bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrity and miss-grouping as support for clusters in agglomerative hierarchical methods—the r-package octopucs
Authors: MacGregor-Fors Ian , Guevara Roger 
Published: August 2024

ABSTRACTThe hierarchical clustering of communities based on species’compositional similarity (and abundance or frequency) is standard in community ecology to unveil large-scale patterns and underlay environmental causes of differentiation among communities. Often, the threshold to discretize clusters is arbitrary despite the existence of methods that minimize this bias. Most available techniques use the exact repeatability of clusters’ memberships under resampling protocols to define robust groups. Here, we propose a novel method to yield cluster support throughout the topology of hierarchical analyses. We acknowledge that the observed dataset may be biased. Instead of using the observed topology as a reference to work out the groups’ support, we compiled a consensus topology. Then, we borrowed the ecological concepts of reciprocal complementarities between a pair of communities and translated them into cluster integrity and contamination. This procedure allows for building support for groups even when there is a partial membership match after resampling the dataset. In addition, we present the R package octopucs in which we implemented the method reported here. Compared with other methods, the new proposal robustly detected changes in the group memberships, resulting in considerable differences in the pattern of supported clusters.
Buzz Pollination: Investigations of Pollen Expulsion using the Discrete Element Method
Authors: Boucher-Bergstedt Caelen , Jankauski Mark , Johnson Erick 
Published: August 2024

AbstractBuzz pollination involves the release of pollen from, primarily, poricidal anthers through vibrations generated by certain bee species. Despite previous experimental and numerical studies, the intricacies of pollen dynamics within vibrating anthers remain elusive due to the challenges in observing these small-scale, opaque systems. This research employs the discrete element method (DEM) to simulate the pollen expulsion process in vibrating anthers. By exploring various frequencies and displacement amplitudes, a correlation between the maximum jerk of anther walls and the initial rate of pollen expulsion is observed under translating oscillations. This study highlights that while increased vibration intensity enhances pollen release, the rate of increase diminishes at higher intensities. Our findings also reveal the significant role of pollen-pollen interactions, which account for upwards of one-third of the total collisions. Comparisons between poricidal and pseudoporicidal anther geometries suggest that pore size and shape also influence expulsion rates. This research provides a foundation for more comprehensive models that can incorporate additional factors such as cohesion, adhesion, and Coulomb forces, paving the way for deeper insights into the mechanics of buzz pollination and its variability across different anther types and vibration parameters.
Factors affecting the individual probability of infection with a prevalent pathogen (Mycoplasma) and the effect on Griffon vultures’ movement behavior
Authors: Anglister Nili , Crafton Miranda May , Avraham On , Acácio Marta , Vaadia Gideon , Hatzofe Ohad , Miller Yigal , Mikula Inna , Pinter-Wollman Noa , Lysnyansky Inna , Spiegel Orr 
Published: August 2024

AbstractMycoplasmas are known as commensals and pathogenic bacteria of various raptor species causing clinical or subclinical infections. However, little is known about the prevalence of mycoplasma in captive and wild raptors and its significance to their health. In Israel, the Griffon vulture (Gyps fulvus; hereafter Griffons) is considered critically endangered, and its intensive management program includes population monitoring and restocking (captive-born or imported rehabilitated wild Spanish Griffons). Here we survey the prevalence ofMycoplasmaspecies in both the wild and captive populations. During 2019-2020, we collected 244 tracheal swab samples from 167 unique individuals. We used PCR analysis to identifyMycoplasmaspecies. First, we identified nine spp., including species not yet described in Israel or for Griffon vultures. Second, imported Griffons showed a higher prevalence and a different diversity of species in comparison to the local ones, suggesting that at least oneMycoplasmaspecies (Sp 18b) was introduced into the native population. Third, juvenile Griffons had a higher prevalence, different species composition, and stronger reduction in movement compared to adults, confirming the susceptibility of this group to mycoplasma infections. GPS-tracking of 60 free-ranging individuals showed that even in the absence of apparent clinical signs, Griffons infected with mycoplasma, and especially sub-adults flew less (shorter distances and periods). These findings underscore the importance of considering potential pathogen introductions in population reinforcement and reintroduction initiatives, providing valuable insights for similar conservation programs globally. Further, they demonstrate the potential of long-term tracking for detecting subclinical effects that are unnoticeable in clinical examination.
SeuratExtend: Streamlining Single-Cell RNA-Seq Analysis Through an Integrated and Intuitive Framework
Authors: Hua Yichao , Weng Linqian , Zhao Fang , Rambow Florian 
Published: August 2024

