bluuebunny/crossref_metadata_2025_split huggingface dataset:
North Atlantic deep-sea benthic biodiversity unveiled through sponge natural sampler DNA
Authors: Riesgo Ana , Arias María Belén , Gallego Ramon , Díez-Vives Cristina , Neave Erika , Wang Cai , Cárdenas Paco , Steffen Karin , Taboada Sergio , Villamor Adriana , Drewery Jim , Kenchington Ellen , Mariani Stefano 
Published: January 2024

Abstract

The deep sea remains the biggest challenge to biodiversity exploration, and anthropogenic disturbances extend well into this realm, calling for urgent management strategies. One of the most diverse, productive, and vulnerable ecosystems in the deep sea are sponge grounds. Currently, environmental DNA (eDNA) metabarcoding is revolutionising the field of biodiversity monitoring, yet complex deep-sea benthic ecosystems remain challenging to assess even with these novel technologies. Here, we evaluate the effectiveness of whole-community metabarcoding to characterise metazoan diversity in sponge grounds across the North Atlantic by leveraging the natural eDNA sampling properties of deep-sea sponges themselves. We sampled 97 sponge tissues from four species across four North-Atlantic biogeographic regions in the deep sea and screened them at the universal COI barcode region. We recovered unprecedented levels of taxonomic diversity per unit effort, especially across the phyla Chordata, Cnidaria, Echinodermata and Porifera, with at least 406 metazoan species. These assemblages identify strong spatial patterns in relation to both latitude and depth, and detect emblematic species currently employed as indicators for these vulnerable habitats. We unveil the remarkable performance of sponges as high-resolution natural samplers of environmental DNA from across the whole animal kingdom and illustrate their vast potential as accurate, low-impact biomonitoring solutions for highly diverse, vulnerable deep-sea ecosystems.
Toward Best Practice in Identifying Subtle Differential Expression with RNA-seq: A Real-World Multi-Center Benchmarking Study Using Quartet and MAQC Reference Materials
Authors: Zhang Rui , Wang Duo , Liu Yaqing , Zhang Yuanfeng , Chen Qingwang , Han Yanxi , Hou Wanwan , Liu Cong , Yu Ying , Li Ziyang , Li Ziqiang , Zhao Jiaxin , Zheng Yuanting , Shi Leming , Li Jinming 
Published: January 2024

Abstract

Translating RNA-seq into clinical diagnostics requires ensuring the reliability of detecting clinically relevant subtle differential expressions, such as those between different disease subtypes or stages. Moreover, cross-laboratory reproducibility and consistency under diverse experimental and bioinformatics workflows urgently need to be addressed. As part of the Quartet project, we presented a comprehensive RNA-seq benchmarking study utilizing Quartet and MAQC RNA reference samples spiked with ERCC controls in 45 independent laboratories, each employing their in-house RNA-seq workflows. We assessed the data quality, accuracy and reproducibility of gene expression and differential gene expression and compared over 40 experimental processes and 140 combined differential analysis pipelines based on multiple 'ground truths'. Here we show that real-world RNA-seq exhibited greater inter-laboratory variations when detecting subtle differential expressions between Quartet samples. Experimental factors including mRNA enrichment methods and strandedness, and each bioinformatics step, particularly normalization, emerged as primary sources of variations in gene expression and have a more pronounced impact on the subtle differential expression measurement. We underscored the pivotal role of experimental execution over the choice of experimental protocols, the importance of strategies for filtering low-expression genes, and optimal gene annotation and analysis tools. In summary, this study provided best practice recommendations for the development, optimization, and quality control of RNA-seq for clinical diagnostic purposes.
The risk of diabetes associated with DDE exposure and its interaction with a common FTO gene variant: the Pro-Saude study, Brazil
Authors: Meyer Armando , Sichieri Rosely , Porta Miquel , Robinson Oliver , Verly Eliseu , Neto José , Rosa Ana , Vineis Paolo , Faerstein Eduardo 
Published: January 2024

Abstract

Exposure to dichlorodiphenyldichloroethylene (DDE) is suspected to be associated with an increased risk of type 2 diabetes (T2D). Other studies suggested that the fat mass and obesity-associated gene (FTO) is associated with T2D risk, regardless of adiposity. Dichlorodiphenyltrichloroethane (DDT) was used in Brazil until the mid-2000s, but no previous studies investigated the association between diabetes and body concentrations of DDE in that country. We investigated that association in a population of Rio de Janeiro, as well as how the FTO-rs9939609 genotypes might affect it. In this cross-sectional study nested in the Pro-Saude cohort, participants were randomly selected according to age, sex, and educational level at the cohort's baseline up to n = 520. Individuals who self-reported diabetes or presented glycated hemoglobin (HbA1c) ≥ 6.5% in the study's phase 4 were considered diabetic. We used logistic regression to estimate the odds ratio of diabetes according to serum levels of DDE, adjusting for age, sex, and total fat mass. We stratified the adjusted odds ratio by FTO-rs9939609 variant genotypes. Serum levels of DDE were associated with a higher chance of having diabetes (OR: 1.43; 95%CI: 1.11–1.84). Across quartiles of DDE concentrations, the dose-response relationship was statistically significant (p-trend = 0.003). The magnitude of the association was higher among individuals with the homozygous allele for the FTO-rs9939609 gene (OR: 3.33; 0.45–24.13). Exposure to DDE may increase the risk of developing diabetes in the Brazilian population, especially in individuals homozygous allele for the FTO-rs9939609 variant.
First isolation and genotyping of pathogenic Leptospira spp. from Austria
Authors: Sohm Cynthia , Willixhofer Denise , Fasching Eva , Waldner Karoline , Deitzer Nicole , Steiner Janina , Jöbstl Julia , Schleicher Corina , Schwarz Marcel , Fuchs Reinhard , Bourhy Pascale , Käsbohrer Annemarie , Wittek Thomas , Firth Clair , Steinparzer Romana , Desvars-Larrive Amélie 
Published: January 2024

Abstract
Leptospirosis is a globally distributed zoonotic disease. The standard serological test, known as Microscopic Agglutination Test (MAT), requires the use of live Leptospirastrains. To enhance its sensitivity and specificity, the usage of locally circulating strains is recommended. However, to date, no local strain is available from Austria. This study aimed to isolate circulating Leptospira strains from cattle in Austria to enhance the performances of the routine serological test for both humans and animals. We used a statistical approach combined with a comprehensive literature search to profile cattle with greater risk of leptospirosis infection and implemented a targeted sampling between November 2021 and October 2022. Urine and/or kidney tissue were sampled from 410 cattle considered at higher risk of infection. Samples were inoculated into EMJH-STAFF culture media within 2-6 hours and a PCR assay was used to confirm the presence/absence of pathogenic Leptospira in each sample. Isolates were further characterised by core genome multilocus sequence typing (cgMLST). Nine out of 429 samples tested positive by PCR, from which three isolates were successfully cultured and identified as Leptospira borgpetersenii serogroup Sejroe serovar Hardjobovis, cgMLST cluster 40. This is the first report on the isolation and genotyping of local zoonotic Leptospira in Austria, which holds the potential for a significant improvement in diagnostic performance in the country. Although the local strain was identified as a cattle-adapted serovar, it possesses significant zoonotic implications. Furthermore, this study contributes to a better understanding of the epidemiology of leptospirosis in Europe.
Water motifs in zirconium metal-organic frameworks induced by nanoconfinement and hydrophilic adsorption sites
Authors: Speybroeck Veronique Van , Lamaire Aran , Rogge Sven , Wieme Jelle 
Published: January 2024

Abstract

The intricate hydrogen bond network of water gives rise to various structures with anomalous properties at different thermodynamic conditions. Nanoconfinement can further modify the water structure and properties, and induce specific water motifs, which are instrumental for technological applications such as atmospheric water harvesting. However, so far, a causal relationship between nanoconfinement and the presence of specific hydrophilic adsorption sites is lacking, hampering the further design of nanostructured materials for water templating. Therefore, this work investigates the organisation of water in a series of zirconium-based metal-organic frameworks (MOFs), with varying topologies, pore sizes, and chemical composition, to extract design rules to shape water. The highly tuneable pores and hydrophilicity of MOFs makes them ideally suited for this purpose. We find that small nanopores favour orderly water clusters that nucleate at hydrophilic adsorption sites. Favourably positioning the secondary adsorption sites, hydrogen-bonded to the primary adsorption sites, allows larger clusters to form. To disentangle the importance of nanoconfinement and hydrophilic nucleation sites in this process, we introduce an analytical model with precise control of the adsorption sites. This sheds a new light on design parameters to induce specific water clusters and hydrogen-bonded networks, thus rationalising the application space of water in nanoconfinement.
Sulfur metabolism promotes the progression of Liver Hepatocellular Carcinoma via the PPAR signaling pathway.
Authors: wei peng , Chen Bendong , Zhou Hongcai , zhang Xusheng , Song Lili , Ding Ling , Chen Long , Ma Weihu 
Published: January 2024

Abstract

More and more studies have shown that sulfur metabolism plays an important role in various cancers, but not much research has been done on Liver Hepatocellular Carcinoma (LIHC). This study aimed to discovered genes with high correlation between sulfur metabolism and LIHC. GSE148985, a dataset containing 10 experimental samples and 5 control samples was used to find differentially expressed genes (DEGs) in sulfur metabolism; and DEGs in LIHC were found from The Cancer Genome Atlas(TCGA)database. Subsequently, 11 DEGs were obtained, through various bioinformatics methods and further analysis to obtain the target genes, our results showed that the sulfur metabolism promotes the progression of LIHC. As a result, we illustrate that the sulfur metabolism promotes the progression of LIHC via the PPAR signaling pathway.
Alien fish species in the North Aegean Sea: a review of their distributions integrating unpublished fisheries data
Authors: Evangelopoulos Athanasios , Karampetsis Dimitrios , Christidis Aris , Gubili Chrysoula , Sapounidis Argyrios , Adamidou Angeliki , Kamidis Nikolaos , Koutrakis Emmanouil 
Published: January 2024

Abstract

Fisheries-dependent data and information gathered through fisheries-related scientific surveys can significantly contribute to researching the patterns and processes underlying marine biological invasions and their interactions with fisheries. This study presents an overview of the presence of non-indigenous (NIS) fish species in the North Aegean Sea, offering insights into their distributions and impact on fisheries. The findings are based on a comprehensive compilation of commercial fisheries-dependent and scientific survey data collected in Greece from 2016 to 2023, along with an up-to-date systematic review of the international scientific literature. The study resulted in the identification of 37 non-indigenous fish species, including several recorded for the first time in the area. The results suggest that fish NIS invasions in the North Aegean Sea are dynamic: While most species were classified as casual, and the frequencies of occurrence as well as the quantities in commercial fisheries catches of established species are smaller than in the South Aegean Sea, an increasing trend in species introductions, extent of occurrence, and the area of occupancy of several species was identified. The significance of non-indigenous fish species is growing in relevance to commercial fisheries in the study area, especially in the Northeastern Aegean Sea. There, fish NIS catches are increasing, and new species of potential commercial interest have emerged in the last few years.
The distribution and drivers of tree cover in India
Authors: Gopalakrishna Trisha , Rifai Sami , Ratnam Jayashree , Menor Imma Oliveras , Stevens Nicola , Malhi Yadvinder 
Published: January 2024

Abstract

The distribution of forest and savanna biomes and the role of resources (climate and soil) and disturbances (fire and herbivory) in determining tree-grass dynamics remains elusive and variable across geographies. This is especially problematic in Indian savannas which have been historically misclassified as degraded forests and are targeted for tree-planting. Here, we examine biome distribution and determinants through the lens of tree cover across India. Our analyses reveal four distinct zones of differing tree cover, with intermediate zones containing savanna vegetation. Rainfall seasonality determines maximum possible tree cover non-linearly. Once rainfall seasonality is factored out, soil sand fraction and topography partially explain residual variation of tree cover. High domestic livestock herbivory and other anthropogenic pressures reduce tree cover. Lastly, lack of detectable fires precludes robust conclusions about the relationship between fire and tree cover. By considering these environmental drivers in restoration planning, we can improve upon simplistic tree planting initiatives that may be detrimental to Indian savannas.
Stability and inter-family associations of hair endocannabinoid and N-acyl-ethanolamines across the perinatal period in mothers, fathers, and children
Authors: Bergunde Luisa , Steudte-Schmiedgen Susann , Karl Marlene , Jaramillo Isabel , Gao Wei , von Soest Tilmann , Garthus-Niegel Susan 
Published: January 2024

Abstract

Analysis of endocannabinoids (ECs) and endocannabinoid-related compounds (ERCs) in hair is assumed to retrospectively assess long-term EC/ERC concentrations. To inform their use, this study investigated stability of EC/ERC hair concentrations in mothers, fathers, and their children across the perinatal period as well as associations between family members. In a prospective cohort study, EC (AEA, 1-AG/2-AG) and ERC (SEA, PEA, OEA) levels were quantified in hair samples taken four times in mothers (n =336)and their partners (n =225) from pregnancy to two years postpartum and in offspring (n =319) from shortly after birth to two years postpartum. Across the perinatal period, maternal and paternal hair ECs/ERCs showed fair-to-good multiple-test consistency and variable relative stability, and inconsistent absolute stability for mothers. Regarding children, hair ECs/ERCs evidenced poor multiple-test consistency, no absolute stability, and either no or variable relative stability. Hair ECs/ERCs were significantly related across the perinatal period within couples and parent-child dyads. Findings suggest hair ECs/ERCs during the perinatal period possess some trait-like stability in adults, highlighting the utility of hair analysis. The first two years of life may be a dynamic phase for the endocannabinoid system in children, potentially characterized by endocannabinoid system synchrony within the family.
Frequency of Cul-de-sac Obliteration in Surgery for Pelvic Organ Prolapse: A Retrospective Analysis
Authors: Hirata Go , Miyagi Etsuko , Maruyama Yasuyo , Ishikawa Rena , Hirabuki Tomoo 
Published: January 2024

Abstract
Introduction and Hypothesis: We aimed to clarify the frequency of cul-de-sac obliteration in patients undergoing POP surgery.
Methods: We retrospectively reviewed patients who underwent laparoscopic POP surgery at our hospital between April 2017 and September 2021.
Results: In total, 191 cases were included in the analysis. Ten patients (5.2%) had cul-de-sac obliteration. No difference in age (73 years vs. 72 years, P = 0.99), parity (2 vs. 2, P = 0.64), or body mass index (BMI) (25.7kg/m2 vs. 24.7kg/m2, P = 0.34) was observed between the cul-de-sac obliteration and normal groups. No significant differences were observed in the rate of previous abdominal surgery (50.0% vs. 32.6%, P = 0.46), rate of POP – quantification system (POP-Q) ≥2 posterior prolapse (40.0% vs. 46.4%, P = 0.98), and effect of defecation symptoms on the prolapse quality of life (p-QOL) score (vaginal bulge emptying bowels: 2.5 vs. 3.5, P = 0.15; empty bowel feeling: 3 vs. 3, P = 0.72, constipation: 3.5 vs. 3, P = 0.58; straining to open bowels: 3.5 vs. 3, P=0.82; empty bowels with fingers: 1 vs. 1, P = 0.55) between the cul-de-sac obliteration and normal groups. Multivariate analysis of risk factors for the cul-de-sac obliteration was performed for age, number of births, previous abdominal surgery, and presence of rectocele; however no significant risk factors were extracted.
Conclusion: Predicting cul-de-sac obliteration preoperatively in patients undergoing POP surgery based on age, number of previous surgeries, previous abdominal surgeries, rectocele, and defecation symptoms is difficult.
A simple and sequential strategy for the introduction of complexity and hierarchy in hydrogen-bonded organic (HOFs) crystals for environmental applications
Authors: Fernández Antonio , Halliwell Chris , Jolley Kenny , Yendall Keith , Elsegood Mark R.J. , Parkinson Gary 
Published: January 2024

Abstract
Hydrogen-bonded organic frameworks (HOFs) are a new class of crystalline porous organic molecular materials (POMMs) with great potential for a diverse range of applications. HOFs face common challenges to POMMs, and in general to purely organic crystals, that is, the difficulty of integrating multiple hierarchies in crystals. Herein, we proposed a simple and sequential strategy for the formation of hierarchical HOFs, including combined hierarchies in composition, architecture, and porosity. The strategy is based on controlling the assembly conditions, avoiding the use of any surface functionalization or template and obtaining hierarchical crystalline porous structures in an easy manner. As proof of concept, we demonstrate that hierarchical HOF crystals can be used to assemble crystals with superhydrophobicity and trapping abilities for the capture of persistent water contaminants such as oils and microplastics. We expect that this strategy could serve as inspiration for the construction of more intricated multiscale structures that could greatly expand the library of HOFs materials.
Effects of exogenous organic acids and biological substrates on the structural characteristics of soil bacterial communities in coastal mudflat soils of salt-tolerant forage growth field
Authors: xiaoyu Liu , Liang Zhong , Ruixue Yang , Huiyan Wang , Xinbao Liu , Wei Xue , He Yang , Yixin Shen , Jianlong Li , Zhengguo Sun 
Published: January 2024

Abstract
Aims
The high salinity of soil, nutrient scarcity, and poor aggregate structure limit the exploitation and utilization of coastal mudflat resources and the sustainable development of saline soil agriculture. In this paper, the effects of applying exogenous organic acids combined with biological substrate on the composition and diversity of soil bacterial community were studied in moderately saline mudflats in Jiangsu Province.
Methods
A combination of three exogenous organic acids (humic acid, fulvic acid, and citric acid) and four biological substrates (cottonseed hull, cow manure, grass charcoal, and pine needle) was set up. A total of 120 kg ha− 1 of organic acids and 5000 kg ha− 1 of substrates were used, plus two treatments, CK without application of organic acids and substrates and CK0 in bare ground, for a total of 14 treatments.
Results
No significant difference was found in the alpha diversity of soil bacterial community among all treatments (P > 0.05), with the fulvic acid composite pine needle (FPN) treatment showing the largest increase in each index. The beta diversity differed significantly (P ≤ 0.05) among all treatments, and the difference between citric acid–grass charcoal (CGC) and CK treatments was greater than that of other treatments. All treatments were effective in increasing the number of bacterial ASVs and affecting the structural composition of the community. Citric acid–cow manure, FPN, and CGC treatments were found to be beneficial for the relative abundance of Proteobacteria, Chloroflexi, and Actinobacteria, respectively. By contrast, all treatments triggered a decrease in the relative abundance of Acidobacteria. The changes in soil bacterial communities were closely related to the changes in soil salt alkali and nutrient characteristics induced by the addition of exogenous organic acids and biological substrates.
Conclusions
Adding exogenous organic acids and biological substrates provides a relatively independent microenvironment and sufficient nutrients for the life activities of different energy-type bacteria. It regulates the species composition and functional characteristics of bacterial communities by changing the structural characteristics of these communities in mudflats.
Social alienation and self-care ability in old age among rural empty-nest elderly multiple mediating effects through psychological resilience and subjective well-being
Authors: Jiang Zhaoquan , Sun Qi , Zhang Huijun , Zhou Shixue 
Published: January 2024

Abstract
Background
This study aims to explore the roles of psychological resilience and subjective well-being as multiple mediators in the relationship between social alienation and the ability for self-care in elderly individuals living alone in rural areas, particularly focusing on the empty-nest segment of this population.
Methods
From February 17, 2021, to April 20, 2023, A multistage stratified sampling approach was utilized to conduct a survey among 425 elderly individuals (aged 60 and above) living in rural areas without the company of their children, commonly referred to as 'empty-nesters'. These participants were recruited from rural areas of Liaoning Province, China. The questionnaire included the Generalized Social Alienation Scale, the Psychological Resilience Scale, the Subjective Well-being Scale, and the Self-care Ability In Old Age Scale. The analysis was designed to define the characteristics of the sample. We employed linear regression to examine how social alienation influences self-care capabilities in the elderly. To assess the compound mediating effects of psychological resilience and subjective well-being, the PROCESS macro (Model 6) was utilized.
Results
Social alienation significantly impacts self-care ability in the elderly living alone in rural areas, with a direct effect size of β = -0.678 (95% CI = -0.750–0.607), accounting for 66.67% of the total influence. Additionally, three indirect pathways play a role in shaping self-care ability in old age: 1) The psychological resilience route, contributing 42.37% of the total effect (β=-0.431, 95% CI=-0.515–-0.350); 2) The subjective well-being route, adding 4.32% to the total effect (β = 0.044, 95% CI = 0.010–0.089); and 3) A combined pathway involving both psychological resilience and subjective well-being, which adds 4.71% to the overall effect (β = 0.048, 95% CI = 0.029–0.073). The cumulative mediating effect of these pathways is 33.33%.
Conclusions
In rural areas, the well-being and self-care capabilities of older adults living alone are significantly influenced by their psychological resilience and sense of subjective well-being. As such, it's imperative for healthcare professionals and relevant stakeholders to focus on the mental health and psychological resilience of these individuals. By doing so, and by prioritizing their subjective well-being, targeted interventions can be effectively implemented to bolster the resilience and overall happiness of these elderly members of our rural communities.