dataset, where the number and types of compounds identified were comparable (or identical) to those identified with the traditional manual peak annotation process, and NMDS analysis of the compounds produced the same pattern of significance as in the original study. Both the speed and accuracy of GC -MS data processing are drastically improved with uafR because it allows users to fluidly interact with their experiment following tentative library identifications [i.e. after the m/z spectra have been matched against an installed chemical fragmentation database (e.g. NIST)]. Use of uafR will allow larger datasets to be collected and systematically interpreted quickly. Furthermore, the functions of uafR could allow backlogs of previously collected and annotated data to be processed by new personnel or students as they are being trained. This is critical as we enter the era of exposomics, metabolomics, volatilomes, and landscape level, high-throughput chemotyping. This package was developed to advance collective understanding of chemical data and is applicable to any research that benefits from GC -MS analysis. It can be downloaded for free along with sample datasets from Github at github.org/castratton/uafR or installed directly from R or RStudio using the developer tools: 'devtools::install_github("castratton/uafR")'.},
}

*Gas Chromatography-Mass Spectrometry/methods
*Algorithms
*Software
Cheminformatics/methods

@article {pmid38967613,
year = {2024},
author = {Hanners, A and Melnyk, B and Bedell, T and Conroy, S and Volek, J and Brock, G and Kelley, M},
title = {A pilot study of Keto Prescribed+: A healthy thinking and eating educational program for African American women.},
journal = {Journal of the American Association of Nurse Practitioners},
volume = {36},
number = {7},
pages = {377-384},
pmid = {38967613},
issn = {2327-6924},
support = {L30 HL159699/HL/NHLBI NIH HHS/United States ; UL1TR002733//Center for Clinical and Translational Science, Ohio State University/ ; TL1TR002735//Center for Clinical and Translational Science, Ohio State University/ ; },
mesh = {Humans ; Female ; Pilot Projects ; *Black or African American/psychology/statistics & numerical data ; Adult ; Middle Aged ; Obesity/therapy/psychology ; },
abstract = {African American (AA) women have the highest prevalence of obesity in addition to health disparities in preventable diet-related diseases (i.e., diabetes, hypertension), which places them at increased risk for cardiovascular disease. The purpose of this pilot study was to assess the feasibility, acceptability, and preliminary effectiveness of the Keto Prescribed+ (KetoRx+) program on associated physical and psychosocial outcomes among this population. The KetoRx+ program is a healthy eating and thinking educational intervention. The program combined online and in-person community group sessions over 8 weeks. The Keto Prescribed+ was found to be feasible and acceptable with comments on ways to increase acceptability from participants completing program (n = 10). Physical outcomes changed showed an average decrease in weight of 10lbs (SD = 5), baseline average 226lbs. Waist-to-hip ratio and systolic blood pressure also trended down. Psychosocial outcomes showed improvement trends. The KetoRx+ program is feasible and acceptable for overweight or obese AA women. Preliminary efficacy was established for most physical and psychosocial outcomes. However, more research is needed to identify specific program components contributing to healthy lifestyle behavior change and to establish program efficacy and effectiveness. Culturally adapted community-based biopsychosocial interventions using ketogenic nutrition therapy may help improve cardiovascular health of adult AA women.},
}

Humans
Female
Pilot Projects
*Black or African American/psychology/statistics & numerical data
Adult
Middle Aged
Obesity/therapy/psychology

@article {pmid38966305,
year = {2024},
author = {Crowley, LM and Roy, HE and Brown, PMJ and , and , and , and , and , and , and , },
title = {The genome sequence of the ten-spot ladybird, Adalia decempunctata (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {106},
pmid = {38966305},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Adalia decempunctata (the ten-spot ladybird; Arthropoda; Insecta; Coleoptera; Coccinellidae). The genome sequence is 489.4 megabases in span. Most of the assembly is scaffolded into 12 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 19.68 kilobases in length.},
}

@article {pmid38964062,
year = {2024},
author = {Jeon, Y and Kwon, YS and Noh, YJ and Lee, SM and Song, JW and Kim, JH and Seo, JS},
title = {Unraveling the mechanisms of benzo[a]pyrene degradation by Pigmentiphaga kullae strain KIT-003 using a multi-omics approach.},
journal = {Ecotoxicology and environmental safety},
volume = {281},
number = {},
pages = {116665},
doi = {10.1016/j.ecoenv.2024.116665},
pmid = {38964062},
issn = {1090-2414},
mesh = {*Benzo(a)pyrene/metabolism/toxicity ; *Biodegradation, Environmental ; Republic of Korea ; Proteomics ; Water Pollutants, Chemical/metabolism/toxicity ; Gas Chromatography-Mass Spectrometry ; Catechols/metabolism ; Rivers/chemistry/microbiology ; Multiomics ; },
abstract = {Polycyclic aromatic hydrocarbons (PAHs), notably benzo[a]pyrene (BaP), are environmental contaminants with multiple adverse ecological implications. Numerous studies have suggested the use of BaP biodegradation using various bacterial strains to remove BaP from the environment. This study investigates the BaP biodegradation capability of Pigmentiphaga kullae strain KIT-003, isolated from the Nak-dong River (South Korea) under specific environmental conditions. The optimum conditions of biodegradation were found to be pH 7.0, 35°C, and a salinity of 0 %. GC-MS analysis suggested alternative pathways by which KIT-003 produced catechol from BaP through several intermediate metabolites, including 4-formylchrysene-5-carboxylic acid, 5,6-dihydro-5,6-dihydroxychrysene-5-carboxylic acid (isomer: 3,4-dihydro-3,4-dihydroxychrysene-4-carboxylic acid), naphthalene-1,2-dicarboxylic acid, and 2-hydroxy-1-naphthoic acid. Proteomic profiles indicated upregulation of enzymes associated with aromatic compound degradation, such as nahAc and nahB, and of those integral to the tricarboxylic acid cycle, reflecting the strain's adaptability to and degradation of BaP. Lipidomic analysis of KIT-003 demonstrated that BaP exposure induced an accumulation of glycerolipids such as diacylglycerol and triacylglycerol, indicating their crucial role in bacterial adaptation mechanisms under BaP stress. This study provides significant scientific knowledge regarding the intricate mechanisms involved in BaP degradation by microorganisms.},
}

*Benzo(a)pyrene/metabolism/toxicity
*Biodegradation, Environmental
Republic of Korea
Proteomics
Water Pollutants, Chemical/metabolism/toxicity
Gas Chromatography-Mass Spectrometry
Catechols/metabolism
Rivers/chemistry/microbiology
Multiomics

@article {pmid38960861,
year = {2024},
author = {Dolenz, S and van der Valk, T and Jin, C and Oppenheimer, J and Sharif, MB and Orlando, L and Shapiro, B and Dalén, L and Heintzman, PD},
title = {Unravelling reference bias in ancient DNA datasets.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {7},
pages = {},
pmid = {38960861},
issn = {1367-4811},
support = {2021.0048//Knut and Alice Wallenberg Foundation/ ; },
mesh = {*DNA, Ancient/analysis ; Humans ; *Sequence Analysis, DNA/methods ; Software ; Animals ; Sequence Alignment/methods ; Computational Biology/methods ; Algorithms ; },
abstract = {MOTIVATION: The alignment of sequencing reads is a critical step in the characterization of ancient genomes. However, reference bias and spurious mappings pose a significant challenge, particularly as cutting-edge wet lab methods generate datasets that push the boundaries of alignment tools. Reference bias occurs when reference alleles are favoured over alternative alleles during mapping, whereas spurious mappings stem from either contamination or when endogenous reads fail to align to their correct position. Previous work has shown that these phenomena are correlated with read length but a more thorough investigation of reference bias and spurious mappings for ancient DNA has been lacking. Here, we use a range of empirical and simulated palaeogenomic datasets to investigate the impacts of mapping tools, quality thresholds, and reference genome on mismatch rates across read lengths.

RESULTS: For these analyses, we introduce AMBER, a new bioinformatics tool for assessing the quality of ancient DNA mapping directly from BAM-files and informing on reference bias, read length cut-offs and reference selection. AMBER rapidly and simultaneously computes the sequence read mapping bias in the form of the mismatch rates per read length, cytosine deamination profiles at both CpG and non-CpG sites, fragment length distributions, and genomic breadth and depth of coverage. Using AMBER, we find that mapping algorithms and quality threshold choices dictate reference bias and rates of spurious alignment at different read lengths in a predictable manner, suggesting that optimized mapping parameters for each read length will be a key step in alleviating reference bias and spurious mappings.

AMBER is available for noncommercial use on GitHub (https://github.com/tvandervalk/AMBER.git). Scripts used to generate and analyse simulated datasets are available on Github (https://github.com/sdolenz/refbias_scripts).},
}

*DNA, Ancient/analysis
Humans
*Sequence Analysis, DNA/methods
Software
Animals
Sequence Alignment/methods
Computational Biology/methods
Algorithms

@article {pmid38956468,
year = {2024},
author = {Li, X and Cao, T and Liu, H and Fu, L and Wang, Q},
title = {Identification and expression analysis of Sox family genes in echinoderms.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {655},
pmid = {38956468},
issn = {1471-2164},
support = {ZR2021QD158//Natural Science Foundation of Shandong Province, China/ ; ZR2021MC151//Natural Science Foundation of Shandong Province, China/ ; 2023XBZD003//Scientific Research Project of Yantai Vocational College/ ; },
mesh = {Animals ; *SOX Transcription Factors/genetics/metabolism ; *Phylogeny ; *Echinodermata/genetics ; *Multigene Family ; Gene Expression Profiling ; Evolution, Molecular ; Gene Expression Regulation, Developmental ; Computational Biology/methods ; },
abstract = {The Sox gene family, a collection of transcription factors widely distributed throughout the animal kingdom, plays a crucial role in numerous developmental processes. Echinoderms occupy a pivotal position in many research fields, such as neuroscience, sex determination and differentiation, and embryonic development. However, to date, no comprehensive study has been conducted to characterize and analyze Sox genes in echinoderms. In the present study, the evolution and expression of Sox family genes across 11 echinoderms were analyzed using bioinformatics methods. The results revealed a total of 70 Sox genes, with counts ranging from 5 to 8 across different echinoderms. Phylogenetic analysis revealed that the identified Sox genes could be categorized into seven distinct classes: the SoxB1 class, SoxB2 class, SoxC class, SoxD class, SoxE class, SoxF class and SoxH class. Notably, the SoxB1, SoxB2, and SoxF genes were ubiquitously present in all the echinoderms studied, which suggests that these genes may be conserved in echinoderms. The spatiotemporal expression patterns observed for Sox genes in the three echinoderms indicated that various Sox members perform distinct functional roles. Notably, SoxB1 is likely involved in echinoderm ovary development, while SoxH may play a crucial role in testis development in starfish and sea cucumber. In general, the present investigation provides a molecular foundation for exploring the Sox gene in echinoderms, providing a valuable resource for future phylogenetic and genomic studies.},
}

Animals
*SOX Transcription Factors/genetics/metabolism
*Phylogeny
*Echinodermata/genetics
*Multigene Family
Gene Expression Profiling
Evolution, Molecular
Gene Expression Regulation, Developmental
Computational Biology/methods

@article {pmid38955825,
year = {2024},
author = {Pan, H and Wattiez, R and Gillan, D},
title = {Soil Metaproteomics for Microbial Community Profiling: Methodologies and Challenges.},
journal = {Current microbiology},
volume = {81},
number = {8},
pages = {257},
pmid = {38955825},
issn = {1432-0991},
support = {No.2023-BSBA-024//Joint Funds of the Natural Science Foundation of Liaoning Province of China/ ; },
mesh = {*Soil Microbiology ; *Proteomics/methods ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Microbiota ; Fungi/classification/genetics/metabolism/isolation & purification ; Soil/chemistry ; Computational Biology/methods ; },
abstract = {Soil represents a complex and dynamic ecosystem, hosting a myriad of microorganisms that coexist and play vital roles in nutrient cycling and organic matter transformation. Among these microorganisms, bacteria and fungi are key members of the microbial community, profoundly influencing the fate of nitrogen, sulfur, and carbon in terrestrial environments. Understanding the intricacies of soil ecosystems and the biological processes orchestrated by microbial communities necessitates a deep dive into their composition and metabolic activities. The advent of next-generation sequencing and 'omics' techniques, such as metagenomics and metaproteomics, has revolutionized our understanding of microbial ecology and the functional dynamics of soil microbial communities. Metagenomics enables the identification of microbial community composition in soil, while metaproteomics sheds light on the current biological functions performed by these communities. However, metaproteomics presents several challenges, both technical and computational. Factors such as the presence of humic acids and variations in extraction methods can influence protein yield, while the absence of high-resolution mass spectrometry and comprehensive protein databases limits the depth of protein identification. Notwithstanding these limitations, metaproteomics remains a potent tool for unraveling the intricate biological processes and functions of soil microbial communities. In this review, we delve into the methodologies and challenges of metaproteomics in soil research, covering aspects such as protein extraction, identification, and bioinformatics analysis. Furthermore, we explore the applications of metaproteomics in soil bioremediation, highlighting its potential in addressing environmental challenges.},
}

*Soil Microbiology
*Proteomics/methods
*Metagenomics/methods
*Bacteria/genetics/classification/metabolism/isolation & purification
*Microbiota
Fungi/classification/genetics/metabolism/isolation & purification
Soil/chemistry
Computational Biology/methods

@article {pmid38954338,
year = {2024},
author = {Yao, Z and Zhou, X and Jin, T and Wang, L and Liu, N and Wu, L},
title = {Remediation of phenanthrene contaminated soil by persulphate coupled with Pseudomonas aeruginosa GZ7 based on oxidation prediction model.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {31},
pages = {44415-44430},
pmid = {38954338},
issn = {1614-7499},
support = {52270171//Innovative Research Group Project of the National Natural Science Foundation of China/ ; 51974314//Innovative Research Group Project of the National Natural Science Foundation of China/ ; },
mesh = {*Phenanthrenes/metabolism ; *Pseudomonas aeruginosa ; *Soil Pollutants ; *Oxidation-Reduction ; *Soil/chemistry ; Soil Microbiology ; Environmental Restoration and Remediation/methods ; Biodegradation, Environmental ; Polycyclic Aromatic Hydrocarbons ; Sulfates/chemistry ; },
abstract = {Chemical oxidation coupled with microbial remediation has attracted widespread attention for the removal of polycyclic aromatic hydrocarbons (PAHs). Among them, the precise evaluation of the feasible oxidant concentration of PAH-contaminated soil is the key to achieving the goal of soil functional ecological remediation. In this study, phenanthrene (PHE) was used as the target pollutant, and Fe[2+]-activated persulphate (PS) was used to remediate four types of soils. Linear regression analysis identified the following important factors influencing remediation: PS dosage and soil PHE content for PHE degradation, Fe[2+] dosage, hydrolysable nitrogen (HN), and available phosphorus for PS decomposition. A comprehensive model of "soil characteristics-oxidation conditions-remediation effect" with a high predictive accuracy was constructed. Based on model identification, Pseudomonas aeruginosa GZ7, which had high PAHs degrading ability after domestication, was further applied to coupling repair remediation. The results showed that the optimal PS dose was 0.75% (w/w). The response relationship between soil physical, chemical, and biological indicators at the intermediate interface and oxidation conditions was analysed. Coupled remediation effects were clarified using microbial diversity sequencing. The introduction of Pseudomonas aeruginosa GZ7 stimulated the relative abundance of Cohnella, Enterobacter, Paenibacillus, and Bacillus, which can promote material metabolism and energy transformation during remediation.},
}

*Phenanthrenes/metabolism
*Pseudomonas aeruginosa
*Soil Pollutants
*Oxidation-Reduction
*Soil/chemistry
Soil Microbiology
Environmental Restoration and Remediation/methods
Biodegradation, Environmental
Polycyclic Aromatic Hydrocarbons
Sulfates/chemistry

@article {pmid38954067,
year = {2024},
author = {Bazkiaee, PA and Kamkar, B and Amiri, E and Kazemi, H and Rezaei, M and Araji, HA},
title = {Multi-criteria GIS-based land suitability analysis for rice cultivation: a case study in Guilan Province, Iran.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {7},
pages = {680},
pmid = {38954067},
issn = {1573-2959},
mesh = {*Oryza/growth & development ; Iran ; *Geographic Information Systems ; *Environmental Monitoring/methods ; *Agriculture/methods ; *Soil/chemistry ; Conservation of Natural Resources ; Climate ; },
abstract = {Ensuring food security and sustainable resource management has become a paramount global concern, prompting significant attention to land suitability analysis for enhancing agricultural production. In this study, an AHP-weighted overlay method was employed to delineate rice cultivation suitability in Guilan province, Iran, a central hub for rice production. Sixteen climatic, topographic, and soil variables were integrated, and individual maps were reclassified to align with the specific requisites for rice production. The results revealed three suitability classes: including 'very suitable,' 'suitable,' and 'moderately suitable', covering 91%, 6%, and 3% of the land, respectively. Soil attributes, particularly organic matter, significantly influenced suitability (weight value of 0.745), with topographic and soil factors outweighing climate in assessment. While salinity is generally absent, organic matter deficiency affects 44% of the land. Phosphorus imbalances are prevalent, with potassium toxicity observed in 10%. Microelement deficiencies, especially in iron and zinc, are noted. Additionally, the results indicated that topographic and soil attributes played a more significant role than climate-related factors in assessing land suitability for rice cultivation within the study area. This research provides a comprehensive spatial analysis of all variables in the study region, shedding light on the complexities of land suitability for rice cultivation. These findings contribute to the understanding of agricultural sustainability and resource management strategies in the context of food security.},
}

*Oryza/growth & development
Iran
*Geographic Information Systems
*Environmental Monitoring/methods
*Agriculture/methods
*Soil/chemistry
Conservation of Natural Resources
Climate

@article {pmid38951915,
year = {2024},
author = {Koci, O and Russell, RK and Shaikh, MG and Edwards, C and Gerasimidis, K and Ijaz, UZ},
title = {CViewer: a Java-based statistical framework for integration of shotgun metagenomics with other omics datasets.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {117},
pmid = {38951915},
issn = {2049-2618},
support = {NE/L011956/1//NERC Environmental Bioinformatics Centre/ ; BB/T010657/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; EP/V030515/1//Engineering and Physical Sciences Research Council/ ; },
mesh = {*Metagenomics/methods ; Humans ; *Software ; Microbiota/genetics ; Gastrointestinal Microbiome/genetics ; Computational Biology/methods ; Metagenome ; Crohn Disease/microbiology/genetics ; },
abstract = {BACKGROUND: Shotgun metagenomics for microbial community survey recovers enormous amount of information for microbial genomes that include their abundances, taxonomic, and phylogenetic information, as well as their genomic makeup, the latter of which then helps retrieve their function based on annotated gene products, mRNA, protein, and metabolites. Within the context of a specific hypothesis, additional modalities are often included, to give host-microbiome interaction. For example, in human-associated microbiome projects, it has become increasingly common to include host immunology through flow cytometry. Whilst there are plenty of software approaches available, some that utilize marker-based and assembly-based approaches, for downstream statistical analyses, there is still a dearth of statistical tools that help consolidate all such information in a single platform. By virtue of stringent computational requirements, the statistical workflow is often passive with limited visual exploration.

RESULTS: In this study, we have developed a Java-based statistical framework (https://github.com/KociOrges/cviewer) to explore shotgun metagenomics data, which integrates seamlessly with conventional pipelines and offers exploratory as well as hypothesis-driven analyses. The end product is a highly interactive toolkit with a multiple document interface, which makes it easier for a person without specialized knowledge to perform analysis of multiomics datasets and unravel biologically relevant patterns. We have designed algorithms based on frequently used numerical ecology and machine learning principles, with value-driven from integrated omics tools which not only find correlations amongst different datasets but also provide discrimination based on case-control relationships.

CONCLUSIONS: CViewer was used to analyse two distinct metagenomic datasets with varying complexities. These include a dietary intervention study to understand Crohn's disease changes during a dietary treatment to include remission, as well as a gut microbiome profile for an obesity dataset comparing subjects who suffer from obesity of different aetiologies and against controls who were lean. Complete analyses of both studies in CViewer then provide very powerful mechanistic insights that corroborate with the published literature and demonstrate its full potential. Video Abstract.},
}

*Metagenomics/methods
Humans
*Software
Microbiota/genetics
Gastrointestinal Microbiome/genetics
Computational Biology/methods
Metagenome
Crohn Disease/microbiology/genetics

@article {pmid38947430,
year = {2024},
author = {Li, S and Mao, Y and Yang, J and Li, Y and Dong, J and Wang, Z and Jiang, L and He, S},
title = {Efficient integration of covalent triazine frameworks (CTFs) for augmented photocatalytic efficacy: A review of synthesis, strategies, and applications.},
journal = {Heliyon},
volume = {10},
number = {11},
pages = {e32202},
pmid = {38947430},
issn = {2405-8440},
abstract = {Heterogeneous photocatalysis emerges as an exceptionally appealing technological avenue for the direct capture, conversion, and storage of renewable solar energy, facilitating the generation of sustainable and ecologically benign solar fuels and a spectrum of other pertinent applications. Heterogeneous nanocomposites, incorporating Covalent Triazine Frameworks (CTFs), exhibit a wide-ranging spectrum of light absorption, well-suited electronic band structures, rapid charge carrier mobility, ample resource availability, commendable chemical robustness, and straightforward synthetic routes. These attributes collectively position them as highly promising photocatalysts with applicability in diverse fields, including but not limited to the production of photocatalytic solar fuels and the decomposition of environmental contaminants. As the field of photocatalysis through the hybridization of CTFs undergoes rapid expansion, there is a pressing and substantive need for a systematic retrospective analysis and forward-looking evaluation to elucidate pathways for enhancing performance. This comprehensive review commences by directing attention to diverse synthetic methodologies for the creation of composite materials. And then it delves into a thorough exploration of strategies geared towards augmenting performance, encompassing the introduction of electron donor-acceptor (D-A) units, heteroatom doping, defect Engineering, architecture of Heterojunction and optimization of morphology. Following this, it systematically elucidates applications primarily centered around the efficient generation of photocatalytic hydrogen, reduction of carbon dioxide through photocatalysis, and the degradation of organic pollutants. Ultimately, the discourse turns towards unresolved challenges and the prospects for further advancement, offering valuable guidance for the potent harnessing of CTFs in high-efficiency photocatalytic processes.},
}

@article {pmid38945180,
year = {2024},
author = {Pearl, RL and Donze, LF and Rosas, LG and Agurs-Collins, T and Baskin, ML and Breland, JY and Shanks, CB and Stowers, KC and Johnson, S and Lee, BY and Martin, MY and Mujuru, P and Odoms-Young, A and Panza, E and Pronk, NP and Calicutt, K and Nadglowski, J and Nece, PM and Tedder, M and Chow, LS and Krishnamurti, H and Jay, M and Xi, D and Jastreboff, AM and Stanford, FC},
title = {Ending Weight Stigma to Advance Health Equity.},
journal = {American journal of preventive medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.amepre.2024.06.021},
pmid = {38945180},
issn = {1873-2607},
}

@article {pmid38941024,
year = {2024},
author = {Holstein, T and Muth, T},
title = {Bioinformatic Workflows for Metaproteomics.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2820},
number = {},
pages = {187-213},
pmid = {38941024},
issn = {1940-6029},
mesh = {*Proteomics/methods ; *Computational Biology/methods ; *Workflow ; *Software ; *Microbiota/genetics ; Humans ; Databases, Protein ; Metagenomics/methods ; },
abstract = {The strong influence of microbiomes on areas such as ecology and human health has become widely recognized in the past years. Accordingly, various techniques for the investigation of the composition and function of microbial community samples have been developed. Metaproteomics, the comprehensive analysis of the proteins from microbial communities, allows for the investigation of not only the taxonomy but also the functional and quantitative composition of microbiome samples. Due to the complexity of the investigated communities, methods developed for single organism proteomics cannot be readily applied to metaproteomic samples. For this purpose, methods specifically tailored to metaproteomics are required. In this work, a detailed overview of current bioinformatic solutions and protocols in metaproteomics is given. After an introduction to the proteomic database search, the metaproteomic post-processing steps are explained in detail. Ten specific bioinformatic software solutions are focused on, covering various steps including database-driven identification and quantification as well as taxonomic and functional assignment.},
}

*Proteomics/methods
*Computational Biology/methods
*Workflow
*Software
*Microbiota/genetics
Humans
Databases, Protein
Metagenomics/methods

@article {pmid38938637,
year = {2024},
author = {Yang, J and Deng, H and Zhang, Y and Zhou, Y and Miao, T},
title = {Application of amodal segmentation for shape reconstruction and occlusion recovery in occluded tomatoes.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1376138},
pmid = {38938637},
issn = {1664-462X},
abstract = {Common object detection and image segmentation methods are unable to accurately estimate the shape of the occluded fruit. Monitoring the growth status of shaded crops in a specific environment is challenging, and certain studies related to crop harvesting and pest detection are constrained by the natural shadow conditions. Amodal segmentation can focus on the occluded part of the fruit and complete the overall shape of the fruit. We proposed a Transformer-based amodal segmentation algorithm to infer the amodal shape of occluded tomatoes. Considering the high cost of amodal annotation, we only needed modal dataset to train the model. The dataset was taken from two greenhouses on the farm and contains rich occlusion information. We introduced boundary estimation in the hourglass structured network to provide a priori information about the completion of the amodal shapes, and reconstructed the occluded objects using a GAN network (with discriminator) and GAN loss. The model in this study showed accuracy, with average pairwise accuracy of 96.07%, mean intersection-over-union (mIoU) of 94.13% and invisible mIoU of 57.79%. We also examined the quality of pseudo-amodal annotations generated by our proposed model using Mask R-CNN. Its average precision (AP) and average precision with intersection over union (IoU) 0.5 (AP50) reached 63.91%,86.91% respectively. This method accurately and rationally achieves the shape of occluded tomatoes, saving the cost of manual annotation, and is able to deal with the boundary information of occlusion while decoupling the relationship of occluded objects from each other. Future work considers how to complete the amodal segmentation task without overly relying on the occlusion order and the quality of the modal mask, thus promising applications to provide technical support for the advancement of ecological monitoring techniques and ecological cultivation.},
}

@article {pmid38937989,
year = {2024},
author = {Wu, H and Mu, C and Li, X and Fan, W and Shen, L and Zhu, W},
title = {Breed-Driven Microbiome Heterogeneity Regulates Intestinal Stem Cell Proliferation via Lactobacillus-Lactate-GPR81 Signaling.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2400058},
doi = {10.1002/advs.202400058},
pmid = {38937989},
issn = {2198-3844},
support = {32030104//National Natural Science Foundation of China/ ; 2022YFD1300402//National Key Research and Development Program of China/ ; },
abstract = {Genetically lean and obese individuals have distinct intestinal microbiota and function. However, the underlying mechanisms of the microbiome heterogeneity and its regulation on epithelial function such as intestinal stem cell (ISC) fate remain unclear. Employing pigs of genetically distinct breeds (obese Meishan and lean Yorkshire), this study reveals transcriptome-wide variations in microbial ecology of the jejunum, characterized by enrichment of active Lactobacillus species, notably the predominant Lactobacillus amylovorus (L. amylovorus), and lactate metabolism network in obese breeds. The L. amylovorus-dominant heterogeneity is paralleled with epithelial functionality difference as reflected by highly expressed GPR81, more proliferative ISCs and activated Wnt/β-catenin signaling. Experiments using in-house developed porcine jejunal organoids prove that live L. amylovorus and its metabolite lactate promote intestinal organoid growth. Mechanistically, L. amylovorus and lactate activate Wnt/β-catenin signaling in a GPR81-dependent manner to promote ISC-mediated epithelial proliferation. However, heat-killed L. amylovorus fail to cause these changes. These findings uncover a previously underrepresented role of L. amylovorus in regulating jejunal stem cells via Lactobacillus-lactate-GPR81 axis, a key mechanism bridging breed-driven intestinal microbiome heterogeneity with ISC fate. Thus, results from this study provide new insights into the role of gut microbiome and stem cell interactions in maintaining intestinal homeostasis.},
}

@article {pmid38936731,
year = {2024},
author = {Li, Y and Hou, K and Chang, Y and Yuan, B and Li, X},
title = {A methodological study on the identification of ecological security change processes and zoning control strategies -- Based on the perspective of sustainable development.},
journal = {The Science of the total environment},
volume = {946},
number = {},
pages = {174190},
doi = {10.1016/j.scitotenv.2024.174190},
pmid = {38936731},
issn = {1879-1026},
abstract = {Ecological security (ES) is a crucial indicator for assessing the sustainable development of a region. Currently, most studies on ES primarily focus on process analysis, and the integration of environmental variability into the development of tailored control strategies for regions with varying ecological quality is overlooked. Therefore, in this study, we identified regional ES change processes, employed an optimized system to calculate the ecological security index (ESI), and identified ecological corridors (ECs) through the Minimum Constrained Resource (MCR) model to determine zoning strategies for typical arid regions, using the Ningxia region in the Yellow River Basin of China as an example. The findings showed that (1) from 2006 to 2020, the ESI values of most regions were between 0.2 and 0.4, with small but consistent increases in the ESI values over the years. (2) The proportion of regions with high ES ratings increased by 9.08 % across all districts and counties, and the center of gravity of ES shifted in a north-south and east-west direction. (3) The ESI exhibited a strong positive spatial correlation, characterized by spatial diffusion and spillover effects in most regions. (4) The ECs were predominantly distributed in a north-south direction, involving a total of 20 districts and counties. Based on the principles of sustainable development, we developed a model for the dynamic identification and zoning control of regional ES, aiming to provide a practical framework for effective ecological restoration and protection measures. Additionally, the strategies and methodologies presented in this study serve as important references for similar regions worldwide to facilitate the zoning control of ES, highlighting the broader significance and applicability of the study.},
}

@article {pmid38935782,
year = {2024},
author = {Louvet, A and Mantoux, C and Machon, N},
title = {Assessing the extinction risk of the spontaneous flora in urban tree bases.},
journal = {PLoS computational biology},
volume = {20},
number = {6},
pages = {e1012191},
pmid = {38935782},
issn = {1553-7358},
mesh = {*Extinction, Biological ; *Trees ; *Bayes Theorem ; *Cities ; *Ecosystem ; Computational Biology ; Markov Chains ; Models, Biological ; Paris ; },
abstract = {As the spatial arrangement of trees planted along streets in cities makes their bases potential ecological corridors for the flora, urban tree bases may be a key contributor to the overall connectivity of the urban ecosystem. However, these tree bases are also a highly fragmented environment in which extinctions are frequent. The goal of this study was to assess the plant species' ability to survive and spread through urban tree bases. To do so, we developed a Bayesian framework to assess the extinction risk of a plant metapopulation using presence/absence data, assuming that the occupancy dynamics was described by a Hidden Markov Model. The novelty of our approach is to take into account the combined effect of low-distance dispersal and the potential presence of a seed bank on the extinction risk. We introduced a metric of the extinction risk and examined its performance over a wide range of metapopulation parameters. We applied our framework to yearly floristic inventories carried out in 1324 tree bases in Paris, France. While local extinction risks were generally high, extinction risks at the street scale varied greatly from one species to another. We identified 10 plant species that could survive and spread through urban tree bases, and three plant traits correlated with the extinction risk at the metapopulation scale: the maximal height, and the beginning and end of the flowering period. Our results suggest that some plant species can use urban tree bases as ecological corridors despite high local extinction risks by forming a seed bank. We also identified other plant traits correlated with the ability to survive in tree bases, related to the action of gardeners. Moreover, our findings demonstrate that our Bayesian estimation framework based on percolation theory has the potential to be extended to more general metapopulations.},
}

*Extinction, Biological
*Trees
*Bayes Theorem
*Cities
*Ecosystem
Computational Biology
Markov Chains
Models, Biological
Paris

@article {pmid38932245,
year = {2024},
author = {Conradie, T and Caparros-Martin, JA and Egan, S and Kicic, A and Koks, S and Stick, SM and Agudelo-Romero, P},
title = {Exploring the Complexity of the Human Respiratory Virome through an In Silico Analysis of Shotgun Metagenomic Data Retrieved from Public Repositories.},
journal = {Viruses},
volume = {16},
number = {6},
pages = {},
pmid = {38932245},
issn = {1999-4915},
support = {NHMRC115648//National Health and Medical Research Council/ ; Synergy grant APP118364//National Health and Medical Research Council/ ; Theme Collaboration Award 2023//Telethon Kids Institute/ ; N/A//Google cloud education program/ ; Investigator grant 2021/GR000216//National Health and Medical Research Council/ ; },
mesh = {Humans ; *Metagenomics/methods ; *Virome ; *Genome, Viral ; *Respiratory System/virology ; *Viruses/genetics/classification/isolation & purification ; Metagenome ; Computer Simulation ; Phylogeny ; Computational Biology/methods ; Microbiota ; Bacteriophages/genetics/classification/isolation & purification ; },
abstract = {BACKGROUND: Respiratory viruses significantly impact global morbidity and mortality, causing more disease in humans than any other infectious agent. Beyond pathogens, various viruses and bacteria colonize the respiratory tract without causing disease, potentially influencing respiratory diseases' pathogenesis. Nevertheless, our understanding of respiratory microbiota is limited by technical constraints, predominantly focusing on bacteria and neglecting crucial populations like viruses. Despite recent efforts to improve our understanding of viral diversity in the human body, our knowledge of viral diversity associated with the human respiratory tract remains limited.

METHODS: Following a comprehensive search in bibliographic and sequencing data repositories using keyword terms, we retrieved shotgun metagenomic data from public repositories (n = 85). After manual curation, sequencing data files from 43 studies were analyzed using EVEREST (pipEline for Viral assEmbly and chaRactEriSaTion). Complete and high-quality contigs were further assessed for genomic and taxonomic characterization.

RESULTS: Viral contigs were obtained from 194 out of the 868 FASTQ files processed through EVEREST. Of the 1842 contigs that were quality assessed, 8% (n = 146) were classified as complete/high-quality genomes. Most of the identified viral contigs were taxonomically classified as bacteriophages, with taxonomic resolution ranging from the superkingdom level down to the species level. Captured contigs were spread across 25 putative families and varied between RNA and DNA viruses, including previously uncharacterized viral genomes. Of note, airway samples also contained virus(es) characteristic of the human gastrointestinal tract, which have not been previously described as part of the lung virome. Additionally, by performing a meta-analysis of the integrated datasets, ecological trends within viral populations linked to human disease states and their biogeographical distribution along the respiratory tract were observed.

CONCLUSION: By leveraging publicly available repositories of shotgun metagenomic data, the present study provides new insights into viral genomes associated with specimens from the human respiratory tract across different disease spectra. Further studies are required to validate our findings and evaluate the potential impact of these viral communities on respiratory tract physiology.},
}

Humans
*Metagenomics/methods
*Virome
*Genome, Viral
*Respiratory System/virology
*Viruses/genetics/classification/isolation & purification
Metagenome
Computer Simulation
Phylogeny
Computational Biology/methods
Microbiota
Bacteriophages/genetics/classification/isolation & purification

@article {pmid38924481,
year = {2024},
author = {Ramos, SR and Reynolds, H and Johnson, C and Melkus, G and Kershaw, T and Thayer, J and Vorderstrasse, A},
title = {Perceptions on HIV-related Comorbidities and Usability of a Virtual Environment as CVD Prevention Education in Sexual Minority Men with HIV: Formative Phases of a Pilot RCT.},
journal = {Journal of medical Internet research},
volume = {},
number = {},
pages = {},
doi = {10.2196/57351},
pmid = {38924481},
issn = {1438-8871},
abstract = {BACKGROUND: Sexual minority men with HIV are at increased risk of cardiovascular disease (CVD) and have been underrepresented in behavioral research and in clinical trials.

OBJECTIVE: To explore perceptions about HIV-related comorbidities and assess the interest and usability of a virtual environment as CVD prevention education in Black and Latinx sexual minority men with HIV.

METHODS: This is a 3-phase pilot randomized control behavioral trial. We report on formative phases 1 and 2 that informed virtual environment content and features using qualitative interviews, usability testing, and beta testing with 25 individuals. In Phase 1, 15 participants completed interviews exploring HIV-related illnesses of concern that would be used to tailor the virtual environment. In Phase 2, usability and beta testing were conducted with 10 participants to assess interest, features, and content.

RESULTS: In Phase 1, we found CVD risk factors included high blood pressure, heart attack, stroke, and diabetes. Cancer (prostate, colon, and others) was a common concern and so were the development of mental health conditions. In Phase 2, all participants completed the 12-item usability checklist with favorable feedback within 30 to 60 minutes. Beta-testing interviews suggested: 1) Mixed perceptions about health and HIV, 2) High risk for comorbid conditions, 3) Virtual environment features were promising, and 4) need for diverse avatar representations.

CONCLUSIONS: We identified several comorbid conditions of concern and findings carry significant implications for mitigating barriers to preventative health screenings given the shared risk factors between HIV and related comorbidities. Highly rated aspects of the virtual environment were anonymity, meeting others who identify as gay or bisexual with HIV, validating LGBTQ+ images and content, and accessibility to CVD prevention education. Critical end-user feedback from beta-testing suggested more options for avatar customization in skin, hair, body representation. Our next phase will test the virtual environment as a new approach to advancing cardiovascular health equity in ethnic and racial sexual minority men with HIV.

CLINICALTRIAL: clinicaltrials.gov (NCT04061915).

RR2-10.2196/38348.},
}

@article {pmid38917233,
year = {2024},
author = {Costa, IB and Pimenta, IDSF and Aiquoc, KM and Oliveira, ÂGRDC},
title = {Congenital syphilis, syphilis in pregnancy and prenatal care in Brazil: An ecological study.},
journal = {PloS one},
volume = {19},
number = {6},
pages = {e0306120},
pmid = {38917233},
issn = {1932-6203},
mesh = {Humans ; Pregnancy ; Female ; Brazil/epidemiology ; *Syphilis, Congenital/epidemiology ; *Prenatal Care ; *Pregnancy Complications, Infectious/epidemiology ; Incidence ; Adult ; Socioeconomic Factors ; Syphilis/epidemiology/diagnosis ; Adolescent ; Young Adult ; },
abstract = {The aim of this research was to evaluate the incidence of congenital syphilis and the ratio between congenital syphilis and syphilis in pregnant women in Brazil according to socioeconomic indicators (inadequate water supply and sanitation; illiteracy at 15 years of age or older; household income per capita; proportion of poor people; Gini index; human development index; and average health expenditure per inhabitant by the health system) and prenatal quality-of-care indicators. We conducted an ecological study using a sample composed of 257 municipalities, each with ≥ 100,000 inhabitants. Data was collected from four public databases: the Brazilian Institute of Geography and Statistics, comprising socioeconomical data from the 2010 census; and the data of 2019 available in the databases of the Department of Informatics of the Brazilian Health System, Information and Management of Primary Care, and the Electronic Citizen Information System. Descriptive analysis of dependent and independent variables and bivariate analysis by Negative Binomial regression were carried out. The mean incidence of congenital syphilis was 38% higher in municipalities with a Human Development Index up to 0.785 (ratio of means [RM] = 1.38; p = 0.049) and 57% higher among populations where less than 50% of primary healthcare services provided a rapid test for syphilis (RM = 1.57; p < 0.001). The ratio between congenital syphilis and syphilis in pregnant women was 29% higher in municipalities with a low household income per capita (RM = 1.29; p < 0.001) and 28% higher in locations where less than 50% of the primary healthcare services provided a rapid test for syphilis (RM = 1.28; p < 0.001). There was no statistical significance of the quality of prenatal care compared to the outcomes. This result underscores the challenges in detecting syphilis infections among pregnant women during prenatal care, consequently increasing the risk of vertical transmission of the disease to the fetus. Traits of inequality in the occurrence of congenital syphilis also draw attention to strategies to reduce health inequities and improve prenatal care.},
}

Humans
Pregnancy
Female
Brazil/epidemiology
*Syphilis, Congenital/epidemiology
*Prenatal Care
*Pregnancy Complications, Infectious/epidemiology
Incidence
Adult
Socioeconomic Factors
Syphilis/epidemiology/diagnosis
Adolescent
Young Adult

@article {pmid38916705,
year = {2024},
author = {Yu, J and Chen, S},
title = {The Use of Big Data Analysis in Digital Empowerment of Sustainable Technological Innovation Management of Ecological Enterprises.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {31},
pages = {43956-43966},
pmid = {38916705},
issn = {1614-7499},
mesh = {*Big Data ; China ; Inventions ; Ecology ; Empowerment ; Environmental Monitoring/methods ; Conservation of Natural Resources ; },
abstract = {With the social economy's rapid progress and the popularization of environmental awareness, ecological enterprises have gradually become a crucial trend in the development of modern enterprises. This work intends to promote the development of ecological enterprises to a higher level. This work first analyzes the management mode of ecological enterprises in the context of big data in China. Then, it establishes various indicators to analyze the role of sustainable technological innovation in enterprise development and the impact of digital empowerment on enterprise development. Finally, this work takes China's manufacturing industry and ecological enterprises in Hubei Province as examples to summarize the digital empowerment of sustainable technological innovation management of ecological enterprises under the background of big data. The final result indicates that sustainable technological innovation significantly reduces ecological enterprises' resource consumption and waste emissions. Additionally, it has a significant positive effect on improving enterprise output value and economic benefits. The digital empowerment of enterprises has a significant driving effect on sustainable technological innovation, with a digital driving coefficient of 26. This work provides a feasible scheme for the specific application of big data analysis in the technology innovation management of ecological enterprises, including market demand analysis, environmental monitoring and governance, technology assessment and risk management. This work expounds the role of big data analysis technology in improving decision-making efficiency, optimizing resource allocation and enhancing the competitiveness of enterprises in the digital empowerment of ecological enterprises.},
}

*Big Data
China
Inventions
Ecology
Empowerment
Environmental Monitoring/methods
Conservation of Natural Resources

@article {pmid38915508,
year = {2024},
author = {Shukla, HG and Chakraborty, M and Emerson, JJ},
title = {Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38915508},
issn = {2692-8205},
support = {S10 OD021718/OD/NIH HHS/United States ; R35 GM153327/GM/NIGMS NIH HHS/United States ; P30 AR075047/AR/NIAMS NIH HHS/United States ; R01 GM123303/GM/NIGMS NIH HHS/United States ; S10 OD010794/OD/NIH HHS/United States ; P30 CA062203/CA/NCI NIH HHS/United States ; R00 GM129411/GM/NIGMS NIH HHS/United States ; },
abstract = {Many essential functions of organisms are encoded in highly repetitive genomic regions, including histones involved in DNA packaging, centromeres that are core components of chromosome segregation, ribosomal RNA comprising the protein translation machinery, telomeres that ensure chromosome integrity, piRNA clusters encoding host defenses against selfish elements, and virtually the entire Y chromosome. These regions, formed by highly similar tandem arrays, pose significant challenges for experimental and informatic study, impeding sequence-level descriptions essential for understanding genetic variation. Here, we report the assembly and variation analysis of such repetitive regions in Drosophila melanogaster, offering significant improvements to the existing community reference assembly. Our work successfully recovers previously elusive segments, including complete reconstructions of the histone locus and the pericentric heterochromatin of the X chromosome, spanning the Stellate locus to the distal flank of the rDNA cluster. To infer structural changes in these regions where alignments are often not practicable, we introduce landmark anchors based on unique variants that are putatively orthologous. These regions display considerable structural variation between different D. melanogaster strains, exhibiting differences in copy number and organization of homologous repeat units between haplotypes. In the histone cluster, although we observe minimal genetic exchange indicative of crossing over, the variation patterns suggest mechanisms such as unequal sister chromatid exchange. We also examine the prevalence and scale of concerted evolution in the histone and Stellate clusters and discuss the mechanisms underlying these observed patterns.},
}

@article {pmid38915006,
year = {2024},
author = {Reininghaus, U and Schwannauer, M and Barne, I and Beames, JR and Bonnier, RA and Brenner, M and Breznoščáková, D and Dančík, D and De Allegri, M and Di Folco, S and Durstewitz, D and Gugel, J and Hajdúk, M and Heretik, A and Izáková, Ľ and Katreniakova, Z and Kiekens, G and Koppe, G and Kurilla, A and Marelli, L and Nagyova, I and Nguyen, H and Pečeňák, J and Schulte-Strathaus, JCC and Sotomayor-Enriquez, K and Uyttebroek, L and Weermeijer, J and Wolters, M and Wensing, M and Boehnke, JR and Myin-Germeys, I and Schick, A},
title = {Strategies, processes, outcomes, and costs of implementing experience sampling-based monitoring in routine mental health care in four European countries: study protocol for the IMMERSE effectiveness-implementation study.},
journal = {BMC psychiatry},
volume = {24},
number = {1},
pages = {465},
pmid = {38915006},
issn = {1471-244X},
support = {945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 389624707//DFG/ ; 101063326//Marie Skłodowska-Curie fellowship/ ; 1204924N//Research Foundation Flanders/ ; APVV-22-0587//Agentúra na Podporu Výskumu a Vývoja/ ; },
mesh = {Humans ; *Mental Health Services/economics ; Germany ; Belgium ; Slovakia ; Mental Disorders/therapy/economics ; Ecological Momentary Assessment ; Europe ; Cost-Benefit Analysis/methods ; },
abstract = {BACKGROUND: Recent years have seen a growing interest in the use of digital tools for delivering person-centred mental health care. Experience Sampling Methodology (ESM), a structured diary technique for capturing moment-to-moment variation in experience and behaviour in service users' daily life, reflects a particularly promising avenue for implementing a person-centred approach. While there is evidence on the effectiveness of ESM-based monitoring, uptake in routine mental health care remains limited. The overarching aim of this hybrid effectiveness-implementation study is to investigate, in detail, reach, effectiveness, adoption, implementation, and maintenance as well as contextual factors, processes, and costs of implementing ESM-based monitoring, reporting, and feedback into routine mental health care in four European countries (i.e., Belgium, Germany, Scotland, Slovakia).

METHODS: In this hybrid effectiveness-implementation study, a parallel-group, assessor-blind, multi-centre cluster randomized controlled trial (cRCT) will be conducted, combined with a process and economic evaluation. In the cRCT, 24 clinical units (as the cluster and unit of randomization) at eight sites in four European countries will be randomly allocated using an unbalanced 2:1 ratio to one of two conditions: (a) the experimental condition, in which participants receive a Digital Mobile Mental Health intervention (DMMH) and other implementation strategies in addition to treatment as usual (TAU) or (b) the control condition, in which service users are provided with TAU. Outcome data in service users and clinicians will be collected at four time points: at baseline (t0), 2-month post-baseline (t1), 6-month post-baseline (t2), and 12-month post-baseline (t3). The primary outcome will be patient-reported service engagement assessed with the service attachment questionnaire at 2-month post-baseline. The process and economic evaluation will provide in-depth insights into in-vivo context-mechanism-outcome configurations and economic costs of the DMMH and other implementation strategies in routine care, respectively.

DISCUSSION: If this trial provides evidence on reach, effectiveness, adoption, implementation and maintenance of implementing ESM-based monitoring, reporting, and feedback, it will form the basis for establishing its public health impact and has significant potential to bridge the research-to-practice gap and contribute to swifter ecological translation of digital innovations to real-world delivery in routine mental health care.

TRIAL REGISTRATION: ISRCTN15109760 (ISRCTN registry, date: 03/08/2022).},
}

Humans
*Mental Health Services/economics
Germany
Belgium
Slovakia
Mental Disorders/therapy/economics
Ecological Momentary Assessment
Europe
Cost-Benefit Analysis/methods

@article {pmid38914930,
year = {2024},
author = {Jiang, G and Zheng, JY and Ren, SN and Yin, W and Xia, X and Li, Y and Wang, HL},
title = {A comprehensive workflow for optimizing RNA-seq data analysis.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {631},
pmid = {38914930},
issn = {1471-2164},
mesh = {*Workflow ; *RNA-Seq/methods ; *Software ; Fungi/genetics ; Computational Biology/methods ; Sequence Analysis, RNA/methods ; Alternative Splicing ; },
abstract = {BACKGROUND: Current RNA-seq analysis software for RNA-seq data tends to use similar parameters across different species without considering species-specific differences. However, the suitability and accuracy of these tools may vary when analyzing data from different species, such as humans, animals, plants, fungi, and bacteria. For most laboratory researchers lacking a background in information science, determining how to construct an analysis workflow that meets their specific needs from the array of complex analytical tools available poses a significant challenge.

RESULTS: By utilizing RNA-seq data from plants, animals, and fungi, it was observed that different analytical tools demonstrate some variations in performance when applied to different species. A comprehensive experiment was conducted specifically for analyzing plant pathogenic fungal data, focusing on differential gene analysis as the ultimate goal. In this study, 288 pipelines using different tools were applied to analyze five fungal RNA-seq datasets, and the performance of their results was evaluated based on simulation. This led to the establishment of a relatively universal and superior fungal RNA-seq analysis pipeline that can serve as a reference, and certain standards for selecting analysis tools were derived for reference. Additionally, we compared various tools for alternative splicing analysis. The results based on simulated data indicated that rMATS remained the optimal choice, although consideration could be given to supplementing with tools such as SpliceWiz.

CONCLUSION: The experimental results demonstrate that, in comparison to the default software parameter configurations, the analysis combination results after tuning can provide more accurate biological insights. It is beneficial to carefully select suitable analysis software based on the data, rather than indiscriminately choosing tools, in order to achieve high-quality analysis results more efficiently.},
}

*Workflow
*RNA-Seq/methods
*Software
Fungi/genetics
Computational Biology/methods
Sequence Analysis, RNA/methods
Alternative Splicing

@article {pmid38911902,
year = {2024},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , },
title = {The genome sequence of the White-point, Mythimna albipuncta (Denis & Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {62},
pmid = {38911902},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Mythimna albipuncta (the White-point; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 698.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.38 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,679 protein coding genes.},
}

@article {pmid38908558,
year = {2024},
author = {Yang, Y and Li, Z and Wen, J},
title = {Long term impact of Wenchuan earthquake on population mental and behavioral disorders in heavily-stricken areas: An ecological study based on big data.},
journal = {Journal of affective disorders},
volume = {361},
number = {},
pages = {589-595},
doi = {10.1016/j.jad.2024.06.070},
pmid = {38908558},
issn = {1573-2517},
mesh = {Humans ; *Earthquakes ; China/epidemiology ; Male ; Female ; Middle Aged ; Adult ; *Mental Disorders/epidemiology ; *Disasters/statistics & numerical data ; *Survivors/psychology/statistics & numerical data ; Prevalence ; Adolescent ; Aged ; *Big Data ; Young Adult ; Risk Factors ; Child ; Urbanization ; },
abstract = {BACKGROUND: This study aimed to explore and evaluate the development trends and differential changes in the prevalence of mental and behavioral disorders among the earthquake survivors in exposure groups (highly hard-hit areas) and control groups (general disaster areas) from 2015 to 2019, as well as to investigate the potential influencing factors.

METHODS: Data was obtained from the Sichuan Health Information System and the Sichuan Health Yearbook, the prevalence of the exposure group and the control group were calculated, the difference between the two groups was evaluated using the prevalence rate ratio, and a fixed effect model was developed to investigate the potential influencing factors of the prevalence.

RESULTS: The prevalence by gender and age in the exposure group was always greater than those in the control group (RR>1), although the disparity between the two proceeded to diminish with time. The urbanization rate (β = 0.0448, P < 0.05) and disaster area levels (β = 0.0104, P < 0.05) were risk factors for the prevalence of mental and behavioral disorders.

LIMITATIONS: The study only collected data at the group level following the Wenchuan earthquake. Consequently, the findings are only applicable at the group level. Furthermore, diagnostic criteria for various types of mental and behavioral disorders diseases were not provided.

CONCLUSIONS: The earthquake has a significant long-term impact on mental health. It is necessary to continuously monitor the mental health of Wenchuan earthquake survivors and take appropriate post-disaster intervention measures.},
}

Humans
*Earthquakes
China/epidemiology
Male
Female
Middle Aged
Adult
*Mental Disorders/epidemiology
*Disasters/statistics & numerical data
*Survivors/psychology/statistics & numerical data
Prevalence
Adolescent
Aged
*Big Data
Young Adult
Risk Factors
Child
Urbanization

@article {pmid38907904,
year = {2024},
author = {Roved, J},
title = {MHCtools 1.5: Analysis of MHC Sequencing Data in R.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2809},
number = {},
pages = {275-295},
pmid = {38907904},
issn = {1940-6029},
mesh = {*Major Histocompatibility Complex/genetics ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Software ; Animals ; *Haplotypes/genetics ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; Genetic Variation ; Genotyping Techniques/methods ; Genotype ; },
abstract = {The genes of the major histocompatibility complex (MHC) play a vital role in the vertebrate immune system and have attracted considerable interest in evolutionary biology. While the MHC has been characterized in detail in humans (human leukocyte antigen, HLA) and in model organisms such as the mouse, studies in non-model organisms often lack prior knowledge about structure, genetic variability, and evolutionary properties of this locus. MHC genotyping in non-model species commonly relies on PCR-based amplicon sequencing, and while several published protocols facilitate generation of MHC sequence data, there is a lack of transparent and standardized tools for downstream data analysis.Here, I present the R package MHCtools version 1.5, which contains 15 tools that (i) assist accurate MHC genotyping from high-throughput amplicon sequencing data, and provide standardized methods to analyze (ii) MHC diversity, (iii) MHC supertypes, and (iv) MHC haplotypes.I hope that MHCtools will be helpful in future studies of the MHC in non-model species and that it may help to advance our understanding of the important roles of the MHC in ecology and evolution.},
}

*Major Histocompatibility Complex/genetics
Humans
*High-Throughput Nucleotide Sequencing/methods
*Software
Animals
*Haplotypes/genetics
Computational Biology/methods
Sequence Analysis, DNA/methods
Genetic Variation
Genotyping Techniques/methods
Genotype

@article {pmid38904377,
year = {2024},
author = {Berasategui, A and Salem, H and Moller, AG and Christopher, Y and Vidaurre Montoya, Q and Conn, C and Read, TD and Rodrigues, A and Ziemert, N and Gerardo, N},
title = {Genomic insights into the evolution of secondary metabolism of Escovopsis and its allies, specialized fungal symbionts of fungus-farming ants.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0057624},
doi = {10.1128/msystems.00576-24},
pmid = {38904377},
issn = {2379-5077},
abstract = {The metabolic intimacy of symbiosis often demands the work of specialists. Natural products and defensive secondary metabolites can drive specificity by ensuring infection and propagation across host generations. But in contrast to bacteria, little is known about the diversity and distribution of natural product biosynthetic pathways among fungi and how they evolve to facilitate symbiosis and adaptation to their host environment. In this study, we define the secondary metabolism of Escovopsis and closely related genera, symbionts in the gardens of fungus-farming ants. We ask how the gain and loss of various biosynthetic pathways correspond to divergent lifestyles. Long-read sequencing allowed us to define the chromosomal features of representative Escovopsis strains, revealing highly reduced genomes composed of seven to eight chromosomes. The genomes are highly syntenic with macrosynteny decreasing with increasing phylogenetic distance, while maintaining a high degree of mesosynteny. An ancestral state reconstruction analysis of biosynthetic pathways revealed that, while many secondary metabolites are shared with non-ant-associated Sordariomycetes, 56 pathways are unique to the symbiotic genera. Reflecting adaptation to diverging ant agricultural systems, we observe that the stepwise acquisition of these pathways mirrors the ecological radiations of attine ants and the dynamic recruitment and replacement of their fungal cultivars. As different clades encode characteristic combinations of biosynthetic gene clusters, these delineating profiles provide important insights into the possible mechanisms underlying specificity between these symbionts and their fungal hosts. Collectively, our findings shed light on the evolutionary dynamic nature of secondary metabolism in Escovopsis and its allies, reflecting adaptation of the symbionts to an ancient agricultural system.IMPORTANCEMicrobial symbionts interact with their hosts and competitors through a remarkable array of secondary metabolites and natural products. Here, we highlight the highly streamlined genomic features of attine-associated fungal symbionts. The genomes of Escovopsis species, as well as species from other symbiont genera, many of which are common with the gardens of fungus-growing ants, are defined by seven chromosomes. Despite a high degree of metabolic conservation, we observe some variation in the symbionts' potential to produce secondary metabolites. As the phylogenetic distribution of the encoding biosynthetic gene clusters coincides with attine transitions in agricultural systems, we highlight the likely role of these metabolites in mediating adaptation by a group of highly specialized symbionts.},
}

@article {pmid38902323,
year = {2024},
author = {Horváth, G and Sos, T and Bóné, G and Lőrincz, CE and Pap, PL and Herczeg, G},
title = {Integrating behavioural thermoregulatory strategy into the animal personality framework using the common lizard, Zootoca vivipara as a model.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {14200},
pmid = {38902323},
issn = {2045-2322},
support = {PD 132041//Nemzeti Kutatási, Fejlesztési és Innovaciós Alap/ ; },
mesh = {Animals ; *Lizards/physiology ; *Body Temperature Regulation/physiology ; *Behavior, Animal/physiology ; Personality/physiology ; Male ; Female ; },
abstract = {The study of consistent between-individual behavioural variation in single (animal personality) and across two or more behavioural traits (behavioural syndrome) is a central topic of behavioural ecology. Besides behavioural type (individual mean behaviour), behavioural predictability (environment-independent within-individual behavioural variation) is now also seen as an important component of individual behavioural strategy. Research focus is still on the 'Big Five' traits (activity, exploration, risk-taking, sociability and aggression), but another prime candidate to integrate to the personality framework is behavioural thermoregulation in small-bodied poikilotherms. Here, we found animal personality in thermoregulatory strategy (selected body temperature, voluntary thermal maximum, setpoint range) and 'classic' behavioural traits (activity, sheltering, risk-taking) in common lizards (Zootoca vivipara). Individual state did not explain the between-individual variation. There was a positive behavioural type-behavioural predictability correlation in selected body temperature. Besides an activity-risk-taking syndrome, we also found a risk-taking-selected body temperature syndrome. Our results suggest that animal personality and behavioural syndrome are present in common lizards, both including thermoregulatory and 'classic' behavioural traits, and selecting high body temperature with high predictability is part of the risk-prone behavioural strategy. We propose that thermoregulatory behaviour should be considered with equal weight to the 'classic' traits in animal personality studies of poikilotherms employing active behavioural thermoregulation.},
}

Animals
*Lizards/physiology
*Body Temperature Regulation/physiology
*Behavior, Animal/physiology
Personality/physiology
Male
Female

@article {pmid38899724,
year = {2024},
author = {Parra, J and Jarmusch, SA and Duncan, KR},
title = {Multi-omics analysis of antagonistic interactions among free-living Pseudonocardia from diverse ecosystems.},
journal = {Environmental microbiology},
volume = {26},
number = {6},
pages = {e16635},
doi = {10.1111/1462-2920.16635},
pmid = {38899724},
issn = {1462-2920},
support = {2-1-4-17-1-037//Ministerio de Ciencia Tecnología y Telecomunicaciones, Costa Rica/ ; NNF19OC0055625//Novo Nordisk Fonden/ ; DNRF137//Danmarks Grundforskningsfond/ ; },
mesh = {Antibiosis ; *Ecosystem ; Genomics ; Geologic Sediments/microbiology ; *Metabolomics ; Multigene Family ; Multiomics ; *Phylogeny ; *Pseudonocardia/genetics ; },
abstract = {Actinomycetes are a phylogenetically diverse bacterial group which are widely distributed across terrestrial and aquatic ecosystems. Within this order, the genus Pseudonocardia and their specialised metabolites have been the focus of previous ecological studies due to their antagonistic interactions with other microorganisms and their mutualistic interactions with insects. However, the chemical ecology of free-living Pseudonocardia remains understudied. This study applies a multi-omics approach to investigate the chemical ecology of free-living actinomycetes from the genus Pseudonocardia. In a comparative genomics analysis, it was observed that the biosynthetic gene cluster family distribution was influenced mainly by phylogenetic distance rather than the geographic or ecological origin of strains. This finding was also observed in the mass spectrometry-based metabolomic profiles of nine Pseudonocardia species isolated from marine sediments and two terrestrial species. Antagonist interactions between these 11 species were examined, and matrix-assisted laser desorption/ionisation-mass spectrometry imaging was used to examine in situ chemical interactions between the Southern Ocean strains and their phylogenetically close relatives. Overall, it was demonstrated that phylogeny was the main predictor of antagonistic interactions among free-living Pseudonocardia. Moreover, two features at m/z 441.15 and m/z 332.20 were identified as metabolites related to these interspecies interactions.},
}

Antibiosis
*Ecosystem
Genomics
Geologic Sediments/microbiology
*Metabolomics
Multigene Family
Multiomics
*Phylogeny
*Pseudonocardia/genetics

@article {pmid38897481,
year = {2024},
author = {Kepp, KP and Aavitsland, P and Ballin, M and Balloux, F and Baral, S and Bardosh, K and Bauchner, H and Bendavid, E and Bhopal, R and Blumstein, DT and Boffetta, P and Bourgeois, F and Brufsky, A and Collignon, PJ and Cripps, S and Cristea, IA and Curtis, N and Djulbegovic, B and Faude, O and Flacco, ME and Guyatt, GH and Hajishengallis, G and Hemkens, LG and Hoffmann, T and Joffe, AR and Klassen, TP and Koletsi, D and Kontoyiannis, DP and Kuhl, E and La Vecchia, C and Lallukka, T and Lambris, J and Levitt, M and Makridakis, S and Maltezou, HC and Manzoli, L and Marusic, A and Mavragani, C and Moher, D and Mol, BW and Muka, T and Naudet, F and Noble, PW and Nordström, A and Nordström, P and Pandis, N and Papatheodorou, S and Patel, CJ and Petersen, I and Pilz, S and Plesnila, N and Ponsonby, AL and Rivas, MA and Saltelli, A and Schabus, M and Schippers, MC and Schünemann, H and Solmi, M and Stang, A and Streeck, H and Sturmberg, JP and Thabane, L and Thombs, BD and Tsakris, A and Wood, SN and Ioannidis, JPA},
title = {Panel stacking is a threat to consensus statement validity.},
journal = {Journal of clinical epidemiology},
volume = {173},
number = {},
pages = {111428},
doi = {10.1016/j.jclinepi.2024.111428},
pmid = {38897481},
issn = {1878-5921},
abstract = {Consensus statements can be very influential in medicine and public health. Some of these statements use systematic evidence synthesis but others fail on this front. Many consensus statements use panels of experts to deduce perceived consensus through Delphi processes. We argue that stacking of panel members toward one particular position or narrative is a major threat, especially in absence of systematic evidence review. Stacking may involve financial conflicts of interest, but nonfinancial conflicts of strong advocacy can also cause major bias. Given their emerging importance, we describe here how such consensus statements may be misleading, by analyzing in depth a recent high-impact Delphi consensus statement on COVID-19 recommendations as a case example. We demonstrate that many of the selected panel members and at least 35% of the core panel members had advocated toward COVID-19 elimination (Zero-COVID) during the pandemic and were leading members of aggressive advocacy groups. These advocacy conflicts were not declared in the Delphi consensus publication, with rare exceptions. Therefore, we propose that consensus statements should always require rigorous evidence synthesis and maximal transparency on potential biases toward advocacy or lobbyist groups to be valid. While advocacy can have many important functions, its biased impact on consensus panels should be carefully avoided.},
}

@article {pmid38896539,
year = {2024},
author = {Sänger, M and De Mecquenem, N and Lewińska, KE and Bountris, V and Lehmann, F and Leser, U and Kosch, T},
title = {A qualitative assessment of using ChatGPT as large language model for scientific workflow development.},
journal = {GigaScience},
volume = {13},
number = {},
pages = {},
pmid = {38896539},
issn = {2047-217X},
support = {//German Research Foundation/ ; },
mesh = {*Workflow ; Programming Languages ; Software ; Computational Biology/methods ; Humans ; },
abstract = {BACKGROUND: Scientific workflow systems are increasingly popular for expressing and executing complex data analysis pipelines over large datasets, as they offer reproducibility, dependability, and scalability of analyses by automatic parallelization on large compute clusters. However, implementing workflows is difficult due to the involvement of many black-box tools and the deep infrastructure stack necessary for their execution. Simultaneously, user-supporting tools are rare, and the number of available examples is much lower than in classical programming languages.

RESULTS: To address these challenges, we investigate the efficiency of large language models (LLMs), specifically ChatGPT, to support users when dealing with scientific workflows. We performed 3 user studies in 2 scientific domains to evaluate ChatGPT for comprehending, adapting, and extending workflows. Our results indicate that LLMs efficiently interpret workflows but achieve lower performance for exchanging components or purposeful workflow extensions. We characterize their limitations in these challenging scenarios and suggest future research directions.

CONCLUSIONS: Our results show a high accuracy for comprehending and explaining scientific workflows while achieving a reduced performance for modifying and extending workflow descriptions. These findings clearly illustrate the need for further research in this area.},
}

*Workflow
Programming Languages
Software
Computational Biology/methods
Humans

@article {pmid38892087,
year = {2024},
author = {Suárez, I and Collado, IG and Garrido, C},
title = {Revealing Hidden Genes in Botrytis cinerea: New Insights into Genes Involved in the Biosynthesis of Secondary Metabolites.},
journal = {International journal of molecular sciences},
volume = {25},
number = {11},
pages = {},
pmid = {38892087},
issn = {1422-0067},
support = {PID-2021-1228990-B-C21 and PID-2021-1228990-B-C22//MCIN/AEI/ 10.13039/501100011033 and ERDF A way of making Europe/ ; },
mesh = {*Botrytis/genetics/pathogenicity ; *Secondary Metabolism/genetics ; *Peptide Synthases/genetics/metabolism ; *Polyketide Synthases/genetics/metabolism ; Fungal Proteins/genetics/metabolism ; Computational Biology/methods ; Multigene Family ; Genes, Fungal ; },
abstract = {Utilizing bioinformatics tools, this study expands our understanding of secondary metabolism in Botrytis cinerea, identifying novel genes within polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS), sesquiterpene cyclase (STC), diterpene cyclase (DTC), and dimethylallyltryptophan synthase (DMATS) families. These findings enrich the genetic framework associated with B. cinerea's pathogenicity and ecological adaptation, offering insights into uncharted metabolic pathways. Significantly, the discovery of previously unannotated genes provides new molecular targets for developing targeted antifungal strategies, promising to enhance crop protection and advance our understanding of fungal biochemistry. This research not only broadens the scope of known secondary metabolites but also opens avenues for future exploration into B. cinerea's biosynthetic capabilities, potentially leading to novel antifungal compounds. Our work underscores the importance of integrating bioinformatics and genomics for fungal research, paving the way for sustainable agricultural practices by pinpointing precise molecular interventions against B. cinerea. This study sets a foundation for further investigations into the fungus's secondary metabolism, with implications for biotechnology and crop disease management.},
}

*Botrytis/genetics/pathogenicity
*Secondary Metabolism/genetics
*Peptide Synthases/genetics/metabolism
*Polyketide Synthases/genetics/metabolism
Fungal Proteins/genetics/metabolism
Computational Biology/methods
Multigene Family
Genes, Fungal

@article {pmid38888768,
year = {2024},
author = {Sanderson, H and White, AP},
title = {Methods for Genomic Epidemiology of Bacterial Pathogens: Example Salmonella.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2813},
number = {},
pages = {19-37},
pmid = {38888768},
issn = {1940-6029},
mesh = {*Salmonella/genetics ; Humans ; *Genomics/methods ; *Salmonella Infections/microbiology/epidemiology ; *Phylogeny ; *Genome, Bacterial ; *Molecular Epidemiology/methods ; Virulence Factors/genetics ; Disease Outbreaks ; Drug Resistance, Bacterial/genetics ; Interspersed Repetitive Sequences/genetics ; },
abstract = {Genomics has revolutionized how we characterize and monitor infectious diseases for public health. The surveillance and characterization of Salmonella has improved drastically within the past decade. In this chapter, we discuss the prerequisites for good bacterial genomics studies and make note of advantages and disadvantages of this research approach. We discuss methods for outbreak detection and the evolutionary and epidemiological characterization of Salmonella spp. We provide an outline for determining the sequence type and serotype of isolates, building a core genome phylogenetic tree, and detecting antimicrobial resistance genes, virulence factors, and mobile genetic elements. These methods can be used to study other pathogenic bacterial species.},
}

*Salmonella/genetics
Humans
*Genomics/methods
*Salmonella Infections/microbiology/epidemiology
*Phylogeny
*Genome, Bacterial
*Molecular Epidemiology/methods
Virulence Factors/genetics
Disease Outbreaks
Drug Resistance, Bacterial/genetics
Interspersed Repetitive Sequences/genetics

@article {pmid38882711,
year = {2023},
author = {Waterhouse, RM and Adam-Blondon, AF and Balech, B and Barta, E and Ying Shi Chua, P and Di Cola, V and Heil, KF and Hughes, GM and Jermiin, LS and Kalaš, M and Lanfear, J and Pafilis, E and Palagi, PM and Papageorgiou, AC and Paupério, J and Psomopoulos, F and Raes, N and Burgin, J and Gabaldón, T},
title = {The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity.},
journal = {F1000Research},
volume = {12},
number = {},
pages = {},
pmid = {38882711},
issn = {2046-1402},
mesh = {Humans ; *Biodiversity ; Conservation of Natural Resources ; },
abstract = {Biodiversity loss is now recognised as one of the major challenges for humankind to address over the next few decades. Unless major actions are taken, the sixth mass extinction will lead to catastrophic effects on the Earth's biosphere and human health and well-being. ELIXIR can help address the technical challenges of biodiversity science, through leveraging its suite of services and expertise to enable data management and analysis activities that enhance our understanding of life on Earth and facilitate biodiversity preservation and restoration. This white paper, prepared by the ELIXIR Biodiversity Community, summarises the current status and responses, and presents a set of plans, both technical and community-oriented, that should both enhance how ELIXIR Services are applied in the biodiversity field and how ELIXIR builds connections across the many other infrastructures active in this area. We discuss the areas of highest priority, how they can be implemented in cooperation with the ELIXIR Platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for a Biodiversity Community in ELIXIR and is an appeal to identify and involve new stakeholders.},
}

Humans
*Biodiversity
Conservation of Natural Resources

@article {pmid38882082,
year = {2024},
author = {Fei, J and Jiang, X and Yang, H and Fan, K and Che, Y and Sun, B and Guo, T},
title = {Research and Development of a Big Data Application Platform for Intelligent Blast Furnace Intensive Management and Control.},
journal = {ACS omega},
volume = {9},
number = {23},
pages = {24674-24684},
pmid = {38882082},
issn = {2470-1343},
abstract = {The blast furnaces of Anshan Iron and Steel have completed large-scale modernization, and a large amount of information technology has been popularized and applied to the process of blast furnaces. This paper takes the Anshan Iron and Steel blast furnace group as the research background. Based on big data and industrial Internet technology, combining the smelting process mechanism of blast furnace production and using artificial intelligence, cloud analysis, and other technologies, the data management platform was used to effectively integrate the data of each process of the blast furnace and design the data asset catalogue. The big data application platform for the intensive control of the blast furnace was established. The data were in multidimensional in-depth mining, and the intelligent application model of the blast furnace was established. The visual intelligent monitoring of the safe production and operation of the blast furnace was realized, and the production operation of the blast furnace was guided. The overall information and intelligent level of production operation and management of the blast furnace have been improved.},
}

@article {pmid38880940,
year = {2024},
author = {Medo, A and Ohte, N and Doi, H and Kamdee, K and Koba, K and Arai, N and Mitsunaga, Y and Kume, M and Kojima, D and Nose, T and Yokoyama, A and Viputhanumas, T and Mitamura, H},
title = {Trophic niche partitioning and intraspecific variation in food resource use in the genus Pangasianodon in a reservoir revealed by stable isotope analysis of multiple tissues.},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.15842},
pmid = {38880940},
issn = {1095-8649},
support = {16H05792//Japan Society for the Promotion of Science/ ; 22J13642//Japan Society for the Promotion of Science/ ; 202180216//Japan Society for the Promotion of Science/ ; //Shikata Memorial Trust for Nature Conservation/ ; 25610919060008//Thailand Institute of Nuclear Technology/ ; },
abstract = {Understanding the mechanism by which non-native fish species integrate into native communities is crucial for evaluating the possibility of their establishment success. The genus Pangasianodon, comprising Pangasianodon gigas and Pangasianodon hypophthalmus, has been introduced into reservoirs, which are non-native habitats, for fishery stock enhancement. P. gigas and P. hypophthalmus often successfully establish and co-occur in several Thai reservoirs, but there is little information on differences in food resource use between the two species. To investigate the trophic niche width of P. gigas and P. hypophthalmus in a Thai reservoir, we conducted stable carbon and nitrogen ratio (δ[13]C and δ[15]N) analyses. We examined the degree of individual specialization in both species using the δ[13]C and δ[15]N values of muscle and liver tissues, which provides long- and short-term diet information. The isotopic niches did not overlap between P. gigas and P. hypophthalmus. The δ[15]N value of P. gigas was significantly higher than that of P. hypophthalmus, whereas the δ[13]C value did not significantly differ between the two species. The isotopic niche sizes were larger in P. hypophthalmus than in P. gigas. Individual specialization was observed in P. hypophthalmus but not in P. gigas, indicating that intraspecific variation in food resource use was larger in P. hypophthalmus compared to P. gigas. These findings suggest that trophic niche partitioning was one of the factors facilitating the establishment success of P. gigas and P. hypophthalmus in a reservoir, but the establishment process may differ between the two species.},
}

@article {pmid38873190,
year = {2023},
author = {Boyes, D and Hammond, J and , and , and , and , and , and , },
title = {The genome sequence of the Notch-wing Button, Acleris emargana (Fabricius, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {376},
pmid = {38873190},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Acleris emargana (the Notch-wing Button; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 691.4 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.34 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,886 protein coding genes.},
}

@article {pmid38870844,
year = {2024},
author = {Rocha, LP and Machado, ÍE and Fogal, AS and Malta, DC and Velasquez-Melendez, G and Felisbino-Mendes, MS},
title = {Burden of disease and direct costs to the health system attributable to high body mass index in Brazil.},
journal = {Public health},
volume = {233},
number = {},
pages = {121-129},
doi = {10.1016/j.puhe.2024.05.013},
pmid = {38870844},
issn = {1476-5616},
mesh = {Humans ; Brazil/epidemiology ; *Body Mass Index ; Cross-Sectional Studies ; Male ; *Cost of Illness ; Female ; Middle Aged ; Adult ; *Health Care Costs/statistics & numerical data ; Hospitalization/statistics & numerical data/economics ; National Health Programs/economics/statistics & numerical data ; Obesity/epidemiology/economics ; Aged ; Disability-Adjusted Life Years ; },
abstract = {OBJECTIVES: Excess weight, measured by a high body mass index (BMI), is associated with the onset of many diseases, which can, in turn, lead to disability and premature death, subsequently placing a significant burden on healthcare services. This study analysed the burden of disease and the direct costs to the Brazilian Unified Health System (Sistema Único de Saúde [SUS]) attributable to high BMI in the Brazilian population.

STUDY DESIGN: Ecological study.

METHODS: This ecological study had two components: (1) a time-series assessment to analyse the burden of diseases attributable to high BMI from 1990 to 2019 in Brazil; and (2) a cross-sectional design to estimate the direct costs of SUS hospitalisations and outpatient procedures attributable to high BMI in 2019. Estimates from the Global Burden of Disease study and the costs of hospital admissions and outpatient procedures from the Department of Informatics of the Brazilian Unified Health System were used. Deaths, years of life lost to premature death (YLLs), years lived with disability (YLDs), and years of life lost adjusted for disability (DALYs) were analysed. The direct health cost was obtained in Brazilian Real (R$) and converted in international Dollars (INT$).

RESULTS: The current study found a reduction in the number of DALYs, YLLs, and deaths per 100,000 population of cardiovascular disease (CVD) attributable to high BMI and an increase in YLD due to diabetes and cardiovascular disease attributable to high BMI from 1990 to 2019. In 2019, high BMI resulted in 2404 DALYs, 658 YLDs, 1746 YLLs, and 76 deaths per 100,000 inhabitants. In the same year, INT$377.30 million was spent on hospitalisations and high- and medium-complexity procedures to control non-communicable diseases attributable to high BMI. The states in the South and Southeast regions of Brazil presented the highest total cost per 10,000 inhabitants. CVDs and chronic kidney disease showed the highest costs per hospital admission, whereas neoplasms and CVDs presented the highest costs for outpatient procedures.

CONCLUSIONS: High BMI causes significant disease burden and financial costs. The highest expenses observed were not in locations with the highest burden of disease attributable to high BMI. These findings highlight the need to improve current public policies and apply cost-effective intervention packages, focussing on equity and the promotion of healthier lifestyles to reduce overweight/obesity, especially in localities with low socioeconomic status.},
}

Humans
Brazil/epidemiology
*Body Mass Index
Cross-Sectional Studies
Male
*Cost of Illness
Female
Middle Aged
Adult
*Health Care Costs/statistics & numerical data
Hospitalization/statistics & numerical data/economics
National Health Programs/economics/statistics & numerical data
Obesity/epidemiology/economics
Aged
Disability-Adjusted Life Years

@article {pmid38870774,
year = {2024},
author = {Bucci, S and Berry, N and Ainsworth, J and Berry, K and Edge, D and Eisner, E and Emsley, R and Forbes, G and Hassan, L and Lewis, S and Machin, M and Haddock, G},
title = {Effects of Actissist, a digital health intervention for early psychosis: A randomized clinical trial.},
journal = {Psychiatry research},
volume = {339},
number = {},
pages = {116025},
doi = {10.1016/j.psychres.2024.116025},
pmid = {38870774},
issn = {1872-7123},
abstract = {Schizophrenia affects 24 million people worldwide. Digital health interventions drawing on psychological principles have been developed, but their effectiveness remains unclear. This parallel, assessor-blinded, randomized clinical trial aimed to investigate whether a cognitive behaviour therapy-informed digital health intervention (Actissist app) confers added benefit on psychotic symptoms over and above remote symptom monitoring (ClinTouch app). Participants recruited from UK community health services were randomized 1:1 to receive either Actissist plus treatment as usual (TAU) or ClinTouch plus TAU. Eligible participants were adults with schizophrenia-spectrum psychosis within five years of first episode onset meeting a criterion level of positive symptoms severity. The primary outcome was Positive and Negative Syndrome Scale (PANSS) symptoms total score at 12 weeks post-randomization. Intention-to-treat analysis included 172 participants, with 149 participants (86.6 %) providing primary outcome data. Actissist plus TAU was not associated with greater reduction than an active control remote symptom monitoring app (ClinTouch) in PANSS total score at post-randomization. There were no significant effects between groups across secondary measures. There were no serious adverse reactions. Both groups improved on the primary psychotic symptoms measure at primary end-point and on secondary measures over time. The Actissist app is safe but not superior to digital symptom monitoring.},
}

@article {pmid38868628,
year = {2023},
author = {Obbard, DJ and , and , and , and , },
title = {The genome sequence of a drosophilid fruit fly, Hirtodrosophila cameraria (Haliday, 1833).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {361},
pmid = {38868628},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Hirtodrosophila cameraria (a drosophilid fruit fly; Arthropoda; Insecta; Diptera; Drosophilidae). The genome sequence is 214.5 megabases in span. Most of the assembly is scaffolded into 4 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.94 kilobases in length.},
}

@article {pmid38867756,
year = {2024},
author = {Boyes, D and Lewis, OT and , and , and , and , and , and , and , },
title = {The genome sequence of the Marbled White Spot, Protodeltote pygarga (Hufnagel, 1766).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {7},
pmid = {38867756},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Protodeltote pygarga (the Marbled White Spot; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 421.1 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.48 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,784 protein coding genes.},
}

@article {pmid38867206,
year = {2024},
author = {Anjos, C and Duarte, D and Fatsini, E and Matias, D and Cabrita, E},
title = {Comparative transcriptome analysis reveals molecular damage associated with cryopreservation in Crassostrea angulata D-larvae rather than to cryoprotectant exposure.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {591},
pmid = {38867206},
issn = {1471-2164},
support = {SFRH/BD/130910/2017//Fundação para a Ciência e a Tecnologia/ ; CCMAR/Multi/04326/2022//Fundação para a Ciência e a Tecnologia/ ; 0139_VENUS_5_E//Interreg POCTEP/ ; JRA2-H2020-INFRAIA-2016-2017//European Commission/ ; EBB-EAPA_501/2016//Interreg Atlantic Area/ ; },
mesh = {Animals ; *Cryopreservation ; *Crassostrea/genetics/growth & development ; *Cryoprotective Agents/pharmacology/toxicity ; *Larva/genetics/drug effects/growth & development ; *Gene Expression Profiling ; Transcriptome ; Gene Ontology ; },
abstract = {BACKGROUND: The Portuguese oyster Crassostrea angulata, a bivalve of significant economic and ecological importance, has faced a decline in both production and natural populations due to pathologies, climate change, and anthropogenic factors. To safeguard its genetic diversity and improve reproductive management, cryopreservation emerges as a valuable strategy. However, the cryopreservation methodologies lead to some damage in structures and functions of the cells and tissues that can affect post-thaw quality. Transcriptomics may help to understand the molecular consequences related to cryopreservation steps and therefore to identify different freezability biomarkers. This study investigates the molecular damage induced by cryopreservation in C. angulata D-larvae, focusing on two critical steps: exposure to cryoprotectant solution and the freezing/thawing process.

RESULTS: Expression analysis revealed 3 differentially expressed genes between larvae exposed to cryoprotectant solution and fresh larvae and 611 differentially expressed genes in cryopreserved larvae against fresh larvae. The most significantly enriched gene ontology terms were "carbohydrate metabolic process", "integral component of membrane" and "chitin binding" for biological processes, cellular components and molecular functions, respectively. Kyoto Encyclopedia of Genes and Genomes enrichment analysis identified the "neuroactive ligand receptor interaction", "endocytosis" and "spliceosome" as the most enriched pathways. RNA sequencing results were validate by quantitative RT-PCR, once both techniques presented the same gene expression tendency and a group of 11 genes were considered important molecular biomarkers to be used in further studies for the evaluation of cryodamage.

CONCLUSIONS: The current work provided valuable insights into the molecular repercussions of cryopreservation on D-larvae of Crassostrea angulata, revealing that the freezing process had a more pronounced impact on larval quality compared to any potential cryoprotectant-induced toxicity. Additionally, was identify 11 genes serving as biomarkers of freezability for D-larvae quality assessment. This research contributes to the development of more effective cryopreservation protocols and detection methods for cryodamage in this species.},
}

Animals
*Cryopreservation
*Crassostrea/genetics/growth & development
*Cryoprotective Agents/pharmacology/toxicity
*Larva/genetics/drug effects/growth & development
*Gene Expression Profiling
Transcriptome
Gene Ontology

@article {pmid38865434,
year = {2024},
author = {Iverson, AR and Humple, DL and Cormier, RL and Hahn, TP and Block, TA and Shizuka, D and Lyon, BE and Chaine, AS and Hudson, EJ and Hull, EM},
title = {Winter GPS tagging reveals home ranges during the breeding season for a boreal-nesting migrant songbird, the Golden-crowned Sparrow.},
journal = {PloS one},
volume = {19},
number = {6},
pages = {e0305369},
pmid = {38865434},
issn = {1932-6203},
mesh = {Animals ; *Seasons ; *Geographic Information Systems ; *Animal Migration/physiology ; *Sparrows/physiology ; *Homing Behavior/physiology ; Breeding ; Ecosystem ; British Columbia ; Alaska ; Nesting Behavior/physiology ; },
abstract = {Determining space use for species is fundamental to understanding their ecology, and tracking animals can reveal insights into their spatial ecology on home ranges and territories. Recent technological advances have led to GPS-tracking devices light enough for birds as small as ~30 g, creating novel opportunities to remotely monitor fine-scale movements and space use for these smaller species. We tested whether miniaturized GPS tags can allow us to understand space use of migratory birds away from their capture sites and sought to understand both pre-breeding space use as well as territory and habitat use on the breeding grounds. We used GPS tags to characterize home ranges on the breeding grounds for a migratory songbird with limited available breeding information, the Golden-crowned Sparrow (Zonotrichia atricapilla). Using GPS points from 23 individuals across 26 tags (three birds tagged twice), we found home ranges in Alaska and British Columbia were on average 44.1 ha (95% kernel density estimate). In addition, estimates of territory sizes based on field observations (mean 2.1 ha, 95% minimum convex polygon [MCP]) were three times smaller than 95% MCPs created using GPS tags (mean 6.5 ha). Home ranges included a variety of land cover classes, with shrubland particularly dominant (64-100% of home range cover for all but one bird). Three birds tracked twice returned to the same breeding area each year, supporting high breeding site fidelity for this species. We found reverse spring migration for five birds that flew up to 154 km past breeding destinations before returning. GPS-tracking technology allowed for critical ecological insights into this migratory species that breeds in very remote locations.},
}

Animals
*Seasons
*Geographic Information Systems
*Animal Migration/physiology
*Sparrows/physiology
*Homing Behavior/physiology
Breeding
Ecosystem
British Columbia
Alaska
Nesting Behavior/physiology

@article {pmid38865431,
year = {2024},
author = {Tedersoo, L and Hosseyni Moghaddam, MS and Mikryukov, V and Hakimzadeh, A and Bahram, M and Nilsson, RH and Yatsiuk, I and Geisen, S and Schwelm, A and Piwosz, K and Prous, M and Sildever, S and Chmolowska, D and Rueckert, S and Skaloud, P and Laas, P and Tines, M and Jung, JH and Choi, JH and Alkahtani, S and Anslan, S},
title = {EUKARYOME: the rRNA gene reference database for identification of all eukaryotes.},
journal = {Database : the journal of biological databases and curation},
volume = {2024},
number = {},
pages = {},
pmid = {38865431},
issn = {1758-0463},
support = {Distinguished Scientist Fellowship Programme//King Saud University/ ; MOBERC66 MOBTP198//European Regional Development Fund/ ; //LOEWE Zentrum AdRIA/ ; Distinguished Scientist Fellowship Programme//King Saud University/ ; MOBERC66 MOBTP198//European Regional Development Fund/ ; //LOEWE Zentrum AdRIA/ ; },
mesh = {*Eukaryota/genetics ; RNA, Ribosomal, 18S/genetics ; Databases, Genetic ; Databases, Nucleic Acid ; Animals ; Genes, rRNA/genetics ; Phylogeny ; },
abstract = {Molecular identification of micro- and macroorganisms based on nuclear markers has revolutionized our understanding of their taxonomy, phylogeny and ecology. Today, research on the diversity of eukaryotes in global ecosystems heavily relies on nuclear ribosomal RNA (rRNA) markers. Here, we present the research community-curated reference database EUKARYOME for nuclear ribosomal 18S rRNA, internal transcribed spacer (ITS) and 28S rRNA markers for all eukaryotes, including metazoans (animals), protists, fungi and plants. It is particularly useful for the identification of arbuscular mycorrhizal fungi as it bridges the four commonly used molecular markers-ITS1, ITS2, 18S V4-V5 and 28S D1-D2 subregions. The key benefits of this database over other annotated reference sequence databases are that it is not restricted to certain taxonomic groups and it includes all rRNA markers. EUKARYOME also offers a number of reference long-read sequences that are derived from (meta)genomic and (meta)barcoding-a unique feature that can be used for taxonomic identification and chimera control of third-generation, long-read, high-throughput sequencing data. Taxonomic assignments of rRNA genes in the database are verified based on phylogenetic approaches. The reference datasets are available in multiple formats from the project homepage, http://www.eukaryome.org.},
}

*Eukaryota/genetics
RNA, Ribosomal, 18S/genetics
Databases, Genetic
Databases, Nucleic Acid
Animals
Genes, rRNA/genetics
Phylogeny

@article {pmid38863181,
year = {2024},
author = {Wong, RE and Berner, LT and Sullivan, PF and Potter, CS and Dial, RJ},
title = {Pixel walking along the boreal forest-Arctic tundra ecotone: Large scale ground-truthing of satellite-derived greenness (NDVI).},
journal = {Global change biology},
volume = {30},
number = {6},
pages = {e17374},
doi = {10.1111/gcb.17374},
pmid = {38863181},
issn = {1365-2486},
support = {80NSSC22K1247/NASA/NASA/United States ; 80NSSC20M0070//Alaska Space Grant Program/ ; DEB-2133494//National Science Foundation/ ; OPP-1748773//National Science Foundation/ ; OPP-1748849//National Science Foundation/ ; 80NSSC19M0062//Alaska NASA EPSCoR/ ; },
mesh = {Alaska ; Arctic Regions ; *Satellite Imagery ; *Tundra ; Remote Sensing Technology/methods ; Taiga ; Environmental Monitoring/methods ; },
abstract = {In this Technical Advance, we describe a novel method to improve ecological interpretation of remotely sensed vegetation greenness measurements that involved sampling 24,395 Landsat pixels (30 m) across 639 km of Alaska's central Brooks Range. The method goes well beyond the spatial scale of traditional plot-based sampling and thereby more thoroughly relates ground-based observations to satellite measurements. Our example dataset illustrates that, along the boreal-Arctic boundary, vegetation with the greatest Landsat Normalized Difference Vegetation Index (NDVI) is taller than 1 m, woody, and deciduous; whereas vegetation with lower NDVI tends to be shorter, evergreen, or non-woody. The field methods and associated analyses advance efforts to inform satellite data with ground-based vegetation observations using field samples collected at spatial scales that closely match the resolution of remotely sensed imagery.},
}

Alaska
Arctic Regions
*Satellite Imagery
*Tundra
Remote Sensing Technology/methods
Taiga
Environmental Monitoring/methods

@article {pmid38862613,
year = {2024},
author = {Venu, V and Roth, C and Adikari, SH and Small, EM and Starkenburg, SR and Sanbonmatsu, KY and Steadman, CR},
title = {Multi-omics analysis reveals the dynamic interplay between Vero host chromatin structure and function during vaccinia virus infection.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {721},
pmid = {38862613},
issn = {2399-3642},
support = {20210134ER//DOE | LDRD | Los Alamos National Laboratory (Los Alamos Lab)/ ; },
mesh = {*Chromatin/metabolism/genetics ; Animals ; *Vaccinia virus/genetics/physiology ; Chlorocebus aethiops ; Vero Cells ; Vaccinia/virology/immunology ; Host-Pathogen Interactions/genetics ; Multiomics ; },
abstract = {The genome folds into complex configurations and structures thought to profoundly impact its function. The intricacies of this dynamic structure-function relationship are not well understood particularly in the context of viral infection. To unravel this interplay, here we provide a comprehensive investigation of simultaneous host chromatin structural (via Hi-C and ATAC-seq) and functional changes (via RNA-seq) in response to vaccinia virus infection. Over time, infection significantly impacts global and local chromatin structure by increasing long-range intra-chromosomal interactions and B compartmentalization and by decreasing chromatin accessibility and inter-chromosomal interactions. Local accessibility changes are independent of broad-scale chromatin compartment exchange (~12% of the genome), underscoring potential independent mechanisms for global and local chromatin reorganization. While infection structurally condenses the host genome, there is nearly equal bidirectional differential gene expression. Despite global weakening of intra-TAD interactions, functional changes including downregulated immunity genes are associated with alterations in local accessibility and loop domain restructuring. Therefore, chromatin accessibility and local structure profiling provide impactful predictions for host responses and may improve development of efficacious anti-viral counter measures including the optimization of vaccine design.},
}

*Chromatin/metabolism/genetics
Animals
*Vaccinia virus/genetics/physiology
Chlorocebus aethiops
Vero Cells
Vaccinia/virology/immunology
Host-Pathogen Interactions/genetics
Multiomics

@article {pmid38862357,
year = {2024},
author = {Knight, E and Rhinehart, T and de Zwaan, DR and Weldy, MJ and Cartwright, M and Hawley, SH and Larkin, JL and Lesmeister, D and Bayne, E and Kitzes, J},
title = {Individual identification in acoustic recordings.},
journal = {Trends in ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tree.2024.05.007},
pmid = {38862357},
issn = {1872-8383},
abstract = {Recent advances in bioacoustics combined with acoustic individual identification (AIID) could open frontiers for ecological and evolutionary research because traditional methods of identifying individuals are invasive, expensive, labor-intensive, and potentially biased. Despite overwhelming evidence that most taxa have individual acoustic signatures, the application of AIID remains challenging and uncommon. Furthermore, the methods most commonly used for AIID are not compatible with many potential AIID applications. Deep learning in adjacent disciplines suggests opportunities to advance AIID, but such progress is limited by training data. We suggest that broadscale implementation of AIID is achievable, but researchers should prioritize methods that maximize the potential applications of AIID, and develop case studies with easy taxa at smaller spatiotemporal scales before progressing to more difficult scenarios.},
}

@article {pmid38860489,
year = {2024},
author = {Toga, K and Sakamoto, T and Kanda, M and Tamura, K and Okuhara, K and Tabunoki, H and Bono, H},
title = {Long-read genome assembly of the Japanese parasitic wasp Copidosoma floridanum (Hymenoptera: Encyrtidae).},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkae127},
pmid = {38860489},
issn = {2160-1836},
abstract = {Copidosoma floridanum is a cosmopolitan species and an egg-larval parasitoid of the Plusiine moth. C. floridanum has a unique development mode called polyembryony, in which over two thousands of genetically identical embryos are produced from a single egg. Some embryos develop into sterile soldier larvae precociously, and their emergence period and aggressive behavior are differed between the US and Japanese C. floridanum strains. Genome sequencing expects to contribute our understanding of the molecular bases underlying progression of polyembryony. However, only the genome sequence of the US strain from generating by short-read assembly has been reported. In the present study, we determined the genome sequence of the Japanese strain using Pacific Biosciences high-fidelity reads and generating a highly contiguous assembly (552.7 Mb, N50: 17.9 Mb). Gene prediction and annotation identified 13,886 transcripts derived from 10,786 gene models. We searched the genomic differences between US and Japanese strains. Among gene models predicted in this study, 100 gene loci in the Japanese strain had extremely different gene structure from those in the US strain. This was accomplished through the functional annotation (GGSEARCH) and long-read sequencing. Genomic differences between strains were also reflected to amino acid sequences of vasa that plays a central role in caste determination in this species. The genome assemblies constructed in this study will facilitate the genomic comparisons between Japanese and US strains, leading to our understanding of detail genomic regions responsible for the ecological and physiological characters of C. floridanum.},
}

@article {pmid38856681,
year = {2024},
author = {Dasgupta, S},
title = {Thinking Beyond Disease Silos: Dysregulated Genes Common in Tuberculosis and Lung Cancer as Identified by Systems Biology and Machine Learning.},
journal = {Omics : a journal of integrative biology},
volume = {28},
number = {7},
pages = {347-356},
doi = {10.1089/omi.2024.0116},
pmid = {38856681},
issn = {1557-8100},
mesh = {Humans ; *Machine Learning ; *Lung Neoplasms/genetics ; *Tuberculosis/genetics ; *Systems Biology/methods ; Computational Biology/methods ; Gene Expression Profiling/methods ; Gene Regulatory Networks ; },
abstract = {The traditional way of thinking about human diseases across clinical and narrow phenomics silos often masks the underlying shared molecular substrates across human diseases. One Health and planetary health fields particularly address such complexities and invite us to think across the conventional disease nosologies. For example, tuberculosis (TB) and lung cancer (LC) are major pulmonary diseases with significant planetary health implications. Despite distinct etiologies, they can coexist in a given community or patient. This is both a challenge and an opportunity for preventive medicine, diagnostics, and therapeutics innovation. This study reports a bioinformatics analysis of publicly available gene expression data, identifying overlapping dysregulated genes, downstream regulators, and pathways in TB and LC. Analysis of NCBI-GEO datasets (GSE83456 and GSE103888) unveiled differential expression of CEACAM6, MUC1, ADM, DYSF, PLOD2, and GAS6 genes in both diseases, with pathway analysis indicating association with lysine degradation pathway. Random forest, a machine-learning-based classification, achieved accuracies of 84% for distinguishing TB from controls and 83% for discriminating LC from controls using these specific genes. Additionally, potential drug targets were identified, with molecular docking confirming the binding affinity of warfarin to GAS6. Taken together, the present study speaks of the pressing need to rethink clinical diagnostic categories of human diseases and that TB and LC might potentially share molecular substrates. Going forward, planetary health and One Health scholarship are poised to cultivate new ways of thinking about diseases not only across medicine and ecology but also across traditional diagnostic conventions.},
}

Humans
*Machine Learning
*Lung Neoplasms/genetics
*Tuberculosis/genetics
*Systems Biology/methods
Computational Biology/methods
Gene Expression Profiling/methods
Gene Regulatory Networks

@article {pmid38855721,
year = {2023},
author = {Boyes, D and Broad, GR and Holland, PWH and , and , and , and , and , and , and , },
title = {The genome sequence of the Cloaked Minor, Mesoligia furuncula (Denis & Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {251},
pmid = {38855721},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Mesoligia furuncula (the Cloaked Minor; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 889.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,903 protein coding genes.},
}

@article {pmid38854694,
year = {2024},
author = {Christenhusz, MJM and Pannell, JR and Twyford, AD and , and , and , and , and , and , and , },
title = {The genome sequence of the Annual Mercury, Mercurialis annua L., 1753 (Euphorbiaceae).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {102},
pmid = {38854694},
issn = {2398-502X},
abstract = {We present a genome assembly from a diploid female Mercurialis annua (the Annual Mercury; Tracheophyta; Magnoliopsida; Malpighiales; Euphorbiaceae). The genome sequence is 453.2 megabases in span. Most of the assembly is scaffolded into 8 chromosomal pseudomolecules, including the X chromosome. The organelle genomes have also been assembled, and the mitochondrial genome is 435.28 kilobases in length, while the plastid genome is 169.65 kilobases in length.},
}

@article {pmid38853065,
year = {2024},
author = {O'Connor, JB and Mottlowitz, M and Wagner, BD and Harris, JK and Laguna, TA},
title = {Metabolomics analysis of bronchoalveolar lavage fluid predicts unique features of the lower airway in pediatric cystic fibrosis.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2024.04.017},
pmid = {38853065},
issn = {1873-5010},
abstract = {BACKGROUND: Progressive, obstructive lung disease resulting from chronic infection and inflammation is the leading cause of morbidity and mortality in persons with cystic fibrosis (PWCF). Metabolomics and next -generation sequencing (NGS) of airway secretions can allow for better understanding of cystic fibrosis (CF) pathophysiology. In this study, global metabolomic profiling on bronchoalveolar lavage fluid (BALF) obtained from pediatric PWCF and disease controls (DCs) was performed and compared to lower airway microbiota, inflammation, and lung function.

METHODS: BALF was collected from children undergoing flexible bronchoscopies for clinical indications. Metabolomic profiling was performed using a platform developed by Metabolon Inc. Total bacterial load (TBL) was measured using quantitative polymerase chain reaction (qPCR), and bacterial communities were characterized using 16S ribosomal RNA (rRNA) sequencing. Random Forest Analysis (RFA), principal component analysis (PCA), and hierarchical clustering analysis (HCA) were performed.

RESULTS: One hundred ninety-five BALF samples were analyzed, 142 (73 %) from PWCF. Most metabolites (425/665) and summed categories (7/9) were significantly increased in PWCF. PCA of the metabolomic data revealed CF BALF exhibited more dispersed clustering compared to DC BALF. Higher metabolite concentrations correlated with increased inflammation, increased abundance of Staphylococcus, and decreased lung function.

CONCLUSIONS: The lower airway metabolome of PWCF was defined by a complex expansion of metabolomic activity. These findings could be attributed to heightened inflammation in PWCF and aspects of the CF airway polymicrobial ecology. CF-specific metabolomic features are associated with the unique underlying biology of the CF airway.},
}

@article {pmid38852834,
year = {2024},
author = {Goodus, MT and Alfredo, AN and Carson, KE and Dey, P and Pukos, N and Schwab, JM and Popovich, PG and Gao, J and Mo, X and Bruno, RS and McTigue, DM},
title = {Spinal cord injury-induced metabolic impairment and steatohepatitis develops in non-obese rats and is exacerbated by premorbid obesity.},
journal = {Experimental neurology},
volume = {379},
number = {},
pages = {114847},
doi = {10.1016/j.expneurol.2024.114847},
pmid = {38852834},
issn = {1090-2430},
abstract = {Impaired sensorimotor functions are prominent complications of spinal cord injury (SCI). A clinically important but less obvious consequence is development of metabolic syndrome (MetS), including increased adiposity, hyperglycemia/insulin resistance, and hyperlipidemia. MetS predisposes SCI individuals to earlier and more severe diabetes and cardiovascular disease compared to the general population, which trigger life-threatening complications (e.g., stroke, myocardial infarcts). Although each comorbidity is known to be a risk factor for diabetes and other health problems in obese individuals, their relative contribution or perceived importance in propagating systemic pathology after SCI has received less attention. This could be explained by an incomplete understanding of MetS promoted by SCI compared with that from the canonical trigger diet-induced obesity (DIO). Thus, here we compared metabolic-related outcomes after SCI in lean rats to those of uninjured rats with DIO. Surprisingly, SCI-induced MetS features were equal to or greater than those in obese uninjured rats, including insulin resistance, endotoxemia, hyperlipidemia, liver inflammation and steatosis. Considering the endemic nature of obesity, we also evaluated the effect of premorbid obesity in rats receiving SCI; the combination of DIO + SCI exacerbated MetS and liver pathology compared to either alone, suggesting that obese individuals that sustain a SCI are especially vulnerable to metabolic dysfunction. Notably, premorbid obesity also exacerbated intraspinal lesion pathology and worsened locomotor recovery after SCI. Overall, these results highlight that normal metabolic function requires intact spinal circuitry and that SCI is not just a sensory-motor disorder, but also has significant metabolic consequences.},
}

@article {pmid38845010,
year = {2024},
author = {Wang, S and Lee, HC and Lee, S},
title = {Predicting herb-disease associations using network-based measures in human protein interactome.},
journal = {BMC complementary medicine and therapies},
volume = {24},
number = {Suppl 2},
pages = {218},
pmid = {38845010},
issn = {2662-7671},
support = {GIST Research Institute IIBR//Gwangju Institute of Science and Technology/ ; GIST Research Institute (GRI) GIST-MIT research Collaboration//Gwangju Institute of Science and Technology/ ; 2021M3A9G8022959//Ministry of Science and ICT, South Korea/ ; 2021R1C1C1006336//Ministry of Science and ICT, South Korea/ ; HR22C141105//Ministry of Health and Welfare/ ; },
mesh = {Humans ; *Protein Interaction Maps ; Computer Simulation ; Computational Biology/methods ; },
abstract = {BACKGROUND: Natural herbs are frequently used to treat diseases or to relieve symptoms in many countries. Moreover, as their safety has been proven for a long time, they are considered as main sources of new drug development. However, in many cases, the herbs are still prescribed relying on ancient records and/or traditional practices without scientific evidences. More importantly, the medicinal efficacy of the herbs has to be evaluated in the perspective of MCMT (multi-compound multi-target) effects, but most efforts focus on identifying and analyzing a single compound experimentally. To overcome these hurdles, computational approaches which are based on the scientific evidences and are able to handle the MCMT effects are needed to predict the herb-disease associations.

RESULTS: In this study, we proposed a network-based in silico method to predict the herb-disease associations. To this end, we devised a new network-based measure, WACP (weighted average closest path length), which not only quantifies proximity between herb-related genes and disease-related genes but also considers compound compositions of each herb. As a result, we confirmed that our method successfully predicts the herb-disease associations in the human protein interactome (AUROC = 0.777). In addition, we observed that our method is superior than the other simple network-based proximity measures (e.g. average shortest and closest path length). Additionally, we analyzed the associations between Brassica oleracea var. italica and its known associated diseases more specifically as case studies. Finally, based on the prediction results of the WACP, we suggested novel herb-disease pairs which are expected to have potential relations and their literature evidences.

CONCLUSIONS: This method could be a promising solution to modernize the use of the natural herbs by providing the scientific evidences about the molecular associations between the herb-related genes targeted by multiple compounds and the disease-related genes in the human protein interactome.},
}

Humans
*Protein Interaction Maps
Computer Simulation
Computational Biology/methods

@article {pmid38844398,
year = {2024},
author = {Xiao, Z and Robertson, S and Long, E and Flaig, R and Kirby, L and Romaniuk, L and Murray, A and Whalley, H},
title = {Loneliness in the Digital World: protocol for a co-produced ecological momentary assessment study in adolescents.},
journal = {BMJ open},
volume = {14},
number = {6},
pages = {e087374},
pmid = {38844398},
issn = {2044-6055},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; *Loneliness/psychology ; Adolescent ; *Ecological Momentary Assessment ; *Mental Health ; Female ; Child ; Male ; Social Interaction ; Surveys and Questionnaires ; Research Design ; Depression ; Scotland ; Anxiety ; },
abstract = {INTRODUCTION: Loneliness has been identified as an important public health issue, peaking during adolescence. Previous research has suggested that social interaction is a key factor in loneliness, and positive social interaction can act as a protective factor against loneliness. However, it is unclear whether there are differing impacts of in-person and online social interaction on adolescents' loneliness and mental health. Ecological Momentary Assessment (EMA) designs are ideally suited for better understanding these associations.

METHOD AND ANALYSIS: In the 'Loneliness in the Digital World' study, we will use a co-developed EMA design to capture daily social interactions, loneliness and mental health such as positive and negative emotions, depression and anxiety in approximately 200 adolescents aged 12-15 years. We will combine this with comprehensive information gathered from online surveys. Analysing the data using techniques such as dynamic structural equation modelling, we will examine, among other research questions, the associations between online and in-person social interaction and feelings of loneliness. The results can help inform interventions to support adolescents with high levels of loneliness and poor mental health.

ETHICS AND DISSEMINATION: We received the ethics approval for the data collection from The Academic and Clinical Central Office for Research and Development, followed by the College of Medicine and Veterinary Medicine Ethics panel at University of Edinburgh, and finally reviewed by East of Scotland Research Ethics Service. The results will be disseminated through journal publications, conferences and seminar presentations and to relevant stakeholders such as teachers.},
}

Humans
*Loneliness/psychology
Adolescent
*Ecological Momentary Assessment
*Mental Health
Female
Child
Male
Social Interaction
Surveys and Questionnaires
Research Design
Depression
Scotland
Anxiety

@article {pmid38841890,
year = {2024},
author = {Pedersen, MB and Beedholm, K and Hubancheva, A and Koseva, K and Uebel, AS and Hochradel, K and Madsen, PT and Stidsholt, L},
title = {Clutter resilience via auditory stream segregation in echolocating greater mouse-eared bats.},
journal = {The Journal of experimental biology},
volume = {227},
number = {12},
pages = {},
doi = {10.1242/jeb.246889},
pmid = {38841890},
issn = {1477-9145},
support = {//Frands Christian Frantsen Foundation/ ; FP2 0135-00343B//Natur og Univers, Det Frie Forskningsråd/ ; AU337272//Fonden Frands Christian Frantsens Legat/ ; 41386//Villum Fonden/ ; CF16-0405//Carlsbergfondet/ ; },
mesh = {Animals ; *Chiroptera/physiology ; *Echolocation/physiology ; Male ; Female ; Vocalization, Animal/physiology ; },
abstract = {Bats use echolocation to navigate and hunt in darkness, and must in that process segregate target echoes from unwanted clutter echoes. Bats may do this by approaching a target at steep angles relative to the plane of the background, utilizing their directional transmission and receiving systems to minimize clutter from background objects, but it remains unknown how bats negotiate clutter that cannot be spatially avoided. Here, we tested the hypothesis that when movement no longer offers spatial release, echolocating bats mitigate clutter by calling at lower source levels and longer call intervals to ease auditory streaming. We trained five greater mouse-eared bats (Myotis myotis) to land on a spherical loudspeaker with two microphones attached. We used a phantom-echo setup, where the loudspeaker/target transmitted phantom clutter echoes by playing back the bats' own calls at time delays of 1, 3 and 5 ms with a virtual target strength 7 dB higher than the physical target. We show that the bats successfully landed on the target, irrespective of the clutter echo delays. Rather than decreasing their source levels, the bats used similar source level distributions in clutter and control trials. Similarly, the bats did not increase their call intervals, but instead used the same distribution of call intervals across control and clutter trials. These observations reject our hypothesis, leading us to conclude that bats display great resilience to clutter via short auditory integration times and acute auditory stream segregation rather than via biosonar adjustments.},
}

Animals
*Chiroptera/physiology
*Echolocation/physiology
Male
Female
Vocalization, Animal/physiology

@article {pmid38840517,
year = {2024},
author = {Walker, XJ and Hart, S and Hansen, WD and Jean, M and Brown, CD and Stuart Chapin, F and Hewitt, R and Hollingsworth, TN and Mack, MC and Johnstone, JF},
title = {Factors limiting the potential range expansion of lodgepole pine in Interior Alaska.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {34},
number = {5},
pages = {e2983},
doi = {10.1002/eap.2983},
pmid = {38840517},
issn = {1051-0761},
support = {05-1-2-06//Joint Fire Science Program/ ; //Natural Sciences and Engineering Research Council of Canada/ ; PNW01-JV11261952-23//U.S. Fish and Wildlife Service/ ; RC-2109//Strategic Environmental Research and Development Program/ ; RC-2754//Strategic Environmental Research and Development Program/ ; DEB-0620579//National Science Foundation/ ; DEB-1636476//National Science Foundation/ ; DEB-2224776//National Science Foundation/ ; USFS-PNW01-JV11261952-23//National Science Foundation/ ; RJVA-PNW-20-JV-11261932-018//National Science Foundation/ ; OPP-2116862//National Science Foundation/ ; NNX15AT71A/NASA/NASA/United States ; },
mesh = {*Pinus/physiology ; Alaska ; Climate Change ; Models, Biological ; Seedlings ; Demography ; Animals ; Ecosystem ; },
abstract = {Understanding the factors influencing species range limits is increasingly crucial in anticipating migrations due to human-caused climate change. In the boreal biome, ongoing climate change and the associated increases in the rate, size, and severity of disturbances may alter the distributions of boreal tree species. Notably, Interior Alaska lacks native pine, a biogeographical anomaly that carries implications for ecosystem structure and function. The current range of lodgepole pine (Pinus contorta var. latifolia) in the adjacent Yukon Territory may expand into Interior Alaska, particularly with human assistance. Evaluating the potential for pine expansion in Alaska requires testing constraints on range limits such as dispersal limitations, environmental tolerance limits, and positive or negative biotic interactions. In this study, we used field experiments with pine seeds and transplanted seedlings, complemented by model simulations, to assess the abiotic and biotic factors influencing lodgepole pine seedling establishment and growth after fire in Interior Alaska. We found that pine could successfully recruit, survive, grow, and reproduce across our broadly distributed network of experimental sites. Our results show that both mammalian herbivory and competition from native tree species are unlikely to constrain pine growth and that environmental conditions commonly found in Interior Alaska fall well within the tolerance limits for pine. If dispersal constraints are released, lodgepole pine could have a geographically expansive range in Alaska, and once established, its growth is sufficient to support pine-dominated stands. Given the impacts of lodgepole pine on ecosystem processes such as increases in timber production, carbon sequestration, landscape flammability, and reduced forage quality, natural or human-assisted migration of this species is likely to substantially alter responses of Alaskan forest ecosystems to climate change.},
}

*Pinus/physiology
Alaska
Climate Change
Models, Biological
Seedlings
Demography
Animals
Ecosystem

@article {pmid38839953,
year = {2024},
author = {Senior, RA and Bagwyn, R and Leng, D and Killion, AK and Jetz, W and Wilcove, DS},
title = {Global shortfalls in documented actions to conserve biodiversity.},
journal = {Nature},
volume = {630},
number = {8016},
pages = {387-391},
pmid = {38839953},
issn = {1476-4687},
mesh = {Animals ; *Biodiversity ; *Conservation of Natural Resources/methods/statistics & numerical data ; Databases, Factual ; *Endangered Species/statistics & numerical data ; Extinction, Biological ; *Internationality ; Introduced Species/statistics & numerical data ; },
abstract = {Threatened species are by definition species that are in need of assistance. In the absence of suitable conservation interventions, they are likely to disappear soon[1]. There is limited understanding of how and where conservation interventions are applied globally, or how well they work[2,3]. Here, using information from the International Union for Conservation of Nature Red List and other global databases, we find that for species at risk from three of the biggest drivers of biodiversity loss-habitat loss, overexploitation for international trade and invasive species[4]-many appear to lack the appropriate types of conservation interventions. Indeed, although there has been substantial recent expansion of the protected area network, we still find that 91% of threatened species have insufficient representation of their habitats within protected areas. Conservation interventions are not implemented uniformly across different taxa and regions and, even when present, have infrequently led to substantial improvements in the status of species. For 58% of the world's threatened terrestrial species, we find conservation interventions to be notably insufficient or absent. We cannot determine whether such species are truly neglected, or whether efforts to recover them are not included in major conservation databases. If they are indeed neglected, the outlook for many of the world's threatened species is grim without more and better targeted action.},
}

Animals
*Biodiversity
*Conservation of Natural Resources/methods/statistics & numerical data
Databases, Factual
*Endangered Species/statistics & numerical data
Extinction, Biological
*Internationality
Introduced Species/statistics & numerical data

@article {pmid38838462,
year = {2024},
author = {Runge, MC and Shea, K and Howerton, E and Yan, K and Hochheiser, H and Rosenstrom, E and Probert, WJM and Borchering, R and Marathe, MV and Lewis, B and Venkatramanan, S and Truelove, S and Lessler, J and Viboud, C},
title = {Scenario design for infectious disease projections: Integrating concepts from decision analysis and experimental design.},
journal = {Epidemics},
volume = {47},
number = {},
pages = {100775},
doi = {10.1016/j.epidem.2024.100775},
pmid = {38838462},
issn = {1878-0067},
support = {U24 GM132013/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *COVID-19/epidemiology/prevention & control/transmission ; *Decision Support Techniques ; Forecasting ; SARS-CoV-2 ; Communicable Diseases/epidemiology ; Pandemics/prevention & control ; Decision Making ; Research Design ; },
abstract = {Across many fields, scenario modeling has become an important tool for exploring long-term projections and how they might depend on potential interventions and critical uncertainties, with relevance to both decision makers and scientists. In the past decade, and especially during the COVID-19 pandemic, the field of epidemiology has seen substantial growth in the use of scenario projections. Multiple scenarios are often projected at the same time, allowing important comparisons that can guide the choice of intervention, the prioritization of research topics, or public communication. The design of the scenarios is central to their ability to inform important questions. In this paper, we draw on the fields of decision analysis and statistical design of experiments to propose a framework for scenario design in epidemiology, with relevance also to other fields. We identify six different fundamental purposes for scenario designs (decision making, sensitivity analysis, situational awareness, horizon scanning, forecasting, and value of information) and discuss how those purposes guide the structure of scenarios. We discuss other aspects of the content and process of scenario design, broadly for all settings and specifically for multi-model ensemble projections. As an illustrative case study, we examine the first 17 rounds of scenarios from the U.S. COVID-19 Scenario Modeling Hub, then reflect on future advancements that could improve the design of scenarios in epidemiological settings.},
}

Humans
*COVID-19/epidemiology/prevention & control/transmission
*Decision Support Techniques
Forecasting
SARS-CoV-2
Communicable Diseases/epidemiology
Pandemics/prevention & control
Decision Making
Research Design

@article {pmid38837409,
year = {2024},
author = {Rico-Jiménez, M and Udaondo, Z and Krell, T and Matilla, MA},
title = {Auxin-mediated regulation of susceptibility to toxic metabolites, c-di-GMP levels, and phage infection in the rhizobacterium Serratia plymuthica.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0016524},
doi = {10.1128/msystems.00165-24},
pmid = {38837409},
issn = {2379-5077},
abstract = {UNLABELLED: The communication between plants and their microbiota is highly dynamic and involves a complex network of signal molecules. Among them, the auxin indole-3-acetic acid (IAA) is a critical phytohormone that not only regulates plant growth and development, but is emerging as an important inter- and intra-kingdom signal that modulates many bacterial processes that are important during interaction with their plant hosts. However, the corresponding signaling cascades remain largely unknown. Here, we advance our understanding of the largely unknown mechanisms by which IAA carries out its regulatory functions in plant-associated bacteria. We showed that IAA caused important changes in the global transcriptome of the rhizobacterium Serratia plymuthica and multidisciplinary approaches revealed that IAA sensing interferes with the signaling mediated by other pivotal plant-derived signals such as amino acids and 4-hydroxybenzoic acid. Exposure to IAA caused large alterations in the transcript levels of genes involved in amino acid metabolism, resulting in significant metabolic alterations. IAA treatment also increased resistance to toxic aromatic compounds through the induction of the AaeXAB pump, which also confers resistance to IAA. Furthermore, IAA promoted motility and severely inhibited biofilm formation; phenotypes that were associated with decreased c-di-GMP levels and capsule production. IAA increased capsule gene expression and enhanced bacterial sensitivity to a capsule-dependent phage. Additionally, IAA induced the expression of several genes involved in antibiotic resistance and led to changes in the susceptibility and responses to antibiotics with different mechanisms of action. Collectively, our study illustrates the complexity of IAA-mediated signaling in plant-associated bacteria.

IMPORTANCE: Signal sensing plays an important role in bacterial adaptation to ecological niches and hosts. This communication appears to be particularly important in plant-associated bacteria since they possess a large number of signal transduction systems that respond to a wide diversity of chemical, physical, and biological stimuli. IAA is emerging as a key inter- and intra-kingdom signal molecule that regulates a variety of bacterial processes. However, despite the extensive knowledge of the IAA-mediated regulatory mechanisms in plants, IAA signaling in bacteria remains largely unknown. Here, we provide insight into the diversity of mechanisms by which IAA regulates primary and secondary metabolism, biofilm formation, motility, antibiotic susceptibility, and phage sensitivity in a biocontrol rhizobacterium. This work has important implications for our understanding of bacterial ecology in plant environments and for the biotechnological and clinical applications of IAA, as well as related molecules.},
}

@article {pmid38831386,
year = {2024},
author = {Duo, H and Li, Y and Lan, Y and Tao, J and Yang, Q and Xiao, Y and Sun, J and Li, L and Nie, X and Zhang, X and Liang, G and Liu, M and Hao, Y and Li, B},
title = {Systematic evaluation with practical guidelines for single-cell and spatially resolved transcriptomics data simulation under multiple scenarios.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {145},
pmid = {38831386},
issn = {1474-760X},
support = {KJQN202100538//Science and Technology Research Program of Chongqing Municipal Education Commission/ ; 62101087//National Natural Science Foundation of China/ ; 2021MD703942//China Postdoctoral Science Foundation/ ; YKC23027//Graduate Research Innovation Project of Chongqing Normal University/ ; YNPRAEC-2023004//Open Fund of Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology/ ; },
mesh = {*Single-Cell Analysis/methods ; *Gene Expression Profiling/methods ; Humans ; Software ; Computer Simulation ; Transcriptome ; Computational Biology/methods ; Sequence Analysis, RNA/methods ; RNA-Seq/methods/standards ; },
abstract = {BACKGROUND: Single-cell RNA sequencing (scRNA-seq) and spatially resolved transcriptomics (SRT) have led to groundbreaking advancements in life sciences. To develop bioinformatics tools for scRNA-seq and SRT data and perform unbiased benchmarks, data simulation has been widely adopted by providing explicit ground truth and generating customized datasets. However, the performance of simulation methods under multiple scenarios has not been comprehensively assessed, making it challenging to choose suitable methods without practical guidelines.

RESULTS: We systematically evaluated 49 simulation methods developed for scRNA-seq and/or SRT data in terms of accuracy, functionality, scalability, and usability using 152 reference datasets derived from 24 platforms. SRTsim, scDesign3, ZINB-WaVE, and scDesign2 have the best accuracy performance across various platforms. Unexpectedly, some methods tailored to scRNA-seq data have potential compatibility for simulating SRT data. Lun, SPARSim, and scDesign3-tree outperform other methods under corresponding simulation scenarios. Phenopath, Lun, Simple, and MFA yield high scalability scores but they cannot generate realistic simulated data. Users should consider the trade-offs between method accuracy and scalability (or functionality) when making decisions. Additionally, execution errors are mainly caused by failed parameter estimations and appearance of missing or infinite values in calculations. We provide practical guidelines for method selection, a standard pipeline Simpipe (https://github.com/duohongrui/simpipe ; https://doi.org/10.5281/zenodo.11178409), and an online tool Simsite (https://www.ciblab.net/software/simshiny/) for data simulation.

CONCLUSIONS: No method performs best on all criteria, thus a good-yet-not-the-best method is recommended if it solves problems effectively and reasonably. Our comprehensive work provides crucial insights for developers on modeling gene expression data and fosters the simulation process for users.},
}

*Single-Cell Analysis/methods
*Gene Expression Profiling/methods
Humans
Software
Computer Simulation
Transcriptome
Computational Biology/methods
Sequence Analysis, RNA/methods
RNA-Seq/methods/standards