ABSTRACTSingle-cell RNA sequencing (scRNA-seq) has revolutionized the study of cellular heterogeneity, but the rapid expansion of analytical tools has proven to be both a blessing and a curse, presenting researchers with significant challenges. Here, we present SeuratExtend, a comprehensive R package built upon the widely adopted Seurat framework, which streamlines scRNA-seq data analysis by integrating essential tools and databases. SeuratExtend offers a user-friendly and intuitive interface for performing a wide range of analyses, including functional enrichment, trajectory inference, gene regulatory network reconstruction, and denoising. The package seamlessly integrates multiple databases, such as Gene Ontology and Reactome, and incorporates popular Python tools like scVelo, Palantir, and SCENIC through a unified R interface. SeuratExtend enhances data visualization with optimized plotting functions and carefully curated color schemes, ensuring both aesthetic appeal and scientific rigor. We demonstrate SeuratExtend’s performance through case studies investigating tumor-associated high-endothelial venules and autoinflammatory diseases, and showcase its novel applications in pathway-Level analysis and cluster annotation. SeuratExtend empowers researchers to harness the full potential of scRNA-seq data, making complex analyses accessible to a wider audience. The package, along with comprehensive documentation and tutorials, is freely available at GitHub, providing a valuable resource for the single-cell genomics community.Practitioner PointsSeuratExtend streamlines scRNA-seq workflows by integrating R and Python tools, multiple databases (e.g., GO, Reactome), and comprehensive functional analysis capabilities within the Seurat framework, enabling efficient, multi-faceted analysis in a single environment.Advanced visualization features, including optimized plotting functions and professional color schemes, enhance the clarity and impact of scRNA-seq data presentation.A novel clustering approach using pathway enrichment score-cell matrices offers new insights into cellular heterogeneity and functional characteristics, complementing traditional gene expression-based analyses.
Patient-specific therapeutic benefit of MuSK agonist antibody ARGX-119 in MuSK myasthenia gravis passive transfer models
Authors: Lim Jamie L. , Jensen Stine Marie , Plomp Jaap J. , Vankerckhoven Bernhardt , Kneip Christa , Coppejans Rani , Steyaert Christophe , Moens Kathleen , De Clercq Lieselot , Tannemaat Martijn R. , Ulrichts Peter , Silence Karen , van der Maarel Silvère M. , Vergoossen Dana L.E. , Vanhauwaert Roeland , Verschuuren Jan. J. , Huijbers Maartje G. 
Published: August 2024

AbstractMuscle-specific kinase (MuSK) orchestrates establishment and maintenance of neuromuscular synapses, which enable muscle contraction. Autoantibodies targeting MuSK cause myasthenia gravis (MG), a disease characterized by fatigable skeletal muscle weakness which requires chronic immunosuppressive treatment and ventilatory support at some point in ∼30% of patients. MuSK autoantibodies are predominantly IgG4 and are bispecific, functionally monovalent antibodies due to Fab-arm exchange. Through monovalent binding, MuSK IgG4 autoantibodies act as antagonists on the MuSK signalling pathway, impairing neuromuscular synaptic function. In contrast, bivalent MuSK antibodies act as agonists of the MuSK signalling pathway. Since symptoms in MuSK MG are largely caused by antagonistic monovalent MuSK antibodies, we hypothesized that a bivalent MuSK agonist could rescue MuSK MG, bypassing the need for generalized immunosuppression. In this study, we investigated whether an agonist antibody targeting the Frizzled-like domain of MuSK, ARGX-119, can ameliorate disease in MuSK MG models induced by passive transfer of polyclonal IgG4 from unrelated patients. For each patient material we first established the minimal dose for a progressive MG phenotype based on muscle function tests. ARGX-119 significantly improved survival and muscle weakness in a mouse model induced by one patient material, but not by three others. Mechanistically, this patient-specific efficacy could not be explained by autoantibody epitope specificity, titer or competition for ARGX-119 binding, but rather correlated to the presence of MuSK activating antibodies in some patients. We further provide evidence that anin vitroassay may predict which patients potentially benefit from ARGX-119 and that this treatment, when effective in MuSK MG mice, follows a bell-shaped dose-effect curve. These results provide first proof of concept of a MuSK agonist in a clinically relevant model for MuSK MG. We anticipate this to be a starting point for investigating the therapeutic benefit of ARGX-119 in MuSK MG and other neuromuscular diseases hallmarked by neuromuscular synaptic dysfunction.Graphical abstractHighlightsMuSK agonist ARGX-119 can rescue MuSK MG in a patient-specific mannerMuSK agonism follows a bell-shaped efficacy curve in this MuSK MG mouse modelVariation in ARGX-119 efficacy between patient models is not explained by competition for binding on MuSK, but rather appears related to an agonistic fraction of patient antibodiesAnin vitroassay is potentially predictive for treatment efficacy of the MuSK agonist
Socially driven negative feedback regulates activity and energy use in ant colonies
Authors: Porfiri Maurizio , Abaid Nicole , Garnier Simon 
Published: August 2024

ABSTRACTDespite almost a century of research on energetics in biological systems, we still cannot explain energy regulation in social groups, like ant colonies. How do individuals regulate their collective activity without a centralized control system? What is the role of social interactions in distributing the workload amongst group members? And how does the group save energy by avoiding being constantly active? We offer new insight into these questions by studying an intuitive compartmental model, calibrated with and compared to data on ant colonies. The model describes a previously unexplored balance between positive and negative social feedback driven by individual activity: when activity levels are low, the presence of active individuals stimulates inactive individuals to start working; when activity levels are high, however, active individuals inhibit each other, effectively capping the proportion of active individuals at any one time. Through the analysis of the system stability, we demonstrate that this balance results in energetic spending at the group level growing proportionally slower than the group size. Our finding is reminiscent of Kleiber’s law of metabolic scaling in unitary organisms and highlights the critical role of social interactions in driving the collective energetic efficiency of group-living organisms.
Rapid reprogramming and stabilisation of homoeolog expression bias in hexaploid wheat biparental populations
Authors: Glombik Marek , Arunkumar Ramesh , Burrows Samuel , Mogg Sophie Louise , Wang Xiaoming , Borrill Philippa 
Published: August 2024

SummaryDifferences in the relative level of expression of homoeologs, known as homoeolog expression bias (HEB), are widely observed in allopolyploids. While the evolution of homoeolog expression bias through hybridisation has been characterised, on shorter timescales the extent to which homoeolog expression bias is preserved or altered between generations remains elusive.Here we use biparental mapping populations of hexaploid wheat (Triticum aestivum) with a common Paragon parent to explore the inheritance of homoeolog expression bias in the F5generation.We found that homoeolog expression bias is inherited for 26-27% of triads in both populations. Most triads (∼70%) conserved a similar homoeolog expression bias pattern as one or both parents. Inherited patterns were largely driven by changes in the expression of one homoeolog, allowing homoeolog expression bias in subsequent generations to match parental expression. Novel patterns of homoeolog expression bias occurred more frequently in the biparental population from a landrace x elite cross, than in the population with two elite parents.These results demonstrate that there is significant reprogramming and stabilisation of homoeolog expression bias within a small number of generations that differs significantly based on the parental lines used in the crossing.
Involvement of OsS40-14 in ROS and plastid organization related regulatory networks of dark-induced leaf senescence in rice
Authors: Habiba  , Fan Chunlan , Hong Wuqiang , Shi Ximiao , Wang Xiaowei , Wang Weiqi , Lin Wenfang , Li Yanyun , Ain Noor ul , Miao Ying , Zheng Xiangzi 
Published: August 2024

AbstractDark-induced senescence triggers significant metabolic changes that recycle resources and ensure plant survival. In this study, we identified a transcription factor OsS40-14 in rice, which can form homo-oligomers. Theoss40-14knockout mutants exhibited stay-green phenotype of primary leaf and flag leaf during dark-induced condition, with substantial retention of chlorophylls and photosynthetic capacity as well as remarkably reduced reactive oxygen species (ROS), whileOsS40-14overexpressing transgenic lines (oeOsS40-14) showed an accelerated senescence phenotype under dark-induced leaf senescence conditions. Transcriptome analysis revealed that when the detached leaves ofoss40-14and WT were treated in darkness condition for 72 hours, 1585 DEGs (|Log2FC| ≥1, P value<0.05) were reprogrammed inoss40-14relative to WT. CUT&Tag-seq analysis in protoplast transient expression of OsS40-14 system showed that OsS40-14 was 40.95% enriched in the transcription start site (TSS) of the genome. Sequence clustering analysis showed that OsS40-14 protein was mainly enriched and bound to TACCCACAAGACAC conserved elements. The seed region “ACCCA” of OsS40 proteins was identified by single nucleotide mutagenesis EMSA. The integrative analysis of transcriptome and CUT&Tag-seq datasets showed 153 OsS40-14-targeted DEGs, they mainly enriched in plastid organization and photosynthesis process at dark-induced condition inoss40-14relative to WT. Among them, eleven candidate targets of OsS40-14 such as Glucose 6-phosphate/phosphate translocator, Na+/H+ antiporter, Catalase, Chitinase 2, Phosphate transporter 19, OsWAK32, and OsRLCK319 were directly targeted and upregulated confirmed by ChIP-PCR and RT-qPCR. It demonstrates a novel model of OsS40-14 mediating macromolecule metabolism and nutrient recycling controls the plastid organization during dark-induced leaf senescence.Significant statementInvolvement of OsS40-14 in macromolecule catabolism, nutrient recycling, and ROS homeostasis revealed a plastid organization defection of dark-induced senescence in rice
Resources modulate developmental shifts but not infection tolerance upon coinfection in an insect system
Authors: Schulz Nora K.E. , Asgari Danial , