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Bibliography on: Ecological Informatics

The Electronic Scholarly Publishing Project: Providing world-wide, free access to classic scientific papers and other scholarly materials, since 1993.


ESP: PubMed Auto Bibliography 02 Dec 2023 at 01:44 Created: 

Ecological Informatics

Wikipedia: Ecological Informatics Ecoinformatics, or ecological informatics, is the science of information (Informatics) in Ecology and Environmental science. It integrates environmental and information sciences to define entities and natural processes with language common to both humans and computers. However, this is a rapidly developing area in ecology and there are alternative perspectives on what constitutes ecoinformatics. A few definitions have been circulating, mostly centered on the creation of tools to access and analyze natural system data. However, the scope and aims of ecoinformatics are certainly broader than the development of metadata standards to be used in documenting datasets. Ecoinformatics aims to facilitate environmental research and management by developing ways to access, integrate databases of environmental information, and develop new algorithms enabling different environmental datasets to be combined to test ecological hypotheses. Ecoinformatics characterize the semantics of natural system knowledge. For this reason, much of today's ecoinformatics research relates to the branch of computer science known as Knowledge representation, and active ecoinformatics projects are developing links to activities such as the Semantic Web. Current initiatives to effectively manage, share, and reuse ecological data are indicative of the increasing importance of fields like Ecoinformatics to develop the foundations for effectively managing ecological information. Examples of these initiatives are National Science Foundation Datanet projects, DataONE and Data Conservancy.

Created with PubMed® Query: ( "ecology OR ecological" AND ("data management" OR informatics) NOT "assays for monitoring autophagy" ) NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)


RevDate: 2023-12-01

Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Wellcome Sanger Institute Tree of Life programme, et al (2023)

The genome sequence of the Gold Triangle, Hypsopygia costalis (Fabricius, 1775).

Wellcome open research, 8:15.

We present a genome assembly from an individual male Hypsopygia costalis (the Gold Triangle; Arthropoda; Insecta; Lepidoptera; Pyralidae). The genome sequence is 818 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,248 protein coding genes.

RevDate: 2023-12-01

Turk F, Sweetman J, Allsopp G, et al (2023)

Pathways to care for Long COVID and for long-term conditions from patients' and clinicians' perspective.

RevDate: 2023-11-30

Mori Y, Okawara M, Shibao K, et al (2023)

Short-term outcomes of pancreatoduodenectomy in older individuals over a 9-year period using real-world data: A multilevel analysis based on a nationwide administrative database in Japan.

Journal of hepato-biliary-pancreatic sciences [Epub ahead of print].

BACKGROUND: We aimed to evaluate the short-term outcomes of pancreatoduodenectomy (PD) in older individuals.

METHODS: Data from the Japanese Diagnosis Procedure Combination database on 62 275 patients who underwent PD from 1 April 2012 to 31 March 2020 were analyzed. Patients were divided into five age groups: <70, 70-74, 75-79, 80-84, and ≥85 years. The associations between postoperative outcomes and age were investigated using multilevel analysis. The mean differences in length of hospital stay and cost were also compared.

RESULTS: The rate of PD in older individuals increased annually. Compared with the youngest age group (< 70 years), the incidence rate ratios for in-hospital mortality were 1.52 (95% confidence interval [CI]: 1.30-1.76), 2.07 (1.82-2.37), 2.29 (1.94-2.71), and 2.92 (2.20-3.87) in the 70-74, 75-79, 80-84, and ≥ 85-year-old age groups, respectively (all p < .001). Postoperative complications, length of postoperative hospital stay, and cost increased significantly with increasing age.

CONCLUSIONS: These real-world data emphasize the higher levels of morbidity, mortality, and cost in older patients. Careful attention should be paid when considering the indication for PD in older individuals.

RevDate: 2023-12-01
CmpDate: 2023-12-01

Lu Z, Zhong H, Tang L, et al (2023)

Predicting lncRNA-disease associations based on heterogeneous graph convolutional generative adversarial network.

PLoS computational biology, 19(11):e1011634.

There is a growing body of evidence indicating the crucial roles that long non-coding RNAs (lncRNAs) play in the development and progression of various diseases, including cancers, cardiovascular diseases, and neurological disorders. However, accurately predicting potential lncRNA-disease associations remains a challenge, as existing methods have limitations in extracting heterogeneous association information and handling sparse and unbalanced data. To address these issues, we propose a novel computational method, called HGC-GAN, which combines heterogeneous graph convolutional neural networks (GCN) and generative adversarial networks (GAN) to predict potential lncRNA-disease associations. Specifically, we construct a lncRNA-miRNA-disease heterogeneous network by integrating multiple association data and sequence information. The GCN-based generator is then employed to aggregate neighbor information of nodes and obtain node embeddings, which are used to predict lncRNA-disease associations. Meanwhile, the GAN-based discriminator is trained to distinguish between real and fake lncRNA-disease associations generated by the generator, enabling the generator to improve its ability to generate accurate lncRNA-disease associations gradually. Our experimental results demonstrate that HGC-GAN performs better in predicting potential lncRNA-disease associations, with AUC and AUPR values of 0.9591 and 0.9606, respectively, under 10-fold cross-validation. Moreover, our case study further confirms the effectiveness of HGC-GAN in predicting potential lncRNA-disease associations, even for novel lncRNAs without any known lncRNA-disease associations. Overall, our proposed method HGC-GAN provides a promising approach to predict potential lncRNA-disease associations and may have important implications for disease diagnosis, treatment, and drug development.

RevDate: 2023-11-29

Engloner AI, Németh K, Kós PB, et al (2023)

Genetic diversity of the submerged macrophyte Ceratophyllum demersum depends on habitat hydrology and habitat fragmentation.

Frontiers in plant science, 14:1277916.

The adaptability of plant populations to a changing environment depends on their genetic diversity, which in turn is influenced by the degree of sexual reproduction and gene flow from distant areas. Aquatic macrophytes can reproduce both sexually and asexually, and their reproductive fragments are spread in various ways (e.g. by water). Although these plants are obviously exposed to hydrological changes, the degree of vulnerability may depend on the types of their reproduction and distribution, as well as the hydrological differences of habitats. The aim of this study was to investigate the genetic diversity of the cosmopolitan macrophyte Ceratophyllum demersum in hydrologically different aquatic habitats, i.e. rivers and backwaters separated from the main river bed to a different extent. For this purpose, the first microsatellite primer set was developed for this species. Using 10 developed primer pairs, a high level of genetic variation was explored in C. demersum populations. Overall, more than 80% of the loci were found to be polymorphic, a total of 46 different multilocus genotypes and 18 private alleles were detected in the 63 individuals examined. The results demonstrated that microsatellite polymorphism in this species depends on habitat hydrology. The greatest genetic variability was revealed in populations of rivers, where flowing water provides constant longitudinal connections with distant habitats. The populations of the hydrologically isolated backwaters showed the lowest microsatellite polymorphism, while plants from an oxbow occasionally flooded by the main river had medium genetic diversity. The results highlight that in contrast to species that spread independently of water flow or among hydrologically isolated water bodies, macrophytes with exclusive or dominant hydrochory may be most severely affected by habitat fragmentation, for example due to climate change.

RevDate: 2023-11-30
CmpDate: 2023-11-30

Gouvêa ECDP, Ribeiro AM, Aquino EC, et al (2023)

Mortality trend due to chronic kidney disease in Brazil: an ecological study.

Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil, 32(3):e2023313.

OBJECTIVE: To analyze chronic kidney disease mortality in Brazil according to sex, age group and region of residence, from 2009 to 2020.

METHODS: This was a time series study having deaths as its unit of analysis, based on Mortality Information System data. The mortality rate was standardized using the direct method and the temporal trend was analyzed using the Prais-Winsten method.

RESULTS: There was a rising trend in chronic kidney disease mortality, ranging from 2.82, in 2009, to 3.24 in 2020 (average annual increase 1.29%; 95%CI 0.73;1.85), with a greater increase in males (1.14% per year; 95%CI 0.52;1.76), those aged 75 years and over (2.23% per year; 95%CI 1.87; 2.60) and in the Northern Region (3.86% per year; 95%CI 1.86;5.90) and Northeast Region (3.36% per year; 95%CI 2.24;4.50).

CONCLUSION: Chronic kidney disease mortality showed a rising trend in the period, with sociodemographic disparities.

MAIN RESULTS: A rising mortality trend was found for both sexes, with a greater increase in males, those aged over 75 years and in the North and Northeast regions of Brazil; mortality was highest in the Midwest region throughout the entire period.

IMPLICATIONS FOR SERVICES: The results point to the need to implement public policies with guidelines for addressing chronic kidney disease, focused on strengthening Primary Health Care (PHC).

PERSPECTIVES: Expanding access to health services, health education and integration between PHC, health surveillance and specialized care are strategies that would possibly prove to be efficient in managing this chronic health condition.

RevDate: 2023-11-30
CmpDate: 2023-11-30

Yin FF, Shi X, Guo HF, et al (2023)

Performance evaluation of rural water environment governance based on AHP: a case study of the Beitang River Basin.

Water science and technology : a journal of the International Association on Water Pollution Research, 88(10):2661-2676.

Rural water environment governance in China still lacks a systematic and comprehensive assessment protocol to help analyze and improve such governance performance. The Analytic Hierarchy Process (AHP) method was employed in this study to build a governance assessment system that integrates ecological conditions, water pollution control, and public satisfaction. To cover these topics, the assessment system is composed of an indicator layer that is customized to rural water environment governance in China. The Beitang River, located in the rural region of Hangzhou, Zhejiang, China, was presented as a case study. Field investigation provided raw data for this assessment. A questionnaire survey was conducted to interview local residents on the governance performance. An additional survey with executives who played major roles in the governance was performed to reconstruct a water environment assessment on the Beitang River prior to the governance, in order to highlight the effects of the governance through contrast. The results showed consistency in the questionnaire survey and the assessment system. The AHP assessment system was able to reflect the improvement in the water quality, river ecology, and residential welfare after the governance, and suggested limits and future directions in the following upgrade programs for the river basin.

RevDate: 2023-11-30
CmpDate: 2023-11-30

Hulme PE, Ahmed DA, Haubrock PJ, et al (2024)

Widespread imprecision in estimates of the economic costs of invasive alien species worldwide.

The Science of the total environment, 909:167997.

Several hundred studies have attempted to estimate the monetary cost arising from the management and/or impacts of invasive alien species. However, the diversity of methods used to estimate the monetary costs of invasive alien species, the types of costs that have been reported, and the spatial scales at which they have been assessed raise important questions as to the precision of these reported monetary costs. Benford's Law has been increasingly used as a diagnostic tool to assess the accuracy and reliability of estimates reported in financial accounts but has rarely been applied to audit data on environmental costs. Therefore, the distributions of first, second- and leading double-digits of the monetary costs arising from biological invasions, as reported in the InvaCost database, were compared with the null expectations under Benford's Law. There was strong evidence that the reported monetary costs of biological invasions departed considerably from Benford's Law and the departures were of a scale equal to that found in global macroeconomic data. The rounding upwards of costs appears to be widespread. Furthermore, numerical heaping, where values cluster around specific numbers was evident with only 901 unique cost values accounting for half of the 13,553 cost estimates within the InvaCost database. Irrespective of the currency, the value of 1,000,000 was the most common cost estimate. An investigation of anomalous data entries concluded that non-peer reviewed official government reports need to provide greater detail regarding how costs are estimated. Despite the undeniably high economic cost of biological invasions worldwide, individual records of costs were often found to be imprecise and possibly inflated and this emphasises the need for greater transparency and rigour when reporting the costs of biological invasions. Identifying whether the irregularities found for the costs of biological invasions are general for other types of environmental costs should be a research priority.

RevDate: 2023-11-29

Horvatić S, Parmentier E, Malavasi S, et al (2023)

Endemic fish calling: Acoustics and reproductive behaviour of the Neretva dwarf goby Orsinigobius croaticus.

Ecology and evolution, 13(11):e10673 pii:ECE310673.

The Neretva dwarf goby Orsinigobius croaticus (Gobiiformes, Gobionellidae) is an endemic fish native to the freshwaters of the Adriatic Basin in Croatia and Bosnia and Herzegovina, a Mediterranean Biodiversity Hotspot. Due to its limited distribution range, specific karst habitat and endangered status, laboratory studies on reproductive biology are scarce but crucial. Herein, we investigated the sound production and acoustic behaviour of the endangered O. croaticus during reproductive intersexual laboratory encounters, utilising an interdisciplinary approach. We also performed dissections and micro-computed tomography (μCT) scanning of the pectoral girdle to explore its potential involvement in sound production. Finally, comparative acoustic analysis was conducted on sounds produced by previously recorded soniferous sand gobies to investigate whether acoustic features are species-specific. The endemic O. croaticus is a soniferous species. Males of this species emit pulsatile sounds composed of a variable number of short (~15 ms) consecutive pulses when interacting with females, usually during the pre-spawning phase in the nest, but also during courtship outside the nest. Pulsatile sounds were low-frequency and short pulse trains (~140 Hz, <1000 ms). Male visual behaviour rate was higher when co-occurring with sounds and females entered the male's nest significantly more frequently when sounds were present. Characteristic body movements accompanied male sound production, such as head thrust and fin spreading. Furthermore, μCT scans and dissections suggest that O. croaticus shares certain anatomical similarities of the pectoral girdle (i.e. osseous elements and arrangement of levator pectoralis muscles) to previously studied sand gobies that could be involved in sound production. Multivariate comparisons, using sounds produced by eight soniferous European sand gobies, effectively distinguished soniferous (and sympatric) species based on their acoustic properties. However, the discrimination success decreased when temperature-dependent features (sound duration and pulse repetition rate) were excluded from the analysis. Therefore, we suggest both spectral and temporal features are important for the acoustic differentiation of sand gobies.

RevDate: 2023-11-28

Lawler T, Warren Andersen S, Trentham-Dietz A, et al (2023)

Change in alcohol consumption during the Covid-19 pandemic and associations with mental health and financial hardship: results from a survey of Wisconsin patients with cancer.

Journal of cancer survivorship : research and practice [Epub ahead of print].

PURPOSE: Alcohol consumption increases health risks for patients with cancer. The Covid-19 pandemic may have affected drinking habits for these individuals. We surveyed patients with cancer to examine whether changes in drinking habits were related to mental health or financial effects of the pandemic.

METHODS: From October 2020 to April 2021, adult patients (age 18-80 years at diagnosis) treated for cancer in southcentral Wisconsin were invited to complete a survey. Age-adjusted percentages for history of anxiety or depression, emotional distress, and financial impacts of Covid-19 overall and by change in alcohol consumption (non-drinker, stable, decreased, or increased) were obtained via logistic regression.

RESULTS: In total, 1,875 patients were included in the analysis (median age 64, range 19-87 years), including 9% who increased and 23% who decreased drinking. Compared to stable drinkers (32% of sample), a higher proportion of participants who increased drinking alcohol also reported anxiety or depression (45% vs. 26%), moderate to severe emotional distress (61% vs. 37%) and viewing Covid-19 as a threat to their community (67% vs. 55%). Decreased (vs. stable) drinking was associated with higher prevalence of depression or anxiety diagnosis, emotional distress, and negative financial impacts of the pandemic. Compared to non-drinkers (36% of sample), participants who increased drinking were more likely to report emotional distress (61% vs. 48%).

CONCLUSIONS: Patients with cancer from Wisconsin who changed their alcohol consumption during the Covid-19 pandemic were more likely to report poor mental health including anxiety, depression, and emotional distress than persons whose alcohol consumption was stable.

Clinicians working with cancer survivors should be aware of the link between poor mental health and increased alcohol consumption and be prepared to offer guidance or referrals to counseling, as needed.

RevDate: 2023-11-29
CmpDate: 2023-11-29

Badapalli PK, Kottala RB, Madiga R, et al (2023)

An integrated approach for the assessment and monitoring of land degradation and desertification in semi-arid regions using physico-chemical and geospatial modeling techniques.

Environmental science and pollution research international, 30(55):116751-116764.

Land degradation (LD) and desertification are serious ecological, environmental, and social-economic threats in the world, and there is a demanding need to develop accountable and reproducible techniques to assess them at different scales. This study assesses LD and desertification with the help of remote sensing (RS) and geographical information system (GIS) in the study region for the period past 29 years, i.e., from 1990 to 2019. The severity of LD and desertification was assessed quantitatively by collecting twelve soil samples in the study region and analyzing the eleven soil physico-chemical parameters and these values have made correlated with digital number (DN) values with LANDSAT 8 OLI/TIRS satellite image. The land cover analysis of LANDSAT imagery revealed that the water body slightly increased from 0.29% in 1990 to 0.46% in 2019, and built-up-land increased from 2.87% in 1990 to 5.31% in 2019. Vegetation decreased from 52.03% in 1990 to 28.57%. Fallow land, degraded land, and desertified lands increased at alarming rates, respectively 13.71% to 26.35, 18.57% to 22.31%, and 12.53% to 17.00%. It is also established that the multi-temporal analysis of change detection data can provide a sophisticated measure of ecosystem health and variation, and that, over the last 29 years, considerable progress has been made in the respective research.

RevDate: 2023-11-28

Adhurya S, Lee DY, Lee DS, et al (2023)

Functional trait dataset of benthic macroinvertebrates in South Korean streams.

Scientific data, 10(1):838.

Functional traits are the result of evolution and adaptation, providing important ecological insights into how organisms interact with their environment. Benthic macroinvertebrates, in particular, have garnered attention as biomonitoring indicators for freshwater ecosystems. This study presents a functional trait dataset for benthic macroinvertebrates, comprising 447 taxa (393 at genus level, 53 at family level and one at class level) from five phyla (Annelida, Arthropoda, Mollusca, Nematomorpha, and Platyhelmenthes), categorized into nine traits related to life history, morphology, and habit. To account for variation in available trait information, we assigned confidence levels to each taxon and functional trait based on the level of evidence using fuzzy coding. Our dataset provides an important resource for understanding the ecology of benthic macroinvertebrates in South Korea, serving as a valuable baseline dataset for studying their biodiversity, conservation, and biomonitoring in freshwater ecosystems.

RevDate: 2023-11-28

Wang Z, Yang W, Ryan K, et al (2022)

Using Optimal Transport to Improve Spherical Harmonic Quantification of Complex Biological Shapes.

Proceedings. IEEE International Conference on Bioinformatics and Biomedicine, 2022:1255-1261.

The knowledge of the anatomical shape of both gross and microscopic structures is the key to understanding the effects of disease processes on cellular structure. Geometric morphometric methods, such as Procrustes superimposition, and Spherical Harmonics (SPHARM), have been used to capture the biological shape variation and group differences in morphology. Previous SPHARM-MAT techniques use the CALD algorithm to parameterize the mesh surface. It starts from initial mapping and performs local and global smoothing methods alternately to control the area and length distortions simultaneously. However, this parameterization may not be sufficient in complex morphological cases. To bridge this gap, we propose SPHARM-OT, an enhanced SPHARM surface modeling method using optimal transport (OT) for spherical parameterization. First, the genus 0 3D objects are conformally mapped onto a sphere. Then the optimal transport theory via spherical power diagram is introduced to minimize the area distortion. This new algorithm can effectively reduce the area distortion and lead to a better reconstruction result. We demonstrate the effectiveness of the method by applying it to the human sphenoidal paranasal sinuses.

RevDate: 2023-11-27

Wilson J, Sokhansanj BA, Chong WC, et al (2023)

Fragment databases from screened ligands for drug discovery (FDSL-DD).

Journal of molecular graphics & modelling, 127:108669 pii:S1093-3263(23)00267-X [Epub ahead of print].

Fragment-based drug design (FBDD) is one major drug discovery method employed in computer-aided drug discovery. Due to its inherent limitations, this process experiences long processing times and limited success rates. Here we present a new Fragment Databases from Screened Ligands Drug Design method (FDSL-DD) that intelligently incorporates information about fragment characteristics into a fragment-based design approach to the drug development process. The initial step of the FDSL-DD is the creation of a fragment database from a library of docked, drug-like ligands for a specific target, which deviates from the traditional in silico FBDD strategy, incorporating structure-based design screening techniques to combine the advantages of both approaches. Three different protein targets have been tested in this study to demonstrate the potential of the created fragment library and FDSL-DD. Utilizing the FDSL-DD led to an increase in binding affinity for each protein target. The most substantial increase was exhibited by the ligand designed for TIPE2, with a 3.6 kcalmol[-1] difference between the top ligand from the FDSL-DD and top ligand from the high throughput virtual screening (HTVS). Using drug-like ligands in the initial HTVS allows for a greater search of chemical space, with higher efficiency in fragments selection, less grid boxes, and potentially identifying more interactions.

RevDate: 2023-11-27

Jovanović V, Rudnev M, Abdelrahman M, et al (2023)

The Coronavirus Anxiety Scale: Cross-national measurement invariance and convergent validity evidence.

Psychological assessment pii:2024-28534-001 [Epub ahead of print].

Coronavirus Anxiety Scale (CAS) is a widely used measure that captures somatic symptoms of coronavirus-related anxiety. In a large-scale collaboration spanning 60 countries (Ntotal = 21,513), we examined the CAS's measurement invariance and assessed the convergent validity of CAS scores in relation to the fear of COVID-19 (FCV-19S) and the satisfaction with life (SWLS-3) scales. We utilized both conventional exact invariance tests and alignment procedures, with results revealing that the single-factor model fit the data well in almost all countries. Partial scalar invariance was supported in a subset of 56 countries. To ensure the robustness of results, given the unbalanced samples, we employed resampling techniques both with and without replacement and found the results were more stable in larger samples. The alignment procedure demonstrated a high degree of measurement invariance with 9% of the parameters exhibiting noninvariance. We also conducted simulations of alignment using the parameters estimated in the current model. Findings demonstrated reliability of the means but indicated challenges in estimating the latent variances. Strong positive correlations between CAS and FCV-19S estimated with all three different approaches were found in most countries. Correlations of CAS and SWLS-3 were weak and negative but significantly differed from zero in several countries. Overall, the study provided support for the measurement invariance of the CAS and offered evidence of its convergent validity while also highlighting issues with variance estimation. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

RevDate: 2023-11-27
CmpDate: 2023-11-27

Wang Z, Jia Y, Li P, et al (2023)

Study on environmental factors affecting the quality of codonopsis radix based on MaxEnt model and all-in-one functional factor.

Scientific reports, 13(1):20726.

Owing to the increasing market demand of Codonopsis Radix, the cropper blindly cultivates to expand planting area for economic benefits, which seriously affects the quality of Codonopsis Radix. Therefore, this study synthesized 207 batches of Codonopsis Radix and 115 ecological factors, and analyzed the suitable planting areas of Codonopsis pilosula under current and future climate change based on Geographic Information System (GIS) and MaxEnt model. Secondly, we evaluated the quality of Codonopsis Radix based on the all-in-one functional factor including chromatographic fingerprint, the index components, the effective compounds groups, the nutritional components, and the nutritional elements, and the quality regionalization of Codonopsis Radix was analyzed. Finally, the ecological factors affecting the accumulation of effective components of Codonopsis Radix were analyzed. This study found for the first time that the highly suitable area of Codonopsis pilosula was mainly distributed in the Weihe River system and the Bailongjiang River system in Gansu Province. There were differences in the quality of Codonopsis Radix from different ecologically suitable areas based on the all-in-one functional factors, and the comprehensive high-quality area of Codonopsis Radix was mainly distributed in Longnan and Longxi district of Gansu Province. The precipitation, temperature and altitude play a key role in the accumulation of chemical components in the 10 ecological factors affecting the distribution of Codonopsis pilosula. Under future climatic conditions, the highly suitable area of Codonopsis pilosula is decreased.

RevDate: 2023-11-27

Klee B, Diexer S, Sarajan MH, et al (2023)

Regional Differences in Uptake of Vaccination against COVID-19 and Influenza in Germany: Results from the DigiHero Cohort.

Vaccines, 11(11):.

During the COVID-19 pandemic in Germany, vaccination uptake exhibited considerable regional disparities. To assess the factors contributing to this variation, we examined the association of sociodemographic variables with COVID-19, COVID-19 booster, and influenza vaccination status within a cohort of 37,078 participants from 13 German federal states in the digital health cohort study commonly known as DigiHero. Our findings revealed variations in vaccination rates based on sociodemographic factors. However, these factors had limited explanatory power regarding regional differences in vaccine uptake. In contrast, we found substantial correlations between regional support of specific parties during the last local elections and the vaccination uptake at the level of each administrative district. In conclusion, sociodemographic factors alone did not suffice to explain the regional disparities in vaccine uptake. Political stances can play a major role, although the current investigation did not assess individual political orientations but rather used only an ecological approach.

RevDate: 2023-11-27
CmpDate: 2023-11-27

Dougan KE, Deng ZL, Wöhlbrand L, et al (2023)

Multi-omics analysis reveals the molecular response to heat stress in a "red tide" dinoflagellate.

Genome biology, 24(1):265.

BACKGROUND: "Red tides" are harmful algal blooms caused by dinoflagellate microalgae that accumulate toxins lethal to other organisms, including humans via consumption of contaminated seafood. These algal blooms are driven by a combination of environmental factors including nutrient enrichment, particularly in warm waters, and are increasingly frequent. The molecular, regulatory, and evolutionary mechanisms that underlie the heat stress response in these harmful bloom-forming algal species remain little understood, due in part to the limited genomic resources from dinoflagellates, complicated by the large sizes of genomes, exhibiting features atypical of eukaryotes.

RESULTS: We present the de novo assembled genome (~ 4.75 Gbp with 85,849 protein-coding genes), transcriptome, proteome, and metabolome from Prorocentrum cordatum, a globally abundant, bloom-forming dinoflagellate. Using axenic algal cultures, we study the molecular mechanisms that underpin the algal response to heat stress, which is relevant to current ocean warming trends. We present the first evidence of a complementary interplay between RNA editing and exon usage that regulates the expression and functional diversity of biomolecules, reflected by reduction in photosynthesis, central metabolism, and protein synthesis. These results reveal genomic signatures and post-transcriptional regulation for the first time in a pelagic dinoflagellate.

CONCLUSIONS: Our multi-omics analyses uncover the molecular response to heat stress in an important bloom-forming algal species, which is driven by complex gene structures in a large, high-G+C genome, combined with multi-level transcriptional regulation. The dynamics and interplay of molecular regulatory mechanisms may explain in part how dinoflagellates diversified to become some of the most ecologically successful organisms on Earth.

RevDate: 2023-11-27
CmpDate: 2023-11-27

Aksoy H (2023)

Determination of landslide susceptibility with Analytic Hierarchy Process (AHP) and the role of forest ecosystem services on landslide susceptibility.

Environmental monitoring and assessment, 195(12):1525.

The analysis of landslide susceptibility is a crucial tool in the mitigation and management of ecological and economic hazards. The number of studies examining how the form and durability of forest areas affect landslide susceptibility is very limited. This study was conducted in the Marmara region of northwestern Türkiye, where forested areas and industrial zones are intertwined and dense. The landslide susceptibility map was produced by Analytic Hierarchy Process (AHP) method. In the context of AHP, a total of 12 different variables were employed, namely lithology, slope, curvatures, precipitations, aspect, distance to fault lines, distance to streams, distance to roads, land use, soil, elevation, and Normalized Difference Vegetation Index (NDVI). The performance analysis of the landslide susceptibility map was conducted using the Receiver Operating Characteristics (ROC) curve method. The AUC value was computed (0.809) for the landslide susceptibility map generated by using the AHP technique. Forest type maps were used to analyze the impact of forests on landslide susceptibility. In terms of forest structure, 4 main criteria were determined: stand structure, development stage, crown closure, and stand age. Each criterion was analyzed with Geographic Information Systems (GIS) by overlaying it with the landslide susceptibility map of the study area. The results showed that the risk of landslides was lowest in forests with more than one tree species, mature, development stage and of (e) > 52 cm, and crown closure of 41%-70% (2).

RevDate: 2023-11-25

Barnes M, DC Price (2023)

Endogenous Viral Elements in Ixodid Tick Genomes.

Viruses, 15(11): pii:v15112201.

The documentation of endogenous viral elements (EVEs; virus-derived genetic material integrated into the genome of a nonviral host) has offered insights into how arthropods respond to viral infection via RNA interference pathways. Small non-coding RNAs derived from EVE loci serve to direct RNAi pathways in limiting replication and infection from cognate viruses, thus benefiting the host's fitness and, potentially, vectorial capacity. Here we use informatic approaches to analyze nine available genome sequences of hard ticks (Acari: Ixodidae; Rhipicephalus sanguineus, R. microplus, R. annulatus, Ixodes ricinus, I. persulcatus, I. scapularis, Hyalomma asiaticum, Haemaphysalis longicornis, and Dermacentor silvarum) to identify endogenous viral elements and to illustrate the shared ancestry of all elements identified. Our results highlight a broad diversity of viral taxa as having given rise to 1234 identified EVEs in ticks, with Mononegavirales (specifically Rhabdoviridae) well-represented in this subset of hard ticks. Further investigation revealed extensive adintovirus integrations in several Ixodes species, the prevalence of Bunyavirales EVEs (notably not observed in mosquitoes), and the presence of several elements similar to known emerging human and veterinary pathogens. These results will inform subsequent work on current and past associations with tick species with regard to the viruses from which their "viral fossils" are derived and may serve as a reference for quality control of various tick-omics data that may suffer from misidentification of EVEs as viral genetic material.

RevDate: 2023-11-25

Zhu Q, Ruan M, Hu Z, et al (2023)

The Relationship between Acid Production and the Microbial Community of Newly Produced Coal Gangue in the Early Oxidation Stage.

Microorganisms, 11(11): pii:microorganisms11112626.

Coal gangue is a solid waste formed during coal production, and the acid mine drainage it generates during open-pit storage severely pollutes the ecological environment of mining areas. Microorganisms play a crucial catalytic role in acidification, and their species and gene functions change during the oxidation process of coal gangue. In this study, the changes in microbial community structure were investigated during the initial acidification process for newly produced gangue exposed to moisture by monitoring the changes in pH, EC, sulfate ion concentration, and the iron oxidation rate of gangue leaching solutions. Moreover, the composition and functional abundance of microbial communities on the surface of the gangue were analyzed with rainfall simulation experiments and 16S rRNA sequencing. The study yielded the following findings: (1) The critical period for newly produced gangue oxidation spanned from 0~15 d after its exposure to water; the pH of leaching solutions decreased from 4.65 to 4.09 during this time, and the concentration and oxidation rate of iron in the leaching solutions remained at low levels, indicating that iron oxidation was not the main driver for acidification during this stage. (2) When the gangue was kept dry, Burkholderia spp. dominated the gangue microbial community. When the gangue was exposed to moisture, the rate of acidification accelerated, and Pseudomonas replaced Burkholderia as the dominant genus in the community. (3) In terms of gene function, the microbial community of the acidified gangue had stronger nitrogen cycling functions, and an increase in the abundance of microorganisms related to the sulfur cycle occurred after day 15 of the experiment. The microbial community in the acidified gangue had more stress resistance than the community of the newly formed gangue, but its potential to decompose environmental pollutants decreased.

RevDate: 2023-11-24

Zhou L, Wang Y, Li D, et al (2023)

Efficient degradation of phenanthrene by biochar-supported nano zero-valent iron activated persulfate: performance evaluation and mechanism insights.

Environmental science and pollution research international [Epub ahead of print].

Biochar-supported nano zero-valent iron (BC@nZVI) is a novel and efficient non-homogeneous activator for persulfate (PS). This study aimed to identify the primary pathways, the degradation mechanism and the performance of phenanthrene (PHE) with PS activated by BC@nZVI (BC@nZVI/PS). BC@nZVI as an activator for PS was prepared by liquid phase reduction method. BC@nZVI was characterized using scanning electron microscopy, transmission electron microscopy, X-ray diffractometer and Fourier transform infrared spectroscopy. The effects of the iron-carbon mass ratio and BC@nZVI dosage were investigated, and a pseudo-first-order kinetic model was used to evaluate the PHE degradation. The results showed that BC supported nZVI and inhibited the agglomeration of nZVI, improving PS's activation efficiency. The optimal iron-carbon mass ratio was determined to be 1:4, accompanied by a dosage of 0.6 g/L of BC@nZVI. During PS activation, nZVI was transformed to Fe[2+] and Fe[3+], with the majority being Fe[3+]. The reducibility of nZVI in BC@nZVI enabled the reduction of Fe[3+] to Fe[2+] to activate PS. Radical quenching and electron paramagnetic resonance (EPR) revealed that the oxidative radicals in the BC@nZVI/PS system were mainly SO4[-]· and ·OH, where SO4[-]· was the primary free radical under acidic and neutral conditions and ·OH in alkaline conditions. Additionally, BC@nZVI adsorption had a limited role in PHE removal. This study can provide mechanism insights of PHE degradation in water with BC@nZVI activation of the Na2S2O8 system.

RevDate: 2023-11-24

Tan M, Dong J, Qu J, et al (2023)

The Patterns of Migration of Potentially Toxic Elements from Coal Mining Subsidence Areas and Associated Soils to Waterlogged Areas.

Toxics, 11(11): pii:toxics11110888.

It is crucial for effectively controlling potentially toxic element (PTE) pollution to understand the pollution situation, ecological risks, health risks, and migration patterns of PTEs. However, currently, no research has been conducted on the migration patterns of soil PTEs from coal mining subsidence areas to waterlogged areas under different restoration modes. In this study, a total of 15 sediment samples and 60 soil samples were collected from landscaped wetlands, aquaculture wetland, fish-photovoltaic complementary wetland, photovoltaic wetland, and waterlogged areas with untreated coal mining subsidence. The PTE pollution status, ecological risks, health risks, migration patterns, and the important factors influencing the migration were analyzed. The results indicated that the comprehensive pollution level of PTEs in waterlogged areas with coal mining subsidence can be reduced by developing them into landscaped wetlands, aquaculture wetlands, fish-photovoltaic complementary wetlands, and photovoltaic wetlands. Additionally, the closer to the waterlogged area, the higher the Cu content in the subsidence area soil is, reaching its peak in the waterlogged area. The Cd was influenced positively by SOC and pH. The research results were of great significance for formulating reclamation plans for waterlogged areas and controlling PTE pollution.

RevDate: 2023-11-24
CmpDate: 2023-11-24

Jiahui G, Feilong M, Nastase SA, et al (2023)

Cross-movie prediction of individualized functional topography.

eLife, 12:.

Participant-specific, functionally defined brain areas are usually mapped with functional localizers and estimated by making contrasts between responses to single categories of input. Naturalistic stimuli engage multiple brain systems in parallel, provide more ecologically plausible estimates of real-world statistics, and are friendly to special populations. The current study shows that cortical functional topographies in individual participants can be estimated with high fidelity from naturalistic stimuli. Importantly, we demonstrate that robust, individualized estimates can be obtained even when participants watched different movies, were scanned with different parameters/scanners, and were sampled from different institutes across the world. Our results create a foundation for future studies that allow researchers to estimate a broad range of functional topographies based on naturalistic movies and a normative database, making it possible to integrate high-level cognitive functions across datasets from laboratories worldwide.

RevDate: 2023-11-21

Gonzalez A, Vihervaara P, Balvanera P, et al (2023)

Author Correction: A global biodiversity observing system to unite monitoring and guide action.

RevDate: 2023-11-22
CmpDate: 2023-11-22

Howerton E, Contamin L, Mullany LC, et al (2023)

Evaluation of the US COVID-19 Scenario Modeling Hub for informing pandemic response under uncertainty.

Nature communications, 14(1):7260.

Our ability to forecast epidemics far into the future is constrained by the many complexities of disease systems. Realistic longer-term projections may, however, be possible under well-defined scenarios that specify the future state of critical epidemic drivers. Since December 2020, the U.S. COVID-19 Scenario Modeling Hub (SMH) has convened multiple modeling teams to make months ahead projections of SARS-CoV-2 burden, totaling nearly 1.8 million national and state-level projections. Here, we find SMH performance varied widely as a function of both scenario validity and model calibration. We show scenarios remained close to reality for 22 weeks on average before the arrival of unanticipated SARS-CoV-2 variants invalidated key assumptions. An ensemble of participating models that preserved variation between models (using the linear opinion pool method) was consistently more reliable than any single model in periods of valid scenario assumptions, while projection interval coverage was near target levels. SMH projections were used to guide pandemic response, illustrating the value of collaborative hubs for longer-term scenario projections.

RevDate: 2023-11-22
CmpDate: 2023-11-22

Zhao Y, Jia H, Deng H, et al (2024)

Integrated microbiota and multi-omics analysis reveal the differential responses of earthworm to conventional and biodegradable microplastics in soil under biogas slurry irrigation.

The Science of the total environment, 907:168191.

As one of the promising alternatives of conventional plastic mulching film (C-PMF), biodegradable plastic mulching films (B-PMF) were employed in agronomy production to alleviate the environmental burden of C-PMF. However, information regarding the potential toxicity effects of biodegradable microplastics (MPs) in soil still in scarcity, and the available findings were found to be controversial. Additionally, little is known about the molecular toxicity effects of conventional and biodegradable MPs on terrestrial organisms. Thus, 5 % (w/w) biodegradable (polylactic acid, PLA) and conventional (polyvinylchloride, PVC; low-density polyvinylchloride, LDPE) MPs were employed to assess the toxicity effects on Eisenia fetida in agricultural soil with biogas slurry irrigation. In the present study, transcriptomic, metabolomic profiles and individual indexes were selected to reveal the toxicity mechanisms from molecular level to the individual response. Furthermore, dysbiosis of bacterial community in gut was also investigated for obtaining comprehensive knowledge on the MPs toxicity. At the end of the exposure, the number of survival earthworms after MPs exposure was significantly reduced. Compared with the initial body weight, PLA and LDPE increased the biomass of earthworms after MPs exposure, while no significant influence on the biomass was observed in PVC treatment. Microbacterium, Klebsiella and Chryseobacterium were significantly enriched in earthworm gut after PLA, PVC and LDPE exposure, respectively (p < 0.05). Transcriptomic and metabolomic analysis revealed that PLA exposure induced neurotransmission disorder and high energetic expenditure in earthworms. However, PVC and LDPE inhibited the nutrient absorption efficiency and activated the innate immunity responses of earthworms. The PLS-SEM results showed that the effects of MPs were dominated by the polymer types, and hence, significantly and directly influence the gut bacterial community of earthworms. This study provides a better understanding of the similarities and discrepancies in toxicity effects of biodegradable and conventional MPs from the perspectives of individual, gut bacterial community, transcriptome and metabolome.

RevDate: 2023-11-19

Sajjad W, Ilahi N, Kang S, et al (2023)

Microbial diversity and community structure dynamics in acid mine drainage: Acidic fire with dissolved heavy metals.

The Science of the total environment pii:S0048-9697(23)07263-7 [Epub ahead of print].

Acid mine drainage (AMD) is one of the leading causes of environmental pollution and is linked to public health and ecological consequences. Microbes-mineral interaction generates AMD, but microorganisms can also remedy AMD pollution. Exploring the microbial response to AMD effluents may reveal survival strategies in extreme ecosystems. Three distinct sites across a mine (inside the mine, the entrance of the mine, and outside) were selected to study their heavy metal concentrations due to significant variations in pH and physicochemical characteristics, and high-throughput sequencing was carried out to investigate the microbial diversity. The metal and ion concentrations followed the order SO4[2-], Fe, Cu, Zn, Mg, Pb, Co, Cr, and Ni from highest to lowest, respectively. Maximum sequences were allocated to Proteobacteria and Firmicutes. Among archaea, the abundance of Thaumarchaeota and Euryarchaeota was higher outside of mine. Most of the genera (23.12 %) were unclassified and unknown. The average OTUs (operational taxonomic units) were significantly higher outside the mine; however, diversity indices were not significantly different across the mine sites. Hierarchical clustering of selective genera and nMDS ordination of OTUs displayed greater segregation resolution inside and outside of mine, whereas the entrance samples clustered with greater similarity. Heterogeneous selection might be the main driver of community composition outside the mine, whereas stochastic processes became prominent inside the mine. However, the ANOSIM test shows a relatively even distribution of community composition within and between the groups. Microbial phyla showed both positive and negative correlations with physicochemical factors. A greater number of biomarkers were reported outside of the mine. Predictive functional investigation revealed the existence of putative degradative, metabolic, and biosynthetic pathways. This study presents a rare dataset in our understanding of microbial diversity and distribution as shaped by the ecological gradient and potential novelty in phylogenetic/taxonomic diversity in AMD, with potential biotechnological applications.

RevDate: 2023-11-20
CmpDate: 2023-11-20

Clark MS, Hoffman JI, Peck LS, et al (2023)

Multi-omics for studying and understanding polar life.

Nature communications, 14(1):7451.

Polar ecosystems are experiencing amongst the most rapid rates of regional warming on Earth. Here, we discuss 'omics' approaches to investigate polar biodiversity, including the current state of the art, future perspectives and recommendations. We propose a community road map to generate and more fully exploit multi-omics data from polar organisms. These data are needed for the comprehensive evaluation of polar biodiversity and to reveal how life evolved and adapted to permanently cold environments with extreme seasonality. We argue that concerted action is required to mitigate the impact of warming on polar ecosystems via conservation efforts, to sustainably manage these unique habitats and their ecosystem services, and for the sustainable bioprospecting of novel genes and compounds for societal gain.

RevDate: 2023-11-20
CmpDate: 2023-11-20

Stahnke DN, Nied C, Oliveira MLG, et al (2023)

Trends in hospital admissions and mortality from diabetes mellitus in Rio Grande do Sul: historical series 2000-2020.

Revista gaucha de enfermagem, 44:e20230103 pii:S1983-14472023000100480.

OBJECTIVE: To analyze the trends of hospital admissions and deaths from diabetes mellitus in the 18 host municipalities of the 19 regional health coordination offices and in Rio Grande do Sul, 2000-2020.

METHOD: Ecological study with secondary data collected in the Hospital Information System, the Mortality Information System, and the Brazilian Institute of Geography and Statistics, from 2000-2020. Coefficients were standardized using the direct method and Prais-Winsten regression analysis.

RESULTS: A downward trend wasfound in the coefficients of hospitalizations for diabetes mellitus in most cities and states. In 2020, for both areas, hospitalizations for diabetes mellitus were below the average of the period. The mortality trend remained stationary in almost all municipalities and in the state.

CONCLUSION: There was evidence of a decrease in hospitalizations and stationary mortality by DM in most municipalities analyzed, possibly due to the policies and actions implemented in the period, despite the aging of the population.

RevDate: 2023-11-21
CmpDate: 2023-11-21

Ghiotto G, Zampieri G, Campanaro S, et al (2024)

Strain-resolved metagenomics approaches applied to biogas upgrading.

Environmental research, 240(Pt 2):117414.

Genetic heterogeneity is a common trait in microbial populations, caused by de novo mutations and changes in variant frequencies over time. Microbes can thus differ genetically within the same species and acquire different phenotypes. For instance, performance and stability of anaerobic reactors are linked to the composition of the microbiome involved in the digestion process and to the environmental parameters imposing selective pressure on the metagenome, shaping its evolution. Changes at the strain level have the potential to determine variations in microbial functions, and their characterization could provide new insight into ecological and evolutionary processes driving anaerobic digestion. In this work, single nucleotide variant dynamics were studied in two time-course biogas upgrading experiments, testing alternative carbon sources and the response to exogenous hydrogen addition. A cumulative total of 76,229 and 64,289 high-confidence single nucleotide variants were discerned in the experiments related to carbon substrate availability and hydrogen addition, respectively. By combining complementary bioinformatic approaches, the study reconstructed the precise strain count-two for both hydrogenotrophic archaea-and tracked their abundance over time, while also characterizing tens of genes under strong selection. Results in the dominant archaea revealed the presence of nearly 100 variants within genes encoding enzymes involved in hydrogenotrophic methanogenesis. In the bacterial counterparts, 119 mutations were identified across 23 genes associated with the Wood-Ljungdahl pathway, suggesting a possible impact on the syntrophic acetate-oxidation process. Strain replacement events took place in both experiments, confirming the trends suggested by the variants trajectories and providing a comprehensive understanding of the biogas upgrading microbiome at the strain level. Overall, this resolution level allowed us to reveal fine-scale evolutionary mechanisms, functional dynamics, and strain-level metabolic variation that could contribute to the selection of key species actively involved in the carbon dioxide fixation process.

RevDate: 2023-11-21
CmpDate: 2023-11-21

Munley JA, Kelly LS, Park G, et al (2023)

Sex-specific intestinal dysbiosis persists after multicompartmental injury.

Surgery, 174(6):1453-1462.

BACKGROUND: Preclinical studies of the gut microbiome after severe traumatic injury have demonstrated severe dysbiosis in males, with sex-specific microbial differences up to 2 days after injury. However, the impact of host sex on injury-driven dysbiosis over time remains unknown. We hypothesized that sex-specific differences in intestinal microbiome diversity and composition after traumatic injury with and without stress would persist after 7 days.

METHODS: Male and proestrus female Sprague-Dawley rats (n = 8/group) were subjected to either polytrauma (lung contusion, hemorrhagic shock, cecectomy, bifemoral pseudofractures), polytrauma plus chronic restraint stress, or naïve controls. The fecal microbiome was measured on days 0, 3, and 7 using 16S rRNA sequencing and Quantitative Insights into Microbial Ecology bioinformatics analyses. Microbial alpha-diversity (Chao1 and Shannon indices) and beta-diversity were assessed. Analyses were performed in GraphPad and "R," with significance defined as P < .05.

RESULTS: Polytrauma and polytrauma plus chronic restraint stress reduced alpha-diversity (Chao1, Shannon) within 3 days postinjury, which persisted up to day 7 in both sexes; polytrauma and polytrauma plus chronic restraint stress females had significantly decreased Chao1 compared to male counterparts at day 7 (P = .02). At day 7, the microbiome composition in polytrauma females had higher proportion of Mucispirillum, whereas polytrauma plus chronic restraint stress males demonstrated elevated abundance of Ruminococcus and Akkermansia.

CONCLUSION: Multicompartmental trauma induces intestinal dysbiosis that is sex-specific with persistence of decreased diversity and unique "pathobiome" signatures in females after 1 week. These findings underline sex as an important biological variable that may influence variable host-specific responses and outcomes after severe trauma and critical illness. This underscores the need to consider precision medicine strategies to ameliorate these outcomes.

RevDate: 2023-11-19

Iqbal A, Maqsood Ur Rehman M, Sajjad W, et al (2023)

Patterns of bacterial communities in the rhizosphere and rhizoplane of alpine wet meadows.

Environmental research pii:S0013-9351(23)02476-3 [Epub ahead of print].

Wet meadows, a type of wetland, are vulnerable to climate change and human activity, impacting soil properties and microorganisms that are crucial to the ecosystem processes of wet meadows. To decipher the ecological mechanisms and processes involved in wet meadows, it is necessary to examine the bacterial communities associated with plant roots. To gain valuable insight into the microbial dynamics of alpine wet meadows, we used Illumina MiSeq sequencing to investigate how environmental factors shape the bacterial communities thriving in the rhizosphere and rhizoplane of three plant species: Cremanthodium ellisii, Caltha scaposa, and Cremanthodium lineare. The most abundant bacterial phyla in rhizosphere and rhizoplane were Proteobacteria > Firmicutes > Actinobacteria, while Macrococcus, Lactococcus, and Exiguobacterium were the most abundant bacterial genera between rhizosphere and rhizoplane. The mantel test, network, and structure equation models revealed that bacterial communities of rhizosphere were shaped by total nitrogen (TN), soil water content (SWC), soil organic carbon (SOC), microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), pH, however, rhizoplane bacterial communities exhibited varying results. The bacterial communities exhibited significant heterogeneity, with stochastic process predominating in both the rhizosphere and rhizoplane. PICRUSt2 and FAPROTAX analysis revealed substantial differences in key biogeochemical cycles and metabolic functional predictions. It was concluded that root compartments significantly influenced the bacterial communities, although plant species and elevation asserted varying effects. This study portrays how physicochemical properties, plant species, and elevations can shift the overall structure and functional repertoire of bacterial communities in alpine wet meadows.

RevDate: 2023-11-17

Karimian H, Zou W, Chen Y, et al (2023)

Corrigendum to 'Landscape ecological risk assessment and driving factor analysis in Dongjiang river watershed' [Chemosphere 307 (2022)135835].

RevDate: 2023-11-18
CmpDate: 2023-11-17

Swets MC, Kerr S, Scott-Brown J, et al (2023)

Evaluation of pragmatic oxygenation measurement as a proxy for Covid-19 severity.

Nature communications, 14(1):7374.

Choosing optimal outcome measures maximizes statistical power, accelerates discovery and improves reliability in early-phase trials. We devised and evaluated a modification to a pragmatic measure of oxygenation function, the [Formula: see text] ratio. Because of the ceiling effect in oxyhaemoglobin saturation, [Formula: see text] ratio ceases to reflect pulmonary oxygenation function at high [Formula: see text] values. We found that the correlation of [Formula: see text] with the reference standard ([Formula: see text]/[Formula: see text] ratio) improves substantially when excluding [Formula: see text] and refer to this measure as [Formula: see text]. Using observational data from 39,765 hospitalised COVID-19 patients, we demonstrate that [Formula: see text] is predictive of mortality, and compare the sample sizes required for trials using four different outcome measures. We show that a significant difference in outcome could be detected with the smallest sample size using [Formula: see text]. We demonstrate that [Formula: see text] is an effective intermediate outcome measure in COVID-19. It is a non-invasive measurement, representative of disease severity and provides greater statistical power.

RevDate: 2023-11-17
CmpDate: 2023-11-17

Haslbeck J, Ryan O, F Dablander (2023)

Multimodality and skewness in emotion time series.

Emotion (Washington, D.C.), 23(8):2117-2141.

The ability to measure emotional states in daily life using mobile devices has led to a surge of exciting new research on the temporal evolution of emotions. However, much of the potential of these data still remains untapped. In this paper, we reanalyze emotion measurements from seven openly available experience sampling methodology studies with a total of 835 individuals to systematically investigate the modality (unimodal, bimodal, and more than two modes) and skewness of within-person emotion measurements. We show that both multimodality and skewness are highly prevalent. In addition, we quantify the heterogeneity across items, individuals, and measurement designs. Our analysis reveals that multimodality is more likely in studies using an analog slider scale than in studies using a Likert scale; negatively valenced items are consistently more skewed than positive valenced items; and longer time series show a higher degree of modality in positive and a higher skew in negative items. We end by discussing the implications of our results for theorizing, measurement, and time series modeling. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

RevDate: 2023-11-16
CmpDate: 2023-11-16

Hutt Vater C, Biederman J, DiSalvo M, et al (2023)

Growth Trajectories in Stimulant Treated Children and Adolescents: A Qualitative Review of the Literature from Comprehensive Datasets and Registries.

Journal of child and adolescent psychopharmacology, 33(9):344-355.

Objective: Attention-deficit/hyperactivity disorder (ADHD) treatment with stimulant products has been shown to be safe and effective; however, there are remaining concerns about their possible adverse effects on growth trajectories. We conducted a systematic review of the extant literature derived from ecologically valid databases and registries to assess the body of knowledge about the effects of stimulants on growth trajectories in naturalistic samples. Methods: Using PubMed and PsycINFO, we searched for articles published before February 8, 2023 that focused on growth findings associated with stimulant treatment in pediatric ADHD from comprehensive datasets derived from naturalistic population studies. Results: Of the 1070 articles initially identified, 12 met all inclusion criteria. Sample sizes ranged from 157 to 163,820 youths. Seven of 10 articles examining height found significant decreases in height associated with chronic stimulant treatment that normalized over time in 2 studies. Three articles found no significant association between stimulant treatment and height. No clear associations were identified between cumulative duration and dose of stimulant treatment and adult height. All articles examining weight and six of eight articles examining body mass index (BMI) found significant initial decreases that tended to normalize then increase over time. Longer duration of stimulant medication use was predominantly associated with significant weight and BMI reductions. The effects of stimulant dose on weight and BMI were mostly weak and clinically insignificant. Most studies found no significant association between age at start of stimulant treatment and change in height, weight, or BMI. Most studies did not find significant sex effects in relation to growth parameters. Conclusions: This review of ecologically informative samples revealed that the effects of stimulant treatment on growth trajectories are mainly small and transient. These effects seem to be clinically insignificant for most youth with ADHD who receive stimulant treatment from childhood onto adolescence and adulthood.

RevDate: 2023-11-15

Yuan Y, Li X, Li L, et al (2023)

Machine discovery of partial differential equations from spatiotemporal data: A sparse Bayesian learning framework.

Chaos (Woodbury, N.Y.), 33(11):.

This study presents a general framework, namely, Sparse Spatiotemporal System Discovery (S3d), for discovering dynamical models given by Partial Differential Equations (PDEs) from spatiotemporal data. S3d is built on the recent development of sparse Bayesian learning, which enforces sparsity in the estimated PDEs. This approach enables a balance between model complexity and fitting error with theoretical guarantees. The proposed framework integrates Bayesian inference and a sparse priori distribution with the sparse regression method. It also introduces a principled iterative re-weighted algorithm to select dominant features in PDEs and solve for the sparse coefficients. We have demonstrated the discovery of the complex Ginzburg-Landau equation from a traveling-wave convection experiment, as well as several other PDEs, including the important cases of Navier-Stokes and sine-Gordon equations, from simulated data.

RevDate: 2023-11-15

Xue J, Zhu J, Hu L, et al (2023)

EISA-EXPOSOME: One Highly Sensitive and Autonomous Exposomic Platform with Enhanced in-Source Fragmentation/Annotation.

Analytical chemistry [Epub ahead of print].

Lacking a highly sensitive exposome screening technique is one of the biggest challenges in moving exposomic research forward. Enhanced in-source fragmentation/annotation (EISA) has been developed to facilitate molecular identification in untargeted metabolomics and proteomics. In this work, with a mixture of 50 pesticides at three concentration levels (20, 4, and 0.8 ppb), we investigated the analytical performance of the EISA technique over the well-accepted targeted MS/MS mode (TMM) in the detection and identification of chemicals at low levels using a quadrupole time-of-flight (qTOF) instrument. Compared with the TMM method, the EISA technique can recognize additional 1, 20, and 23 chemicals, respectively, at the three concentration levels (20, 4, and 0.8 ppb, respectively) investigated. At the 0.8 ppb level, intensities of precursor ions and fragments observed using the EISA technique are 30-1,154 and 3-80 times higher, respectively, than those observed at the TMM mode. A higher matched fragment ratio (MFR) between the EISA technique and the TMM method was recognized for most chemicals. We further developed a chemical annotation informatics algorithm, EISA-EXPOSOME, which can automatically search each precursor ion (m/z) in the MS/MS library against the EISA MS1 spectra. This algorithm then calculated a weighted score to rank the candidate features by comparing the experimental fragment spectra to those in the library. The peak intensity, zigzag index, and retention time prediction model as well as the peak correlation coefficient were further adopted in the algorithm to filter false positives. The performance of EISA-EXPOSOME was demonstrated using a pooled dust extract with a pesticide mixture (n = 200) spiked at 5 ppb. One urine sample spiked with a contaminant mixture (n = 50) at the 5 ppb level was also used for the validation of the pipeline. Proof-of-principal application of EISA-EXPOSOME in the real sample was further evaluated on the pooled dust sample with a modified T3DB database (n = 1650). Our results show that the EISA-EXPOSOME algorithm can remarkably improve the detection and annotation coverage at trace levels beyond the traditional approach as well as facilitate the high throughput screening of suspected chemicals.

RevDate: 2023-11-15

Zhao H, Zheng J, Ma S, et al (2023)

Spatial distribution and influencing factors analysis of national key rural tourism villages in the Yangtze River Delta region based on geographically weighted regression.

PloS one, 18(11):e0291614 pii:PONE-D-22-27808.

National key rural tourism villages (NKRTVs) can lead to the high-quality development of rural tourism, and their spatial distribution is influenced by a variety of factors. However, existing studies have neglected the fact that influencing factors can have different directions and effects in different geographic spaces. This study investigates 156 NKRTVs in the Yangtze River Delta region of China as the research object and employs ArcGIS spatial analysis technology to examine their spatial distribution characteristics. Additionally, two new indicators of land and culture are introduced to enhance the index system of influencing factors. A geographically weighted regression model is utilized to identify the spatial heterogeneity of various factors that affect the spatial distribution of NKRTVs. The results of this study indicate the following: (1) The spatial distribution of NKRTVs in the Yangtze River Delta region is characterized by "small clustering and large dispersion." The spatial distribution exhibits strong spatial correlation, with Shanghai serving as the primary spatial clustering core and Huangshan city forming a secondary spatial clustering subcore. The distribution of NKRTVs is relatively scattered in other areas, with obvious differences in the spatial distribution of cold and hot spots. (2) The results of the geographically weighted regression model show that with the change in spatial location, the influence effect of each influencing factor on the spatial distribution of NKRTVs has obvious spatial differences. Based on the spatial heterogeneity of the influencing factors, this study proposes targeted suggestions for the development of rural tourism in different regions.

RevDate: 2023-11-15

Radovic I, Krdzic I, Jovanovic A, et al (2023)

Transcultural adaptation and validation of the Serbian version of Functional Assessment of Chronic Illness Therapy-Treatment Satisfaction-Patient Satisfaction (FACIT-TS-PS) questionnaire.

PloS one, 18(11):e0294339 pii:PONE-D-23-22603.

OBJECTIVE: Transcultural adaptation and validation of FACIT-TS-PS questionnaire to Serbian language.

METHODS: Standard forward and backward translation from English to Serbian language was performed. Pilot testing of FACIT-TS-PS was conducted on 12 patients with a confirmed diagnosis of malignant tumor. The study included 154 patients with malignant disease. The Questionnaire of Patient Satisfaction was used as a validated tool to evaluate concurrent validity of FACIT-TS-PS questionnaire. Reproducibility was tested on 30 subjects who answered the questionnaire for the second time two weeks later.

RESULTS: Three FACIT-TS-PS subscales (Physician Communication, Treatment Staff Communication and Nurse Communication) demonstrated satisfactory construct validity using Cronbach's alpha, the remaining two subscales (Technical Competence and Confidence & Trust) showed high ceiling effect. Treatment Staff Communication subscale showed large floor effect. Concurrent validity was demonstrated by correlation with the two dimensions of the Questionnaire of Patient Satisfaction. Satisfactory reproducibility was demonstrated on 30 patients who filled the questionnaire for the second time two weeks after initial interview.

CONCLUSION: The Serbian version of FACIT-TS-PS with the omission of Treatment Staff Communication subscale could be used as a valid instrument to assess patient and treatment satisfaction in chronically ill patients in the Serbian population. Omission of Treatment Staff Communication subscale is necessary because it contains questions not relevant for patients in Serbian healthcare system.

RevDate: 2023-11-15

Schiebelhut LM, Guillaume AS, Kuhn A, et al (2023)

Genomics and conservation: Guidance from training to analyses and applications.

Molecular ecology resources [Epub ahead of print].

Environmental change is intensifying the biodiversity crisis and threatening species across the tree of life. Conservation genomics can help inform conservation actions and slow biodiversity loss. However, more training, appropriate use of novel genomic methods and communication with managers are needed. Here, we review practical guidance to improve applied conservation genomics. We share insights aimed at ensuring effectiveness of conservation actions around three themes: (1) improving pedagogy and training in conservation genomics including for online global audiences, (2) conducting rigorous population genomic analyses properly considering theory, marker types and data interpretation and (3) facilitating communication and collaboration between managers and researchers. We aim to update students and professionals and expand their conservation toolkit with genomic principles and recent approaches for conserving and managing biodiversity. The biodiversity crisis is a global problem and, as such, requires international involvement, training, collaboration and frequent reviews of the literature and workshops as we do here.

RevDate: 2023-11-15

Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, et al (2023)

The genome sequence of the Leopard Moth, Zeuzera pyrina (Linnaeus, 1761).

Wellcome open research, 8:94.

We present a genome assembly from an individual male Zeuzera pyrina (the Leopard Moth, Arthropoda; Insecta; Lepidoptera; Cossidae). The genome sequence is 687 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled 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 22,738 protein coding genes.

RevDate: 2023-11-14

Zang Z, Zhang Y, Zuo C, et al (2023)

Exploring Global Land Coarse-Mode Aerosol Changes from 2001-2021 Using a New Spatiotemporal Coaction Deep-Learning Model.

Environmental science & technology [Epub ahead of print].

Coarse-mode aerosol optical depths (cAODs) are critical for understanding the impact of coarse particle sizes, especially dust aerosols, on climate. Currently, the limited data length and high uncertainty of satellite products diminish the applicability of cAOD for climate research. Here, we propose a spatiotemporal coaction deep-learning model (SCAM) for the retrieval of global land cAOD (500 nm) from 2001-2021. In contrast to conventional deep-learning models, the SCAM considers the impacts of spatiotemporal feature interactions and can simultaneously describe linear and nonlinear relationships for retrievals. Based on these unique characteristics, the SCAM considerably improved global daily cAOD accuracies and coverages (R = 0.82, root-mean-square error [RMSE] = 0.04). Compared to official products from the multiangle imaging spectroradiometer (MISR), the moderate resolution imaging spectroradiometer (MODIS), and the polarization and directionality of Earth's reflectances (POLDER) instrument, as well as the physical-deep learning (Phy-DL) derived cAOD, the SCAM cAOD improved the monthly R from 0.44 to 0.88 and more accurately captured over the desert regions. Based on the SCAM cAOD, daily dust cases decreased over the Sahara, Thar Desert, Gobi Desert, and Middle East during 2001-2021 (>3 × 10[-3]/year). The SCAM-retrieved cAOD can contribute considerably to resolving the climate change uncertainty related to coarse-mode aerosols. Our proposed method is highly valuable for reducing uncertainties regarding coarse aerosols and climate interactions.

RevDate: 2023-11-15
CmpDate: 2023-11-15

Li D, Guan X, Tang T, et al (2023)

The clean energy development path and sustainable development of the ecological environment driven by big data for mining projects.

Journal of environmental management, 348:119426.

Clean energy is urgently needed to realize mining projects' sustainable development (SD). This study aims to discuss the clean energy development path and the related issues of SD in the ecological environment driven by big data for mining projects. This study adopts a comprehensive research approach, including a literature review, case analysis, and model construction. Firstly, an in-depth literature review of the development status of clean energy is carried out, and the existing research results and technology applications are explored. Secondly, some typical mining projects are selected as cases to discuss the practice and effect of their clean energy application. Finally, the corresponding clean energy development path and the SD analysis model of the ecological environment are constructed based on big data technology to evaluate the feasibility and potential benefits of promoting and applying clean energy in mining projects. (1) It is observed that under different Gross Domestic Product (GDP) growth rates, the new and cumulative installed capacities of wind energy show an increasing trend. In 2022, under the low GDP growth rate, the cumulative installed capacity of global wind energy was 370.60 Gigawatt (GW), and the new installed capacity was 45 GW. With the high GDP growth rate, the cumulative and new installed capacities were 367.83 GW and 46 GW. As the economy grows, new wind energy capacity is expected to increase significantly by 2030. In 2046, 2047, and 2050, carbon dioxide (CO2) emissions reductions are projected to be 8183.35, 8539.22, and 9842.73 Million tons (Mt) (low scenario), 8750.68, 9087.16, and 10,468.75 Mt (medium scenario), and 9083.03, 9458.86, and 10,879.58 Mt (high scenario). By 2060, it is expected that CO2 emissions reduction will continue to increase. (2) The proposed clean energy development path model has achieved a good effect. Through this study, it is hoped to provide empirical support and decision-making reference for the development of mining projects in clean energy, and promote the SD of the mining industry, thus achieving a win-win situation of economic and ecological benefits. This is of great significance for protecting the ecological environment and realizing the sustainable utilization of resources.

RevDate: 2023-11-15
CmpDate: 2023-11-15

Li Z, Li X, Li S, et al (2023)

Bibliometric analysis of electrochemical disinfection: current status and development trend from 2002 to 2022.

Environmental science and pollution research international, 30(52):111714-111731.

The removal of waterborne pathogens from water is critical in preventing the spread of waterborne diseases. Electrochemical methods have been extensively researched and implemented for disinfection, primarily owing to their simplicity, efficiency, and eco-friendliness. Thus, it is essential to conduct a review about the research progress and hotspots on this promising technique. In this paper, we provided a comprehensive bibliometric analysis to systematically study and analyze the current status, hotspots, and trends in electrochemical disinfection research from 2002 to 2022. This study analyzed literature related to electrochemical disinfection or electrochemical sterilization published in the Web of Science database from 2002 to 2022 using CiteSpace and Biblioshiny R language software packages. The analysis focused on the visualization and assessment of annual publication volume, discipline and journal distribution, collaborative networks, highly cited papers, and keywords to systematically understand the current status and trends of electrochemical disinfection. The results showed that between 2002 and 2022, 1171 publications related to electrochemical disinfection were published, with an exponential increase in the cumulative number of publications (y=17.518e[0.2147x], R[2]= 0.9788). The publications covered 76 disciplines with many articles published in high-impact journals. However, the research power was characterized by a large number of scattered research efforts and insufficient cooperation, indicating the need for further innovative collaboration. The citation analysis and keyword analysis suggest that future development in this field may focus on optimizing electrode materials, investigating the disinfection performance of ·OH based systems, optimizing conditions for actual wastewater treatment, and reducing energy consumption to promote practical applications.

RevDate: 2023-11-14

Abbas Q, Ahmad G, Alyas T, et al (2023)

Revolutionizing Urban Mobility: IoT-Enhanced Autonomous Parking Solutions with Transfer Learning for Smart Cities.

Sensors (Basel, Switzerland), 23(21): pii:s23218753.

Smart cities have emerged as a specialized domain encompassing various technologies, transitioning from civil engineering to technology-driven solutions. The accelerated development of technologies, such as the Internet of Things (IoT), software-defined networks (SDN), 5G, artificial intelligence, cognitive science, and analytics, has played a crucial role in providing solutions for smart cities. Smart cities heavily rely on devices, ad hoc networks, and cloud computing to integrate and streamline various activities towards common goals. However, the complexity arising from multiple cloud service providers offering myriad services necessitates a stable and coherent platform for sustainable operations. The Smart City Operational Platform Ecology (SCOPE) model has been developed to address the growing demands, and incorporates machine learning, cognitive correlates, ecosystem management, and security. SCOPE provides an ecosystem that establishes a balance for achieving sustainability and progress. In the context of smart cities, Internet of Things (IoT) devices play a significant role in enabling automation and data capture. This research paper focuses on a specific module of SCOPE, which deals with data processing and learning mechanisms for object identification in smart cities. Specifically, it presents a car parking system that utilizes smart identification techniques to identify vacant slots. The learning controller in SCOPE employs a two-tier approach, and utilizes two different models, namely Alex Net and YOLO, to ensure procedural stability and improvement.

RevDate: 2023-11-14

Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, et al (2023)

The genome sequence of the Miller, Acronicta leporina (Linnaeus, 1758).

Wellcome open research, 8:49.

We present a genome assembly from an individual female Acronicta leporina (the Miller; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 466 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.4 kilobases in length.

RevDate: 2023-11-13

Furtado DP, Vieira EA, Nascimento WF, et al (2023)

#DeOlhoNosCorais: a polygonal annotated dataset to optimize coral monitoring.

PeerJ, 11:e16219.

Corals are colonial animals within the Phylum Cnidaria that form coral reefs, playing a significant role in marine environments by providing habitat for fish, mollusks, crustaceans, sponges, algae, and other organisms. Global climate changes are causing more intense and frequent thermal stress events, leading to corals losing their color due to the disruption of a symbiotic relationship with photosynthetic endosymbionts. Given the importance of corals to the marine environment, monitoring coral reefs is critical to understanding their response to anthropogenic impacts. Most coral monitoring activities involve underwater photographs, which can be costly to generate on large spatial scales and require processing and analysis that may be time-consuming. The Marine Ecology Laboratory (LECOM) at the Federal University of Rio Grande do Norte (UFRN) developed the project "#DeOlhoNosCorais" which encourages users to post photos of coral reefs on their social media (Instagram) using this hashtag, enabling people without previous scientific training to contribute to coral monitoring. The laboratory team identifies the species and gathers information on coral health along the Brazilian coast by analyzing each picture posted on social media. To optimize this process, we conducted baseline experiments for image classification and semantic segmentation. We analyzed the classification results of three different machine learning models using the Local Interpretable Model-agnostic Explanations (LIME) algorithm. The best results were achieved by combining EfficientNet for feature extraction and Logistic Regression for classification. Regarding semantic segmentation, the U-Net Pix2Pix model produced a pixel-level accuracy of 86%. Our results indicate that this tool can enhance image selection for coral monitoring purposes and open several perspectives for improving classification performance. Furthermore, our findings can be expanded by incorporating other datasets to create a tool that streamlines the time and cost associated with analyzing coral reef images across various regions.

RevDate: 2023-11-12

Hao W, Shan YF, Kimura T, et al (2023)

Dual decline in subjective gait speed and domain-specific cognition is associated with higher risk of incident dementia in older Japanese adults: A 15-year age-specific cohort study.

Archives of gerontology and geriatrics, 117:105254 pii:S0167-4943(23)00332-1 [Epub ahead of print].

OBJECTIVES: Dual decline in gait speed and cognition has been found to have higher dementia risk than no decline or pure decline. However, evidence from the Asian population is lacking. Therefore, we aimed to investigate the association of dual decline from age 65 to 70 years with late-life dementia in older Japanese adults with different personal characteristics.

METHODS: Data were collected from an age-specific cohort study conducted in 482 Japanese 65-year-old adults. We investigated participant demographics, medical histories, lifestyles, subjective gait speed, and cognition at both 64/65 and 70/71 years old, and confirmed dementia until age of 85 years. Cox proportion hazard models were used to estimate the risk of dementia, with adjustments for covariates, and death was treated as a competing risk.

RESULTS: After a mean follow-up period of 12.5-years, 111 participants developed dementia. Older adults with dual decline are more likely to have hyperlipidemia, diabetes, and smoking habits. And we found that dual decline in gait speed and domain-specific cognition was associated with a higher risk of dementia compared with no decline in most cognitive tests, with the highest risk observed for gait speed combined with memory (sub-distribution hazard ratio:3.89, 95 %, confidence intervals: [1.68-9.01]). However, significant differences only existed in men after stratification by sex.

CONCLUSIONS: A dual decline in subjective gait speed and cognition may serve as a robust predictor of dementia over a decade prior to its onset, particularly in men. These findings highlighted the importance of screening for dual decline at an early age.

RevDate: 2023-11-13
CmpDate: 2023-11-13

Gao H, Wu M, Liu H, et al (2023)

Unraveling the Positive Effect of Soil Moisture on the Bioaugmentation of Petroleum-Contaminated Soil Using Bioinformatics.

Microbial ecology, 86(4):2436-2446.

Petroleum contamination is a severe threat to the soil environment. Previous studies have demonstrated that petroleum degradation efficiency is promoted by enhancing soil moisture content (MC). However, the effects of MC on soil microbial ecological functions during bioremediation remain unclear. Here, we investigated the impacts of 5% and 15% of moisture contents on petroleum degradation, soil microbial structures and functions, and the related genes using high-throughput sequencing and gene function prediction. Results indicated that petroleum biodegradation efficiency was increased by 8.06% in the soils with 15% MC when compared to that with 5% of MC. The complexity and stability of soil microbial community structures with 15% MC were higher than those in the soils with 5% MC when hydrocarbon-degrading bacterial flora (HDBF) were inoculated into the soils. Fifteen percent of moisture content strengthened the interaction of the bacterial community network and reduced the loss of some key bacteria species including Mycobacterium, Sphingomonas, and Gemmatimonas. Some downregulated gene pathways relating to bioaugmentation were enhanced in the soils with 15% MC. The results suggested that the dynamic balances of microbial communities and the metabolic interactions by 15% MC treatment are the driving forces for the enhancement of bioremediation in petroleum-contaminated soil.

RevDate: 2023-11-13

Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, et al (2022)

The genome sequence of the rosy rustic, Hydraecia micacea (Esper, 1789).

Wellcome open research, 7:131.

We present a genome assembly from an individual female Hydraecia micacea (the rosy rustic; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 562 megabases in span. The majority of the assembly (99.98%) is scaffolded into 32 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled. The mitochondrial genome was also assembled, and is 16.3 kilobases in length.

RevDate: 2023-11-11

Waqas M, Wong MS, Stocchino A, et al (2023)

Marine plastic pollution detection and identification by using remote sensing-meta analysis.

Marine pollution bulletin, 197:115746 pii:S0025-326X(23)01181-5 [Epub ahead of print].

The persistent plastic litter, originating from different sources and transported from rivers to oceans, has posed serious biological, ecological, and chemical effects on the marine ecosystem, and is considered a global issue. In the past decade, many studies have identified, monitored, and tracked marine plastic debris in coastal and open ocean areas using remote sensing technologies. Compared to traditional surveying methods, high-resolution (spatial and temporal) multispectral or hyperspectral remote sensing data have been substantially used to monitor floating marine macro litter (FMML). In this systematic review, we present an overview of remote sensing data and techniques for detecting FMML, as well as their challenges and opportunities. We reviewed the studies based on different sensors and platforms, spatial and spectral resolution, ground sampling data, plastic detection methods, and accuracy obtained in detecting marine litter. In addition, this study elaborates the usefulness of high-resolution remote sensing data in Visible (VIS), Near-infrared (NIR), and Short-Wave InfraRed (SWIR) range, along with spectral signatures of plastic, in-situ samples, and spectral indices for automatic detection of FMML. Moreover, the Thermal Infrared (TIR), Synthetic aperture radar (SAR), and Light Detection and Ranging (LiDAR) data were introduced and these were demonstrated that could be used as a supplement dataset for the identification and quantification of FMML.

RevDate: 2023-11-11

Kimotho RN, S Maina (2023)

Unraveling plant-microbe interactions using integrated omics approaches.

Journal of experimental botany pii:7404888 [Epub ahead of print].

Advances in high throughput- omics techniques provide avenues to decipher plant microbiomes. However, there is limited information on how integrated informatics can help provide deeper insights into plant-microbe interactions in a concerted way. Integrating multi-omic datasets can transform our understanding of the plant microbiome from unspecified genetic influences on interacting species to specific gene-by-gene interactions. Here, we highlight recent progress and emerging strategies in crop microbiome omics research and review key aspects of how the integration of host and microbial omics-based datasets can be used to provide a comprehensive outline of the complex crop microbe interactions. We describe how these technological advances have helped unravel crucial plant and microbial genes and pathways that control beneficial, pathogenic, and commensal plant-host interactions. We identify crucial knowledge gaps and synthesize current limitations in our understanding of crop microbiome omics approaches. We highlight recent studies in which multi-omics-based approaches have led to improved models of crop microbial community structure and function. Finally, we recommend holistic approaches in integrating host and microbial omics datasets to achieve precision and efficiency in data analysis which is crucial for biotic and abiotic stress control and in understanding the contribution of the microbiota in shaping plant fitness.

RevDate: 2023-11-11

Skoric D, Rakic JG, Jovanovic V, et al (2023)

Psychosocial school factors and mental health of first grade secondary school students-Results of the Health Behaviour in School-aged Children Survey in Serbia.

PloS one, 18(11):e0293179.

This cross-sectional study aimed to investigate the association between psychosocial school factors and life satisfaction, symptoms of depression and psychosomatic health complaints among first grade secondary school students in Serbia. We analysed data from the 2018 Health Behaviour in School-aged Children (HBSC) study in the Republic of Serbia. Analyzed psychosocial school factors included satisfaction with school, schoolwork pressure, teacher support, classmate support and being bullied at school. Life satisfaction was assessed by the 11-step Cantril's ladder (cutoff >5). Symptoms of depression were measured by the Center for Epidemiologic Studies Depression Scale (CESD-10) and psychosomatic health complaints by using the HBSC symptom checklist. Univariable and multivariable binary logistic regression was used to determine independent predictors of students' life satisfaction, symptoms of depression and psychosomatic health complaints in the school environment, while also considering their socio-demographic characteristics and perceived family and friend support. The study included 1605 students (average age 15.26 ±0.44 years), of whom 50.3% were females. Results from the binary logistic regression analyses showed that life satisfaction was positively related to school satisfaction and classmate support, and negatively to being bullied at school. Symptoms of depression were positively associated with schoolwork pressure and being bullied at school, and negatively with teacher and classmate support. All analyzed factors of the school environment were significantly related to psychosomatic health complaints, whereby schoolwork pressure and being bullied at school were positively associated, while teacher and classmate support and satisfaction with school were negatively associated. Given the established association of psychosocial school factors with mental health, there is a need for targeted measures both at school and community level with the aim of improving social support in the school environment, reducing schoolwork burden and preventing bullying at school, potentially resulting in the overall improvement of mental health of the first grade secondary school students.

RevDate: 2023-11-10
CmpDate: 2023-11-10

Suire A, Kunita I, Harel R, et al (2023)

Estimating individual exposure to predation risk in group-living baboons, Papio anubis.

PloS one, 18(11):e0287357.

In environments with multiple predators, vulnerabilities associated with the spatial positions of group-living prey are non-uniform and depend on the hunting styles of the predators. Theoretically, coursing predators follow their prey over long distances and attack open areas, exposing individuals at the edge of the group to predation risk more than those at the center (marginal predation). In contrast, ambush predators lurk unnoticed by their prey and appear randomly anywhere in the group; therefore, isolated individuals in the group would be more vulnerable to predators. These positions of vulnerability to predation are expected to be taken by larger-bodied males. Moreover, dominant males presumably occupy the center of the safe group. However, identifying individuals at higher predation risk requires both simultaneous recording of predator location and direct observation of predation events; empirical observations leave ambiguity as to who is at risk. Instead, several theoretical methods (predation risk proxies) have been proposed to assess predation risk: (1) the size of the individual 'unlimited domain of danger' based on Voronoi tessellation, (2) the size of the 'limited domain of danger' based on predator detection distance, (3) peripheral/center position in the group (minimum convex polygon), (4) the number and direction of others in the vicinity (surroundedness), and (5) dyadic distances. We explored the age-sex distribution of individuals in at-risk positions within a wild baboon group facing predation risk from leopards, lions, and hyenas, using Global Positioning System collars. Our analysis of the location data from 26 baboons revealed that adult males were consistently isolated at the edge of the group in all predation risk proxies. Empirical evidence from previous studies indicates that adult male baboons are the most frequently preyed upon, and our results highlights the importance of spatial positioning in this.

RevDate: 2023-11-09

Furuya S, Liu J, Sun Z, et al (2023)

The Big (Genetic) Sort? A Research Note on Migration Patterns and Their Genetic Imprint in the United Kingdom.

Demography pii:383457 [Epub ahead of print].

This research note reinvestigates Abdellaoui et al.'s (2019) findings that genetically selective migration may lead to persistent and accumulating socioeconomic and health inequalities between types (coal mining or non-coal mining) of places in the United Kingdom. Their migration measure classified migrants who moved to the same type of place (coal mining to coal mining or non-coal mining to non-coal mining) into "stay" categories, preventing them from distinguishing migrants from nonmigrants. We reinvestigate the question of genetically selective migration by examining migration patterns between places rather than place types and find genetic selectivity in whether people migrate and where. For example, we find evidence of positive selection: people with genetic variants correlated with better education moved from non-coal mining to coal mining places with our measure of migration. Such findings were obscured in earlier work that could not distinguish nonmigrants from migrants.

RevDate: 2023-11-09

Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, et al (2022)

The genome sequence of the lesser treble-bar moth, Aplocera efformata (Guenée, 1857).

Wellcome open research, 7:303.

We present a genome assembly from an individual female Aplocera efformata (the lesser treble-bar; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 350 megabases in span. Most of the assembly (99.97%) is scaffolded into 32 chromosomal pseudomolecules, with W and Z sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl has identified 11,393 protein coding genes.

RevDate: 2023-11-08

Conte L, Gonella F, Giansanti A, et al (2023)

Modeling cell populations metabolism and competition under maximum power constraints.

PLoS computational biology, 19(11):e1011607 pii:PCOMPBIOL-D-23-00265 [Epub ahead of print].

Ecological interactions are fundamental at the cellular scale, addressing the possibility of a description of cellular systems that uses language and principles of ecology. In this work, we use a minimal ecological approach that encompasses growth, adaptation and survival of cell populations to model cell metabolisms and competition under energetic constraints. As a proof-of-concept, we apply this general formulation to study the dynamics of the onset of a specific blood cancer-called Multiple Myeloma. We show that a minimal model describing antagonist cell populations competing for limited resources, as regulated by microenvironmental factors and internal cellular structures, reproduces patterns of Multiple Myeloma evolution, due to the uncontrolled proliferation of cancerous plasma cells within the bone marrow. The model is characterized by a class of regime shifts to more dissipative states for selectively advantaged malignant plasma cells, reflecting a breakdown of self-regulation in the bone marrow. The transition times obtained from the simulations range from years to decades consistently with clinical observations of survival times of patients. This irreversible dynamical behavior represents a possible description of the incurable nature of myelomas based on the ecological interactions between plasma cells and the microenvironment, embedded in a larger complex system. The use of ATP equivalent energy units in defining stocks and flows is a key to constructing an ecological model which reproduces the onset of myelomas as transitions between states of a system which reflects the energetics of plasma cells. This work provides a basis to construct more complex models representing myelomas, which can be compared with model ecosystems.

RevDate: 2023-11-09
CmpDate: 2023-11-09

Li J, Dong Z, Lu S, et al (2023)

CAS(ME)[3]: A Third Generation Facial Spontaneous Micro-Expression Database With Depth Information and High Ecological Validity.

IEEE transactions on pattern analysis and machine intelligence, 45(3):2782-2800.

Micro-expression (ME) is a significant non-verbal communication clue that reveals one person's genuine emotional state. The development of micro-expression analysis (MEA) has just gained attention in the last decade. However, the small sample size problem constrains the use of deep learning on MEA. Besides, ME samples distribute in six different databases, leading to database bias. Moreover, the ME database development is complicated. In this article, we introduce a large-scale spontaneous ME database: CAS(ME) [3]. The contribution of this article is summarized as follows: (1) CAS(ME) [3] offers around 80 hours of videos with over 8,000,000 frames, including manually labeled 1,109 MEs and 3,490 macro-expressions. Such a large sample size allows effective MEA method validation while avoiding database bias. (2) Inspired by psychological experiments, CAS(ME) [3] provides the depth information as an additional modality unprecedentedly, contributing to multi-modal MEA. (3) For the first time, CAS(ME) [3] elicits ME with high ecological validity using the mock crime paradigm, along with physiological and voice signals, contributing to practical MEA. (4) Besides, CAS(ME) [3] provides 1,508 unlabeled videos with more than 4,000,000 frames, i.e., a data platform for unsupervised MEA methods. (5) Finally, we demonstrate the effectiveness of depth information by the proposed depth flow algorithm and RGB-D information.

RevDate: 2023-11-08

Furuya S, Liu J, Sun Z, et al (2023)

Understanding Internal Migration: A Research Note Providing an Assessment of Migration Selection With Genetic Data.

Demography pii:383422 [Epub ahead of print].

Migration is selective, resulting in inequalities between migrants and nonmigrants. However, investigating migration selection is empirically challenging because combined pre- and post-migration data are rarely available. We propose an alternative approach to assessing internal migration selection by integrating genetic data, enabling an investigation of migration selection with cross-sectional data collected post-migration. Using data from the UK Biobank, we utilized standard tools from statistical genetics to conduct a genome-wide association study (GWAS) for migration distance. We then calculated genetic correlations to compare GWAS results for migration with those for other characteristics. Given that individual genetics are determined at conception, these analyses allow a unique exploration of the association between pre-migration characteristics and migration. Results are generally consistent with the healthy migrant literature: genetics correlated with longer migration distance are associated with higher socioeconomic status and better health. We also extended the analysis to 53 traits and found novel correlations between migration and several physical health, mental health, personality, and sociodemographic traits.

RevDate: 2023-11-07

Laporte C, Fortin F, Dupouy J, et al (2023)

The French ecology of medical care. A nationwide population-based cross sectional study.

Family practice pii:7338780 [Epub ahead of print].

PURPOSE: Studies in the United States, Canada, Belgium, and Switzerland showed that the majority of health problems are managed within primary health care; however, the ecology of French medical care has not yet been described.

METHODS: Nationwide, population-based, cross sectional study. In 2018, we included data from 576,125 beneficiaries from the General Sample of Beneficiaries database. We analysed the reimbursement of consultations with (i) a general practitioner (GP), (ii) an outpatient doctor other than a GP, (iii) a doctor from a university or non-university hospital; and the reimbursement of (iv) hospitalization in a private establishment, (v) general hospital, and (vi) university hospital. For each criterion, we calculated the average monthly number of reimbursements reported on 1,000 beneficiaries. For categorical variables, we used the χ2 test, and to compare means we used the z test. All tests were 2-tailed with a P-value < 5% considered significant.

RESULTS: Each month, on average, 454 (out of 1,000) beneficiaries received at least 1 reimbursement, 235 consulted a GP, 74 consulted other outpatient doctors in ambulatory care and 24 in a hospital, 13 were hospitalized in a public non-university hospital and 10 in the private sector, and 5 were admitted to a university hospital. Independently of age, people consulted GPs twice as much as other specialists. The 13-25-year-old group consulted the least. Women consulted more than men. Individuals covered by complementary universal health insurance had more care.

CONCLUSIONS: Our study on reimbursement data confirmed that, like in other countries, in France the majority of health problems are managed within primary health care.

RevDate: 2023-11-08
CmpDate: 2023-11-08

Liang D, Giam X, Hu S, et al (2023)

Assessing the illegal hunting of native wildlife in China.

Nature, 623(7985):100-105.

Illegal harvesting and trading of wildlife have become major threats to global biodiversity and public health[1-3]. Although China is widely recognized as an important destination for wildlife illegally obtained abroad[4], little attention has been given to illegal hunting within its borders. Here we extracted 9,256 convictions for illegal hunting from a nationwide database of trial verdicts in China spanning January 2014 to March 2020. These convictions involved illegal hunting of 21% (n = 673) of China's amphibian, reptile, bird and mammal species, including 25% of imperilled species in these groups. Sample-based extrapolation indicates that many more species were taken illegally during this period. Larger body mass and range size (for all groups), and proximity to urban markets (for amphibians and birds) increase the probability of a species appearing in the convictions database. Convictions pertained overwhelmingly to illegal hunting for commercial purposes and involved all major habitats across China. A small number of convictions represented most of the animals taken, indicating the existence of large commercial poaching operations. Prefectures closer to urban markets show higher densities of convictions and more individual animals taken. Our results suggest that illegal hunting is a major, overlooked threat to biodiversity throughout China.

RevDate: 2023-11-07

Vasileiou D, Karapiperis C, Baltsavia I, et al (2023)

CGG toolkit: Software components for computational genomics.

PLoS computational biology, 19(11):e1011498 pii:PCOMPBIOL-D-23-00660.

Public-domain availability for bioinformatics software resources is a key requirement that ensures long-term permanence and methodological reproducibility for research and development across the life sciences. These issues are particularly critical for widely used, efficient, and well-proven methods, especially those developed in research settings that often face funding discontinuities. We re-launch a range of established software components for computational genomics, as legacy version 1.0.1, suitable for sequence matching, masking, searching, clustering and visualization for protein family discovery, annotation and functional characterization on a genome scale. These applications are made available online as open source and include MagicMatch, GeneCAST, support scripts for CoGenT-like sequence collections, GeneRAGE and DifFuse, supported by centrally administered bioinformatics infrastructure funding. The toolkit may also be conceived as a flexible genome comparison software pipeline that supports research in this domain. We illustrate basic use by examples and pictorial representations of the registered tools, which are further described with appropriate documentation files in the corresponding GitHub release.

RevDate: 2023-11-07

Hofmeister NR, Stuart KC, Warren WC, et al (2023)

Concurrent invasions of European starlings in Australia and North America reveal population-specific differentiation in shared genomic regions.

Molecular ecology [Epub ahead of print].

A species' success during the invasion of new areas hinges on an interplay between the demographic processes common to invasions and the specific ecological context of the novel environment. Evolutionary genetic studies of invasive species can investigate how genetic bottlenecks and ecological conditions shape genetic variation in invasions, and our study pairs two invasive populations that are hypothesized to be from the same source population to compare how each population evolved during and after introduction. Invasive European starlings (Sturnus vulgaris) established populations in both Australia and North America in the 19th century. Here, we compare whole-genome sequences among native and independently introduced European starling populations to determine how demographic processes interact with rapid evolution to generate similar genetic patterns in these recent and replicated invasions. Demographic models indicate that both invasive populations experienced genetic bottlenecks as expected based on invasion history, and we find that specific genomic regions have differentiated even on this short evolutionary timescale. Despite genetic bottlenecks, we suggest that genetic drift alone cannot explain differentiation in at least two of these regions. The demographic boom intrinsic to many invasions as well as potential inversions may have led to high population-specific differentiation, although the patterns of genetic variation are also consistent with the hypothesis that this infamous and highly mobile invader adapted to novel selection (e.g., extrinsic factors). We use targeted sampling of replicated invasions to identify and evaluate support for multiple, interacting evolutionary mechanisms that lead to differentiation during the invasion process.

RevDate: 2023-11-07

Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, et al (2022)

The genome sequence of the black arches, Lymantria monacha (Linnaeus, 1758).

Wellcome open research, 7:128.

We present a genome assembly from an individual male Lymantria monacha (the black arches; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 916 megabases in span. The majority of the assembly (99.99%) is scaffolded into 28 chromosomal pseudomolecules, with the Z sex chromosome assembled. The mitochondrial genome was also assembled, and is 15.6 kilobases in length.

RevDate: 2023-11-06

Crowley LM, Mitchell R, University of Oxford and Wytham Woods Genome Acquisition Lab, et al (2023)

The genome sequence of the Lesser Hornet Hoverfly, Volucella inanis (Linnaeus, 1758).

Wellcome open research, 8:69.

We present a genome assembly from an individual female Volucella inanis (the Lesser Hornet Hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 961 megabases in span. Most of the assembly is scaffolded into six chromosomal pseudomolecules, including the assembled X sex chromosome. The mitochondrial genome has also been assembled and is 16.0 kilobases in length. Gene annotation of this assembly on Ensembl has identified 11,616 protein coding genes.

RevDate: 2023-11-06
CmpDate: 2023-11-06

Srivastava A, De Corte D, Garcia JAL, et al (2023)

Interplay between autotrophic and heterotrophic prokaryotic metabolism in the bathypelagic realm revealed by metatranscriptomic analyses.

Microbiome, 11(1):239.

BACKGROUND: Heterotrophic microbes inhabiting the dark ocean largely depend on the settling of organic matter from the sunlit ocean. However, this sinking of organic materials is insufficient to cover their demand for energy and alternative sources such as chemoautotrophy have been proposed. Reduced sulfur compounds, such as thiosulfate, are a potential energy source for both auto- and heterotrophic marine prokaryotes.

METHODS: Seawater samples were collected from Labrador Sea Water (LSW, ~ 2000 m depth) in the North Atlantic and incubated in the dark at in situ temperature unamended, amended with 1 µM thiosulfate, or with 1 µM thiosulfate plus 10 µM glucose and 10 µM acetate (thiosulfate plus dissolved organic matter, DOM). Inorganic carbon fixation was measured in the different treatments and samples for metatranscriptomic analyses were collected after 1 h and 72 h of incubation.

RESULTS: Amendment of LSW with thiosulfate and thiosulfate plus DOM enhanced prokaryotic inorganic carbon fixation. The energy generated via chemoautotrophy and heterotrophy in the amended prokaryotic communities was used for the biosynthesis of glycogen and phospholipids as storage molecules. The addition of thiosulfate stimulated unclassified bacteria, sulfur-oxidizing Deltaproteobacteria (SAR324 cluster bacteria), Epsilonproteobacteria (Sulfurimonas sp.), and Gammaproteobacteria (SUP05 cluster bacteria), whereas, the amendment with thiosulfate plus DOM stimulated typically copiotrophic Gammaproteobacteria (closely related to Vibrio sp. and Pseudoalteromonas sp.).

CONCLUSIONS: The gene expression pattern of thiosulfate utilizing microbes specifically of genes involved in energy production via sulfur oxidation and coupled to CO2 fixation pathways coincided with the change in the transcriptional profile of the heterotrophic prokaryotic community (genes involved in promoting energy storage), suggesting a fine-tuned metabolic interplay between chemoautotrophic and heterotrophic microbes in the dark ocean. Video Abstract.

RevDate: 2023-11-06
CmpDate: 2023-11-06

Ha LT (2023)

Scrutinizing the nexus between green innovations and the sustainability of environmental system: novel insights from European database.

Environmental science and pollution research international, 30(50):109087-109109.

A study is presented in this paper that examines the effect of environmental innovation (EI) on environmental performance (EP). Six measures are used to reflect environmental innovation, including the percentage of enterprises that invest in environmental innovation, the percentage of enterprises implementing environmental innovation activities, the number of ISO 14001 certificates, patents related to environmental innovation, the total R&D personnel and researchers, and the amount of green early-stage investments. The estimation results show that EI positively impacts EP in 21 European countries using different econometric techniques during the 2011-2019 period. By using various econometric techniques (namely a panel-corrected standard errors (PCSE) model, a feasible generalized least square estimates (FGLS) model, and the two-step general method of moment (the two-step GMM), our research demonstrates how environmental innovation impacts on environmental quality. The short- and long-term effects of autoregressive distributed lag (ARDL) methods were also investigated using pooled mean groups (PMGs) to distinguish the short-run and long-run influences of EI. The relationship between EI and EP is explored by demonstrating how EI affects EP short- and long-term and comparing its influence on EP across many component measures of EI: air quality, sanitation, drinking water, heavy metals, waste management, biodiversity, habitat, ecosystem services, water resources, and agriculture. Notably, we find that the influences of EI become more pronounced in a country characterized by a well-developed institutional system. Our findings suggest policy implications to help countries invest in research and development with concerns about environmental damage mitigations more effectively. These findings are critical to suggest a way to help countries pursue ecological sustainability.

RevDate: 2023-10-31

Liu L, Chen J, Shen M, et al (2023)

A remote sensing method for mapping alpine grasslines based on graph-cut.

Global change biology [Epub ahead of print].

Climate change has induced substantial shifts in vegetation boundaries such as alpine treelines and shrublines, with widespread ecological and climatic influences. However, spatial and temporal changes in the upper elevational limit of alpine grasslands ("alpine grasslines") are still poorly understood due to lack of field observations and remote sensing estimates. In this study, taking the Tibetan Plateau as an example, we propose a novel method for automatically identifying alpine grasslines from multi-source remote sensing data and determining their positions at 30-m spatial resolution. We first identified 2895 mountains potentially having alpine grasslines. On each mountain, we identified a narrow area around the upper elevational limit of alpine grasslands where the alpine grassline was potentially located. Then, we used linear discriminant analysis to adaptively generate from Landsat reflectance features a synthetic feature that maximized the difference between vegetated and unvegetated pixels in each of these areas. After that, we designed a graph-cut algorithm to integrate the advantages of the Otsu and Canny approaches, which was used to determine the precise position of the alpine grassline from the synthetic feature image. Validation against alpine grasslines visually interpreted from a large number of high-spatial-resolution images showed a high level of accuracy (R[2] , .99 and .98; mean absolute error, 22.6 and 36.2 m, vs. drone and PlanetScope images, respectively). Across the Tibetan Plateau, the alpine grassline elevation ranged from 4038 to 5380 m (5th-95th percentile), lower in the northeast and southeast and higher in the southwest. This study provides a method for remotely sensing alpine grasslines for the first-time at large scale and lays a foundation for investigating their responses to climate change.

RevDate: 2023-11-01
CmpDate: 2023-11-01

Zhang HH, Meng XX, Lin YL, et al (2023)

[Prediction of global potential growth areas for Panax ginseng based on GMPGIS system and MaxEnt model].

Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica, 48(18):4959-4966.

The suitable habitat for the endangered and valuable medicinal herb Panax ginseng is gradually decreasing. It is crucial to investigate its suitable growing areas in China for global protection and sustainable utilization of P. ginseng. In this study, 371 distribution points of P. ginseng were collected, and 21 environmental factors were used as ecological indicators. The geographic information system for global medicinal plants(GMPGIS) system, MaxEnt model, and Thiessen polygon method were used to analyze the potential suitable areas for P. ginseng globally. The results showed that the key environmental variables affecting P. ginseng were precipitation in the hottest quarter(Bio18) and the coefficient of temperature seasonality(Bio4). The suitable habitats for P. ginseng were mostly located in the "One Belt, One Road" countries such as China, Japan, South Korea, North Korea, and Russia. The highly suitable habitats were mainly distributed along mountain ranges in southeastern Shandong, southern Shanxi and Shaanxi, northern Jiangsu, and northwestern Henan of China. Data analysis indicated that the current P. ginseng planting sites were all in high suitability zones, and the Thiessen polygon results showed that the geographic locations of P. ginseng production companies were unbalanced and urgently needed optimization. This study provides data support for P. ginseng planting site selection, scientific introduction, production layout, and long-term development planning.

RevDate: 2023-10-31

Lien AM, Banki O, Barik SK, et al (2023)

Widespread support for a global species list with a formal governance system.

Proceedings of the National Academy of Sciences of the United States of America, 120(45):e2306899120.

Taxonomic data are a scientific common. Unlike nomenclature, which has strong governance institutions, there are currently no generally accepted governance institutions for the compilation of taxonomic data into an accepted global list. This gap results in challenges for conservation, ecological research, policymaking, international trade, and other areas of scientific and societal importance. Consensus on a global list and its management requires effective governance and standards, including agreed mechanisms for choosing among competing taxonomies and partial lists. However, governance frameworks are currently lacking, and a call for governance in 2017 generated critical responses. Any governance system to which compliance is voluntary requires a high level of legitimacy and credibility among those by and for whom it is created. Legitimacy and credibility, in turn, require adequate and credible consultation. Here, we report on the results of a global survey of taxonomists, scientists from other disciplines, and users of taxonomy designed to assess views and test ideas for a new system of taxonomic list governance. We found a surprisingly high degree of agreement on the need for a global list of accepted species and their names, and consistent views on what such a list should provide to users and how it should be governed. The survey suggests that consensus on a mechanism to create, manage, and govern a single widely accepted list of all the world's species is achievable. This finding was unexpected given past controversies about the merits of list governance.

RevDate: 2023-10-29

Jin Q, Gheeya J, Nepal S, et al (2023)

Associations of dietary patterns with kidney cancer risk, kidney cancer-specific mortality and all-cause mortality among postmenopausal women.

British journal of cancer [Epub ahead of print].

BACKGROUND: The empirical dietary index for hyperinsulinemia (EDIH) and empirical dietary inflammatory pattern (EDIP) are novel measures of dietary quality associated with insulin hypersecretion or chronic inflammation, respectively, whereas the Healthy Eating Index (HEI-2015) measures adherence to the Dietary Guidelines for Americans (DGA). We evaluated associations of EDIH, EDIP and HEI-2015 on the risk of both kidney cancer development and mortality.

METHODS: We calculated the dietary scores from baseline food frequency questionnaires among 115,830 participants aged 50-79 years in the Women's Health Initiative. Multivariable-adjusted Cox regression was used to estimate hazard ratios (HR) and 95% confidence intervals (95%CI) for kidney cancer risk, kidney cancer-specific mortality and all-cause mortality, per 1-standard deviation increment in dietary pattern scores.

RESULTS: Higher EDIH was associated with greater risk of kidney cancer development [HR, 1.12; 95%CI, (1.01,1.23)], kidney cancer-specific death [1.22(0.99,1.48)], and all-cause mortality, [1.05(1.02,1.08)]. Higher HEI-2015 was associated with lower risk of kidney cancer development, [0.85(0.77, 0.94)], kidney cancer-specific death, [0.84(0.69,1.03)] and all-cause mortality, [0.97(0.95,1.00)]. However, EDIP was not significantly associated with outcomes. Associations did not differ by BMI categories.

CONCLUSIONS: Low-insulinemic dietary patterns and higher quality diets, are worthy of testing in dietary pattern intervention trials for kidney cancer prevention and improved survivorship.

RevDate: 2023-10-30
CmpDate: 2023-10-30

Zhang HS, Zhong XM, Xiong Y, et al (2023)

[Big data analysis of coastal illegal fishing from the perspective of compensation of ecological and environmental damage].

Ying yong sheng tai xue bao = The journal of applied ecology, 34(10):2827-2834.

Illegal fishing is one of the sources of marine ecological damage. The implementation of compensation of ecological and environmental damage in this field is poorly understood. In this study, we examined data pertaining to coastal illegal fishing cases during 2018-2022 using the big data publicly made available by China Judgement Online. The main results included: 1) there are numerous types of illegal fishing, and more efforts should focus on the nature and extent of illegal fishing, with electrofishing and trawl being suitable entry points; 2) Special attention should be paid to the variation characteristics of rakes in the range of high illegal catch weight and value. It was suggested to optimize and adjust its management mode to avoid the frequent occurrence of such illegal fishing cases of rake; 3) The varieties of assessment models increased the uncertainty of damages computation, which might be reduced by establishing strong criteria for value quantification and damage assessment; 4) There is limited scientific support for the compensation for releasing the most popular ecological restoration technique for illegal fishing. As a result, the "compensation" design for "restoration" should be implemented, while the potential for additional restoration methods should be investigated.

RevDate: 2023-10-30
CmpDate: 2023-10-30

Gutiérrez-Hellín J, Del Coso J, Espada MC, et al (2023)

Research Trends in the Effect of Caffeine Intake on Fat Oxidation: A Bibliometric and Visual Analysis.

Nutrients, 15(20):.

In the last few decades, numerous studies pertaining to research groups worldwide have investigated the effects of oral caffeine intake on fat oxidation at rest, during exercise, and after exercise. However, there is no bibliometric analysis to assess the large volume of scientific output associated with this topic. A bibliometric analysis of this topic may be used by researchers to assess the current scientific interest in the application of caffeine as a nutritional strategy to augment fat oxidation, the journals with more interest in this type of publication, and to draw international collaborations between groups working in the same area. For these reasons, the purpose of this study was to assess the research activity regarding oral caffeine intake and fat oxidation rate in the last few decades by conducting a bibliometric and visual analysis. Relevant publications from 1992 to 2022 were retrieved from the Web of Science (WoS) Core Collection database. Quantitative and qualitative variables were collected, including the number of publications and citations, H-indexes, journals of citation reports, co-authorship, co-citation, and the co-occurrence of keywords. There were 182 total publications, while the number of annual publications is saw-shaped with a modest increase of 11.3% from 2000 to 2009 to 2010 to 2019. The United States was the country with the highest number of publications (24.17% of the total number of articles), followed by the Netherlands (17.03%). According to citation analyses, the average number of citations per document is 130, although there are 21 documents that have received more than 100 citations; the most cited document reached 644 citations. These citation data support the overall relevance of this topic in the fields of nutrition and dietetics and sport sciences that when combined harbored 85.71% of all articles published in the WoS. The most productive author was Westerterp-Plantenga with 16 articles (8.79% of the total number of articles). Nutrients was the journal that published the largest number of articles on this topic (6.59% of the total number of articles). Last, there is a tendency to include keywords such as "performance", "carbohydrate", and "ergogenic aid" in the newer articles, while "obesity", "thermogenic", and "tea" are the keywords more commonly included in older documents. Although research into the role of caffeine on fat oxidation has existed since the 1970s, our analysis suggests that the scientific output associated with this topic has progressively increased since 1992, demonstrating that this is a nutritional research area with a strong foundational base of scientific evidence. Based on the findings of this bibliometric analysis, future investigation may consider focusing on the effects of sex and tolerance to caffeine to widen the assessment of the effectiveness of oral caffeine intake as a nutritional strategy to augment the use of fat as a fuel, as these terms rarely appear in the studies included in this analysis. Additionally, more translational research is necessary as the studies that investigate the effect of oral caffeine intake in ecologically valid contexts (i.e., exercise training programs for individuals with excessive adiposity) are only a minor part of the studies on this topic.

RevDate: 2023-10-30
CmpDate: 2023-10-30

Omang BO, Omeka ME, Asinya EA, et al (2023)

Application of GIS and feedforward back-propagated ANN models for predicting the ecological and health risk of potentially toxic elements in soils in Northwestern Nigeria.

Environmental geochemistry and health, 45(11):8599-8631.

Potentially toxic elements (PTEs) occur naturally in most geologic materials. However, recent anthropogenic disturbances such as ore mining have contributed significantly to their enrichment in soils. Their occurrence in soil may portend a myriad of related risks to the environment and biota. Most traditional soil quality evaluation methods involve comparing the background values of the elements to the established guideline values, which is often time-consuming and fraught with computational errors. As a result, to conduct a comprehensive and unbiased evaluation of soil quality and its effects on the ecosystem and human health, this research combined geochemical, numerical, and GIS data for a composite health risk zonation of the entire study area. Furthermore, the multilayer perceptron artificial neural network (MLP-NN) was used to forecast the most important toxic components influencing soil quality. Geochemical, statistical, and quantitative soil pollution evaluation (pollution index and ecological risk index) showed that apart from mining, the spread and association of trace elements and oxides occur as a consequence of surface environmental conditions (e.g., leaching, weathering, and organo-metallic complexation). The hazard quotients (HQs) and hazard index (HI) of all PTEs were greater than one. This indicates that residents (particularly children) are more susceptible to risks from toxic element ingestion than dermal exposure and inhalation. Ingestion of As and Cr resulted in higher cancer risks and lifetime cancer risk levels (> 1.0E 04), with risk levels increasing toward the northeastern, western, and southeastern directions of the study area. The low modeling errors observed from the sum of square errors, relative errors, and coefficient of determination confirmed the efficiency of the MLP-NN in pollution load prediction. Based on the sensitivity analysis, Hg, Sr, Zn, Ba, As, and Zr showed the greatest influence on soil quality. Focus on remediation should therefore be placed on the removal of these elements from the soil.

RevDate: 2023-10-30
CmpDate: 2023-10-30

Debnath J, Sahariah D, Lahon D, et al (2023)

Geospatial modeling to assess the past and future land use-land cover changes in the Brahmaputra Valley, NE India, for sustainable land resource management.

Environmental science and pollution research international, 30(49):106997-107020.

Satellite remote sensing and geographic information system (GIS) have revolutionalized the mapping, quantifying, and assessing the land surface processes, particularly analyzing the past and future land use-land cover (LULC) change patterns. Worldwide river basins have observed enormous changes in the land system dynamics as a result of anthropogenic factors such as population, urbanization, development, and agriculture. As is the scenario of various other river basins, the Brahmaputra basin, which falls in China, Bhutan, India, and Bangladesh, is also witnessing the same environmental issues. The present study has been conducted on the Brahmaputra Valley in Assam, India (a sub-basin of the larger Brahmaputra basin) and assessed its LULC changes using a maximum likelihood classification algorithm. The study also simulated the changing LULC pattern for the years 2030, 2040, and 2050 using the GIS-based cellular automata Markov model (CA-Markov) to understand the implications of the ongoing trends in the LULC change for future land system dynamics. The current rate of change of the LULC in the region was assessed using the 48 years of earth observation satellite data from 1973 to 2021. It was observed that from 1973 to 2021, the area under vegetation cover and water body decreased by 19.48 and 47.13%, respectively. In contrast, cultivated land, barren land, and built-up area increased by 7.60, 20.28, and 384.99%, respectively. It was found that the area covered by vegetation and water body has largely been transitioned to cultivated land and built-up classes. The research predicted that, by the end of 2050, the area covered by vegetation, cultivated land, and water would remain at 39.75, 32.31, and 4.91%, respectively, while the area covered by built-up areas will increase by up to 18.09%. Using the kappa index (ki) as an accuracy indicator of the simulated future LULCs, the predicted LULC of 2021 was validated against the observed LULC of 2021, and the very high ki observed validated the generated simulation LULC products. The research concludes that significant LULC changes are taking place in the study area with a decrease in vegetation cover and water body and an increase of area under built-up. Such trends will continue in the future and shall have disastrous environmental consequences unless necessary land resource management strategies are not implemented. The main factors responsible for the changing dynamics of LULC in the study area are urbanization, population growth, climate change, river bank erosion and sedimentation, and intensive agriculture. This study is aimed at providing the policy and decision-makers of the region with the necessary what-if scenarios for better decision-making. It shall also be useful in other countries of the Brahmaputra basin for transboundary integrated river basin management of the whole region.

RevDate: 2023-10-28

Huang C, Guan K, Qi X, et al (2023)

Spatial distribution, conversion, and ecological risk assessment of hexabromocyclododecanes in the sediments of black-odorous urban rivers nationwide in China.

The Science of the total environment pii:S0048-9697(23)06684-6 [Epub ahead of print].

Hexabromocyclododecanes (HBCDs) have become a global pollution problem, particularly in China-a major producer and user of HBCDs. However, little is known about the HBCD pollution status in urban rivers nationwide in China. In this study, we comprehensively investigated the pollution characteristics of HBCDs in 173 sediment samples from black-odorous urban rivers across China. Total HBCD concentrations ranged from not-detected to 848 ng/g dw, showing significant differences among the various sampling cities, but generally increasing from west to east China. This distribution pattern of HBCDs was strongly associated with the local industrial output, gross domestic product, and daily wastewater treatment capacity. α-HBCD was the predominant diastereoisomer in most sediments, with an average proportion of 63.8 ± 18.8 %, followed by γ-HBCD (23.8 ± 19.5 %) and β-HBCD (12.4 ± 6.49 %), showing a significant increase of the α-HBCD proportions relative to those in HBCD commercial mixtures and an opposite trend for that of γ-HBCD. These results suggested that HBCDs might undergo isomerization from γ- to α-HBCD and biotic/abiotic degradation with preference for γ-HBCD. Of these conversions, the microbial degradation of HBCDs was further verified by the preferential transformation of (-)-α-, (+)-β-, and (-)-γ-HBCDs and the detection of HBCD-degrading bacteria, including Dehalococcoides, Bacillus, Sphingobium, and Pseudomonas. A risk assessment indicated that HBCDs pose low to moderate risks to aquatic organisms in most black-odorous urban river sediments.

RevDate: 2023-10-28

Karakurt-Fischer S, Johnson DR, Fenner K, et al (2023)

Making waves: Enhancing pollutant biodegradation via rational engineering of microbial consortia.

Water research, 247:120756 pii:S0043-1354(23)01196-X [Epub ahead of print].

Biodegradation holds promise as an effective and sustainable process for the removal of synthetic chemical pollutants. Nevertheless, rational engineering of biodegradation for pollutant remediation remains an unfulfilled goal, while chemical pollution of waters and soils continues to advance. Efforts to (i) identify functional bacteria from aquatic and soil microbiomes, (ii) assemble them into biodegrading consortia, and (iii) identify maintenance and performance determinants, are challenged by large number of pollutants and the complexity in the enzymology and ecology of pollutant biodegradation. To overcome these challenges, approaches that leverage knowledge from environmental bio-chem-informatics and metabolic engineering are crucial. Here, we propose a novel high-throughput bio-chem-informatics pipeline, to link chemicals and their predicted biotransformation pathways with potential enzymes and bacterial strains. Our framework systematically selects the most promising candidates for the degradation of chemicals with unknown biotransformation pathways and associated enzymes from the vast array of aquatic and soil bacteria. We substantiated our perspective by validating the pipeline for two chemicals with known or predicted pathways and show that our predicted strains are consistent with strains known to biotransform those chemicals. Such pipelines can be integrated with metabolic network analysis built upon genome-scale models and ecological principles to rationally design fit-for-purpose bacterial communities for augmenting deficient biotransformation functions and study operational and design parameters that influence their structure and function. We believe that research in this direction can pave the way for achieving our long-term goal of enhancing pollutant biodegradation.

RevDate: 2023-10-28

Dudek M, Sąsiadek-Andrzejczak E, Jaszczak-Kuligowska M, et al (2023)

The Surface Modification of Papers Using Laser Processing towards Applications.

Materials (Basel, Switzerland), 16(20):.

This work presents the results of paper laser processing. It begins with the selection and examination of the processing parameters, then an examination of the properties of the modified papers and examples of applications of the developed modification method. The properties of laser-modified paper were studied using reflectance spectrophotometry to examine the colour aspects of the modified papers, scanning electron microscopy (SEM) and confocal microscopy for a morphological analysis, and Raman spectroscopy to analyse the papers under the influence of laser light. The influence of laser processing on the wettability of paper and the evenness of unprinted and printed paper was also investigated. The knowledge gained on paper surface modification with laser light was used to propose several applications, such as methods of marking, tactile detection, the controlled removal of optical brightener, ink, and metallised coatings from paper packaging, highlighting the design and aesthetics of paper. The developed laser-assisted method shows a promising, ecological approach to the design of many value-added paper products.

RevDate: 2023-10-27

Zhu X, Ji H, Hua G, et al (2023)

Dynamic Release Characteristics and Kinetics of a Persulfate Sustained-Release Material.

Toxics, 11(10):.

Sustained-release materials are increasingly being used in the delivery of oxidants for in situ chemical oxidation (ISCO) for groundwater remediation. Successful implementation of sustained-release materials depends on a clear understanding of the mechanism and kinetics of sustained release. In this research, a columnar sustained-release material (PS@PW) was prepared with paraffin wax and sodium persulfate (PS), and column experiments were performed to investigate the impacts of the PS@PW diameter and PS/PW mass ratio on PS release. The results demonstrated that a reduction in diameter led to an increase in both the rate and proportion of PS release, as well as a diminished lifespan of release. The release process followed the second-order kinetics, and the release rate constant was positively correlated with the PS@PW diameter. A matrix boundary diffusion model was utilized to determine the PS@PW diffusion coefficient of the PS release process, and the release lifespan of a material with a length of 500 mm and a diameter of 80 mm was predicted to be more than 280 days. In general, this research provided a better understanding of the release characteristics and kinetics of persulfate from a sustained-release system and could lead to the development of columnar PS@PW as a practical oxidant for in situ chemical oxidation of contaminated aquifers.

RevDate: 2023-10-27

Boyes D, Chua P, University of Oxford and Wytham Woods Genome Acquisition Lab, et al (2023)

The genome sequence of the Oak Hook-tip, Watsonalla binaria (Hufnagel, 1767).

Wellcome open research, 8:324.

We present a genome assembly from an individual female Watsonalla binaria (the Oak Hook-tip; Arthropoda; Insecta; Lepidoptera; Drepanidae). The genome sequence is 333.0 megabases in span. Most of the assembly is scaffolded into 33 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.24 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,002 protein coding genes.

RevDate: 2023-10-26

Kinkade JA, Seetharam AS, Sachdev S, et al (2023)

Extracellular vesicles from mouse trophoblast cells: effects on neural progenitor cells and potential participants in the placenta-brain Axis.

Biology of reproduction pii:7330548 [Epub ahead of print].

The fetal brain of the mouse is thought to be dependent upon the placenta as a source of serotonin (5-hydroxytryptamine; 5-HT) and other factors. How factors reach the developing brain remains uncertain but are postulated here to be part of the cargo carried by placental extracellular vesicles (EV). We have analyzed the protein, catecholamine, and small RNA content of EV from mouse trophoblast stem cells (TSC) and TSC differentiated into parietal trophoblast giant cells (pTGC), potential primary purveyors of 5-HT. We have examined how exposure of mouse neural progenitor cells (NPC) to EV from either TSC or pTGC affect their transcriptome profiles. The EV from TB cells contained relatively high amounts of 5-HT, as well as dopamine and norepinephrine, but there were no significant differences between EV derived from pTGC and from TSC. Content of miRNA and small nucleolar (sno)RNA, however, did differ according to EV source, and snoRNA were upregulated in EV from pTGC. The primary inferred targets of the miRNA from both pTGC and TSC were mRNA enriched in the fetal brain. NPC readily internalized EV, leading to changes in their transcriptome profiles. Transcripts regulated were mainly ones enriched in neural tissues. The transcripts in EV-treated NPC that demonstrated a likely complementarity with miRNA in EV were mainly up- rather than down-regulated, with functions linked to neuronal processes. Our results are consistent with placenta-derived EV providing direct support for fetal brain development and being an integral part of the placenta-brain axis.

RevDate: 2023-10-27
CmpDate: 2023-10-27

Sonkoly J, Tóth E, Balogh N, et al (2023)

PADAPT 1.0 - the Pannonian Dataset of Plant Traits.

Scientific data, 10(1):742.

The existing plant trait databases' applicability is limited for studies dealing with the flora and vegetation of the eastern and central part of Europe and for large-scale comparisons across regions, mostly because their geographical data coverage is limited and they incorporate records from several different sources, often from regions with markedly different climatic conditions. These problems motivated the compilation of a regional dataset for the flora of the Pannonian region (Eastern Central Europe). PADAPT, the Pannonian Dataset of Plant Traits relies on regional data sources and collates data on 54 traits and attributes of the plant species of the Pannonian region. The current version covers approximately 90% of the species of the region and consists of 126,337 records on 2745 taxa. By including species of the eastern part of Europe not covered by other databases, PADAPT can facilitate studying the flora and vegetation of the eastern part of the continent. Although data coverage is far from complete, PADAPT meets the longstanding need for a regional database of the Pannonian flora.

RevDate: 2023-10-27
CmpDate: 2023-10-27

Oza A (2023)

Reproducibility trial: 246 biologists get different results from same data sets.

Nature, 622(7984):677-678.

RevDate: 2023-10-27
CmpDate: 2023-10-27

Zhao D, Zhang Y, Ren H, et al (2023)

Multi-omics analysis reveals the evolutionary origin of diterpenoid alkaloid biosynthesis pathways in Aconitum.

Journal of integrative plant biology, 65(10):2320-2335.

Diterpenoid alkaloids (DAs) have been often utilized in clinical practice due to their analgesic and anti-inflammatory properties. Natural DAs are prevalent in the family Ranunculaceae, notably in the Aconitum genus. Nevertheless, the evolutionary origin of the biosynthesis pathway responsible for DA production remains unknown. In this study, we successfully assembled a high-quality, pseudochromosome-level genome of the DA-rich species Aconitum vilmorinianum (A. vilmorinianum) (5.76 Gb). An A. vilmorinianum-specific whole-genome duplication event was discovered using comparative genomic analysis, which may aid in the evolution of the DA biosynthesis pathway. We identified several genes involved in DA biosynthesis via integrated genomic, transcriptomic, and metabolomic analyses. These genes included enzymes encoding target ent-kaurene oxidases and aminotransferases, which facilitated the activation of diterpenes and insertion of nitrogen atoms into diterpene skeletons, thereby mediating the transformation of diterpenes into DAs. The divergence periods of these genes in A. vilmorinianum were further assessed, and it was shown that two major types of genes were involved in the establishment of the DA biosynthesis pathway. Our integrated analysis offers fresh insights into the evolutionary origin of DAs in A. vilmorinianum as well as suggestions for engineering the biosynthetic pathways to obtain desired DAs.

RevDate: 2023-10-26

Bald L, Gottwald J, D Zeuss (2023)

spatialMaxent: Adapting species distribution modeling to spatial data.

Ecology and evolution, 13(10):e10635.

Conventional practices in species distribution modeling lack predictive power when the spatial structure of data is not taken into account. However, choosing a modeling approach that accounts for overfitting during model training can improve predictive performance on spatially separated test data, leading to more reliable models. This study introduces spatialMaxent (, a software that combines state-of-the-art spatial modeling techniques with the popular species distribution modeling software Maxent. It includes forward-variable-selection, forward-feature-selection, and regularization-multiplier tuning based on spatial cross-validation, which enables addressing overfitting during model training by considering the impact of spatial dependency in the training data. We assessed the performance of spatialMaxent using the National Center for Ecological Analysis and Synthesis dataset, which contains over 200 anonymized species across six regions worldwide. Our results show that spatialMaxent outperforms both conventional Maxent and models optimized according to literature recommendations without using a spatial tuning strategy in 80 percent of the cases. spatialMaxent is user-friendly and easily accessible to researchers, government authorities, and conservation practitioners. Therefore, it has the potential to play an important role in addressing pressing challenges of biodiversity conservation.

RevDate: 2023-10-25

Bernardini I, Quagliariello A, Peruzza L, et al (2023)

Contaminants from dredged sediments alter the transcriptome of Manila clam and induce shifts in microbiota composition.

BMC biology, 21(1):234.

BACKGROUND: The reuse of dredged sediments in ports and lagoons is a big issue as it should not affect the quality and the equilibrium of ecosystems. In the lagoon of Venice, sediment management is of crucial importance as sediments are often utilized to built-up structures necessary to limit erosion. However, the impact of sediment reuse on organisms inhabiting this delicate area is poorly known. The Manila clam is a filter-feeding species of high economic and ecological value for the Venice lagoon experiencing a drastic decline in the last decades. In order to define the molecular mechanisms behind sediment toxicity, we exposed clams to sediments sampled from different sites within one of the Venice lagoon navigable canals close to the industrial area. Moreover, we investigated the impacts of dredged sediments on clam's microbial communities.

RESULTS: Concentrations of the trace elements and organic chemicals showed increasing concentrations from the city of Venice to sites close to the industrial area of Porto Marghera, where PCDD/Fs and PCBs concentrations were up to 120 times higher than the southern lagoon. While bioaccumulation of organic contaminants of industrial origin reflected sediments' chemical concentrations, metal bioaccumulation was not consistent with metal concentrations measured in sediments probably due to the activation of ABC transporters. At the transcriptional level, we found a persistent activation of the mTORC1 signalling pathway, which is central in the coordination of cellular responses to chemical stress. Microbiota characterization showed the over-representation of potential opportunistic pathogens following exposure to the most contaminated sediments, leading to host immune response activation. Despite the limited acquisition of new microbial species from sediments, the latter play an important role in shaping Manila clam microbial communities.

CONCLUSIONS: Sediment management in the Venice lagoon will increase in the next years to maintain and create new canals as well as to allow the operation of the new mobile gates at the three Venice lagoon inlets. Our data reveal important transcriptional and microbial changes of Manila clams after exposure to sediments, therefore reuse of dredged sediments represents a potential risk for the conservation of this species and possibly for other organisms inhabiting the Venice lagoon.

RevDate: 2023-10-26
CmpDate: 2023-10-26

Mwangungulu SP, Dorothea D, Ngereja ZR, et al (2023)

Geospatial based model for malaria risk prediction in Kilombero valley, South-eastern, Tanzania.

PloS one, 18(10):e0293201.

BACKGROUND: Malaria continues to pose a major public health challenge in tropical regions. Despite significant efforts to control malaria in Tanzania, there are still residual transmission cases. Unfortunately, little is known about where these residual malaria transmission cases occur and how they spread. In Tanzania for example, the transmission is heterogeneously distributed. In order to effectively control and prevent the spread of malaria, it is essential to understand the spatial distribution and transmission patterns of the disease. This study seeks to predict areas that are at high risk of malaria transmission so that intervention measures can be developed to accelerate malaria elimination efforts.

METHODS: This study employs a geospatial based model to predict and map out malaria risk area in Kilombero Valley. Environmental factors related to malaria transmission were considered and assigned valuable weights in the Analytic Hierarchy Process (AHP), an online system using a pairwise comparison technique. The malaria hazard map was generated by a weighted overlay of the altitude, slope, curvature, aspect, rainfall distribution, and distance to streams in Geographic Information Systems (GIS). Finally, the risk map was created by overlaying components of malaria risk including hazards, elements at risk, and vulnerability.

RESULTS: The study demonstrates that the majority of the study area falls under moderate risk level (61%), followed by the low risk level (31%), while the high malaria risk area covers a small area, which occupies only 8% of the total area.

CONCLUSION: The findings of this study are crucial for developing spatially targeted interventions against malaria transmission in residual transmission settings. Predicted areas prone to malaria risk provide information that will inform decision-makers and policymakers for proper planning, monitoring, and deployment of interventions.

RevDate: 2023-10-25

Santos CAQ, Tseng M, Martinez AI, et al (2023)

Comparative antimicrobial use in coronavirus disease 2019 (COVID-19) and non-COVID-19 inpatients from 2019 to 2020: A multicenter ecological study.

Infection control and hospital epidemiology pii:S0899823X23001800 [Epub ahead of print].

OBJECTIVE: We sought to determine whether increased antimicrobial use (AU) at the onset of the coronavirus disease 2019 (COVID-19) pandemic was driven by greater AU in COVID-19 patients only, or whether AU also increased in non-COVID-19 patients.

DESIGN: In this retrospective observational ecological study from 2019 to 2020, we stratified inpatients by COVID-19 status and determined relative percentage differences in median monthly AU in COVID-19 patients versus non-COVID-19 patients during the COVID-19 period (March-December 2020) and the pre-COVID-19 period (March-December 2019). We also determined relative percentage differences in median monthly AU in non-COVID-19 patients during the COVID-19 period versus the pre-COVID-19 period. Statistical significance was assessed using Wilcoxon signed-rank tests.

SETTING: The study was conducted in 3 acute-care hospitals in Chicago, Illinois.

PATIENTS: Hospitalized patients.

RESULTS: Facility-wide AU for broad-spectrum antibacterial agents predominantly used for hospital-onset infections was significantly greater in COVID-19 patients versus non-COVID-19 patients during the COVID-19 period (with relative increases of 73%, 66%, and 91% for hospitals A, B, and C, respectively), and during the pre-COVID-19 period (with relative increases of 52%, 64%, and 66% for hospitals A, B, and C, respectively). In contrast, facility-wide AU for all antibacterial agents was significantly lower in non-COVID-19 patients during the COVID-19 period versus the pre-COVID-19 period (with relative decreases of 8%, 7%, and 8% in hospitals A, B, and C, respectively).

CONCLUSIONS: AU for broad-spectrum antimicrobials was greater in COVID-19 patients compared to non-COVID-19 patients at the onset of the pandemic. AU for all antibacterial agents in non-COVID-19 patients decreased in the COVID-19 period compared to the pre-COVID-19 period.

RevDate: 2023-10-24

Ahmad K, Shankar Pacha A, Yahya Naqash R, et al (2023)

Evolutionary insights on critically endangered Kashmir red deer or hangul (Cervus hanglu hanglu) through a mitogenomic lens.

PeerJ, 11:e15746.

BACKGROUND: The Kashmir red deer or Hangul (Cervus hanglu hanglu) is the only Tarim red deer species endemic to India. With a current estimated population size of fewer than 200 individuals, this critically endangered species is confined to the greater Dachigam landscape in Jammu and Kashmir. Poaching, habitat loss and fragmentation, resource competition with livestock, and small population size are the major conservation challenges for this species.

METHODS: Blood sampling was conducted from two wild Hangul individuals during radio-collaring operations at Dachigam National Park, Kashmir in 2013 and 2020, respectively. Using next-generation sequencing approach, we sequenced the 16,351 bp long mitogenome of two wild-caught Hangul individuals (1 M:1 F at ~14× and ~10× coverage, respectively) from Dachigam National Park.

RESULTS: The annotated sequences were identical with an AT-rich composition, including 13 protein-coding genes (11,354 bp), 22 tRNA genes (1,515 bp), two ribosomal genes (2,526 bp) and a non-coding control region (917 bp) in a conserved order like other red deer species. Bayesian phylogenetic reconstruction of the red deer complex revealed two major groups: the elaphoid and the wapitoid clades. Hangul formed a distinct clade with its other subspecies C. hanglu yarkandensis and is sister to the Hungarian red deer (C. elaphus hippelaphus). Divergence time analyses suggested that the Tarim deer species group separated ~1.55 Mya from their common ancestors and Hangul diverged ~0.75 Mya from closely related C. yarkandensis, corroborating with the known paleobiogeographic events related to refugia during glaciations in the Pleistocene era. This study provides baseline information on Hangul mitogenome for further research on phylogeography and other population parameters and helps in developing suitable conservation plans for this species.

RevDate: 2023-10-23

Marceglia S, Manzelli V, Caruso A, et al (2023)

PainRE-Life: A FHIR Based Telemonitoring Ecosystem for the Management of Patients with Chronic Pain.

Studies in health technology and informatics, 309:183-184.

Chronic pain is a condition in which the use of digital health technologies, ecological momentary assessments, and digital communication tools may boost patient's engagement and coping. Here we present the results of the PainRE-Life a project, financed by the Lombardy Region (Italy), aimed to develop a dynamic and integrated technology ecosystem based on big data management and analysis to allow care continuity in patients with pain, and able to act as a decision aid for patients and caregivers.

RevDate: 2023-10-23
CmpDate: 2023-10-23

Xu P, Zhang W, Wang X, et al (2023)

Multiomics analysis reveals a link between Brassica-specific miR1885 and rapeseed tolerance to low temperature.

Plant, cell & environment, 46(11):3405-3419.

Brassica crops include various edible vegetable and plant oil crops, and their production is limited by low temperature beyond their tolerant capability. The key regulators of low-temperature resistance in Brassica remain largely unexplored. To identify posttranscriptional regulators of plant response to low temperature, we performed small RNA profiling, and found that 16 known miRNAs responded to cold treatment in Brassica rapa. The cold response of seven of those miRNAs were further confirmed by qRT-PCR and/or northern blot analyses. In parallel, a genome-wide association study of 220 accessions of Brassica napus identified four candidate MIRNA genes, all of which were cold-responsive, at the loci associated with low-temperature resistance. Specifically, these large-scale data analyses revealed a link between miR1885 and the plant response to low temperature in both B. rapa and B. napus. Using 5' rapid amplification of cDNA ends approach, we validated that miR1885 can cleave its putative target gene transcripts, Bn.TIR.A09 and Bn.TNL.A03, in B. napus. Furthermore, overexpression of miR1885 in Semiwinter type B. napus decreased the mRNA abundance of Bn.TIR.A09 and Bn.TNL.A03 and resulted in increased sensitivity to low temperature. Knocking down of miR1885 in Spring type B. napus led to increased mRNA abundance of its targets and improved rapeseed tolerance to low temperature. Together, our results suggested that the loci of miR1885 and its targets could be potential candidates for the molecular breeding of low temperature-tolerant Spring type Brassica crops.

RevDate: 2023-10-23
CmpDate: 2023-10-23

Riva F, L Fahrig (2023)

Obstruction of biodiversity conservation by minimum patch size criteria.

Conservation biology : the journal of the Society for Conservation Biology, 37(5):e14092.

Minimum patch size criteria for habitat protection reflect the conservation principle that a single large (SL) patch of habitat has higher biodiversity than several small (SS) patches of the same total area (SL > SS). Nonetheless, this principle is often incorrect, and biodiversity conservation requires placing more emphasis on protection of large numbers of small patches (SS > SL). We used a global database reporting the abundances of species across hundreds of patches to assess the SL > SS principle in systems where small patches are much smaller than the typical minimum patch size criteria applied for biodiversity conservation (i.e., ∼85% of patches <100 ha). The 76 metacommunities we examined included 4401 species in 1190 patches. From each metacommunity, we resampled species-area accumulation curves to evaluate how biodiversity responded to habitat existing as a few large patches or as many small patches. Counter to the SL > SS principle and consistent with previous syntheses, species richness accumulated more rapidly when adding several small patches (45.2% SS > SL vs. 19.9% SL > SS) to reach the same cumulative area, even for the very small patches in our data set. Responses of taxa to habitat fragmentation differed, which suggests that when a given total area of habitat is to be protected, overall biodiversity conservation will be most effective if that habitat is composed of as many small patches as possible, plus a few large ones. Because minimum patch size criteria often require larger patches than the small patches we examined, our results suggest that such criteria hinder efforts to protect biodiversity.

RevDate: 2023-10-22

Koludarov I, Velasque M, Senoner T, et al (2023)

Prevalent bee venom genes evolved before the aculeate stinger and eusociality.

BMC biology, 21(1):229.

BACKGROUND: Venoms, which have evolved numerous times in animals, are ideal models of convergent trait evolution. However, detailed genomic studies of toxin-encoding genes exist for only a few animal groups. The hyper-diverse hymenopteran insects are the most speciose venomous clade, but investigation of the origin of their venom genes has been largely neglected.

RESULTS: Utilizing a combination of genomic and proteo-transcriptomic data, we investigated the origin of 11 toxin genes in 29 published and 3 new hymenopteran genomes and compiled an up-to-date list of prevalent bee venom proteins. Observed patterns indicate that bee venom genes predominantly originate through single gene co-option with gene duplication contributing to subsequent diversification.

CONCLUSIONS: Most Hymenoptera venom genes are shared by all members of the clade and only melittin and the new venom protein family anthophilin1 appear unique to the bee lineage. Most venom proteins thus predate the mega-radiation of hymenopterans and the evolution of the aculeate stinger.

RevDate: 2023-10-22
CmpDate: 2023-10-22

Yang L, Wu S, Li G, et al (2023)

Explore public concerns about environmental protection on Sina Weibo: evidence from text mining.

Environmental science and pollution research international, 30(47):104067-104085.

The increasingly serious problem of ecological environmental pollution warns the importance of human environmental protection behavior. However, public attention to environmental protection plays an important role in solving environmental problems. Therefore, in order to explore the environmental concerns of Chinese residents, the trends in time and space, the relationship between online retweets, and the extraction of environmental concerns, this study analyzed the data of Sina Weibo users and their comments on related posts. At the same time, we used the text mining analysis method to analyze the social media text data, and the results are as follows. In that analysis of concern about environmental protection, women show a stronger attitude and willingness to protect the environment than men, and the public in economically developed areas is more concerned. In order to further investigate the public's environmental concerns, this study also utilized the PageRank algorithm to further study the forwarding relationships between users. The study found that celebrities and some good media organizations can attract environmental attention. Finally, we use pyLDAvis technology to visualize and analyze popular environmental themes and propose reasonable countermeasures and suggestions to enhance public environmental awareness based on the research results.

RevDate: 2023-10-22
CmpDate: 2023-10-22

Sun M, Yan H, Zhang A, et al (2023)

Milletdb: a multi-omics database to accelerate the research of functional genomics and molecular breeding of millets.

Plant biotechnology journal, 21(11):2348-2357.

Millets are a class of nutrient-rich coarse cereals with high resistance to abiotic stress; thus, they guarantee food security for people living in areas with extreme climatic conditions and provide stress-related genetic resources for other crops. However, no platform is available to provide a comprehensive and systematic multi-omics analysis for millets, which seriously hinders the mining of stress-related genes and the molecular breeding of millets. Here, a free, web-accessible, user-friendly millets multi-omics database platform (Milletdb, has been developed. The Milletdb contains six millets and their one related species genomes, graph-based pan-genomics of pearl millet, and stress-related multi-omics data, which enable Milletdb to be the most complete millets multi-omics database available. We stored GWAS (genome-wide association study) results of 20 yield-related trait data obtained under three environmental conditions [field (no stress), early drought and late drought] for 2 years in the database, allowing users to identify stress-related genes that support yield improvement. Milletdb can simplify the functional genomics analysis of millets by providing users with 20 different tools (e.g., 'Gene mapping', 'Co-expression', 'KEGG/GO Enrichment' analysis, etc.). On the Milletdb platform, a gene PMA1G03779.1 was identified through 'GWAS', which has the potential to modulate yield and respond to different environmental stresses. Using the tools provided by Milletdb, we found that the stress-related PLATZs TFs (transcription factors) family expands in 87.5% of millet accessions and contributes to vegetative growth and abiotic stress responses. Milletdb can effectively serve researchers in the mining of key genes, genome editing and molecular breeding of millets.

RevDate: 2023-10-22
CmpDate: 2023-10-22

Zhong X, Xu M, Li T, et al (2023)

Development of EST-SSRs based on the transcriptome of Castanopsis carlesii and cross-species transferability in other Castanopsis species.

PloS one, 18(7):e0288999.

Castanopsis carlesii (Hemsl.) Hay. is a widely distributed and dominant tree species native to subtropical China with significant ecological and economic value. Due to serious human-related disturbance, its wild resources have been increasingly reduced, and whether may result in the loss of genetic diversity. However, no population genetics studies of natural C. carlesii have been reported to date. Microsatellite markers have been a useful tool in population genetics. Therefore, we developed EST-SSR markers based on the transcriptome sequencing of C. carlesii leaves. A total of 149,380,224 clean reads were obtained, and 63,012 nonredundant unigenes with a mean length of 1,034 bp were assembled and annotated based on sequence similarity searches in the Nr, Nt, KO, SwissProt, PFAM, KOG, and GO databases. The results showed that only 5,559 (8.82%) unigenes were annotated in all seven databases, but 46,338 (73.53%) could be annotated in at least one database. A total of 31,459 potential EST-SSRs were identified in 18,690 unigenes, with an average frequency of one SSR approximately 2 kb. Among the 100 EST-SSR primer pairs designed, 49 primer pairs successfully produced the expected product by amplification, with a success rate of 49%, but only 20 primer pairs showed abundant polymorphisms. Polymorphisms were verified using 25 samples from C. carlesii in Qimen, Anhui. A total of 119 alleles were detected, with a mean number of alleles (Na) of 5.95 per locus and a mean polymorphism information content (PIC) of 0.6125. All the 20 newly developed EST-SSR markers were verified in other Castanopsis species (C. sclerophylla, C. lamontii, C. fargesii, C. eyrei and C. jucunda). Sixteen primer pairs showed successful amplification in all five Castanopsis species (80%), and the transferability ratios ranged from 90% to 100%. These developed EST-SSR markers can be applied to population genetic and germplasm evaluations of C. carlesii and related species.

RevDate: 2023-10-22
CmpDate: 2023-10-22

Shafee T, Mietchen D, Lubiana T, et al (2023)

Ten quick tips for editing Wikidata.

PLoS computational biology, 19(7):e1011235.

RevDate: 2023-10-22
CmpDate: 2023-10-22

Brown MJM, Walker BE, Black N, et al (2023)

rWCVP: a companion R package for the World Checklist of Vascular Plants.

The New phytologist, 240(4):1355-1365.

The World Checklist of Vascular Plants (WCVP) is an extremely valuable resource that is being used to address many fundamental and applied questions in plant science, conservation, ecology and evolution. However, databases of this size require data manipulation skills that pose a barrier to many potential users. Here, we present rWCVP, an open-source R package that aims to facilitate the use of the WCVP by providing clear, intuitive functions to execute many common tasks. These functions include taxonomic name reconciliation, geospatial integration, mapping and generation of multiple different summaries of the WCVP in both data and report format. We have included extensive documentation and tutorials, providing step-by-step guides that are accessible even to users with minimal programming experience. rWCVP is available on cran and GitHub.


ESP Quick Facts

ESP Origins

In the early 1990's, Robert Robbins was a faculty member at Johns Hopkins, where he directed the informatics core of GDB — the human gene-mapping database of the international human genome project. To share papers with colleagues around the world, he set up a small paper-sharing section on his personal web page. This small project evolved into The Electronic Scholarly Publishing Project.

ESP Support

In 1995, Robbins became the VP/IT of the Fred Hutchinson Cancer Research Center in Seattle, WA. Soon after arriving in Seattle, Robbins secured funding, through the ELSI component of the US Human Genome Project, to create the original ESP.ORG web site, with the formal goal of providing free, world-wide access to the literature of classical genetics.

ESP Rationale

Although the methods of molecular biology can seem almost magical to the uninitiated, the original techniques of classical genetics are readily appreciated by one and all: cross individuals that differ in some inherited trait, collect all of the progeny, score their attributes, and propose mechanisms to explain the patterns of inheritance observed.

ESP Goal

In reading the early works of classical genetics, one is drawn, almost inexorably, into ever more complex models, until molecular explanations begin to seem both necessary and natural. At that point, the tools for understanding genome research are at hand. Assisting readers reach this point was the original goal of The Electronic Scholarly Publishing Project.

ESP Usage

Usage of the site grew rapidly and has remained high. Faculty began to use the site for their assigned readings. Other on-line publishers, ranging from The New York Times to Nature referenced ESP materials in their own publications. Nobel laureates (e.g., Joshua Lederberg) regularly used the site and even wrote to suggest changes and improvements.

ESP Content

When the site began, no journals were making their early content available in digital format. As a result, ESP was obliged to digitize classic literature before it could be made available. For many important papers — such as Mendel's original paper or the first genetic map — ESP had to produce entirely new typeset versions of the works, if they were to be available in a high-quality format.

ESP Help

Early support from the DOE component of the Human Genome Project was critically important for getting the ESP project on a firm foundation. Since that funding ended (nearly 20 years ago), the project has been operated as a purely volunteer effort. Anyone wishing to assist in these efforts should send an email to Robbins.

ESP Plans

With the development of methods for adding typeset side notes to PDF files, the ESP project now plans to add annotated versions of some classical papers to its holdings. We also plan to add new reference and pedagogical material. We have already started providing regularly updated, comprehensive bibliographies to the ESP.ORG site.


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This is a must read book for anyone with an interest in invasion biology. The full title of the book lays out the author's premise — The New Wild: Why Invasive Species Will Be Nature's Salvation. Not only is species movement not bad for ecosystems, it is the way that ecosystems respond to perturbation — it is the way ecosystems heal. Even if you are one of those who is absolutely convinced that invasive species are actually "a blight, pollution, an epidemic, or a cancer on nature", you should read this book to clarify your own thinking. True scientific understanding never comes from just interacting with those with whom you already agree. R. Robbins

Electronic Scholarly Publishing
961 Red Tail Lane
Bellingham, WA 98226

E-mail: RJR8222 @

Papers in Classical Genetics

The ESP began as an effort to share a handful of key papers from the early days of classical genetics. Now the collection has grown to include hundreds of papers, in full-text format.

Digital Books

Along with papers on classical genetics, ESP offers a collection of full-text digital books, including many works by Darwin (and even a collection of poetry — Chicago Poems by Carl Sandburg).


ESP now offers a much improved and expanded collection of timelines, designed to give the user choice over subject matter and dates.


Biographical information about many key scientists.

Selected Bibliographies

Bibliographies on several topics of potential interest to the ESP community are now being automatically maintained and generated on the ESP site.

ESP Picks from Around the Web (updated 07 JUL 2018 )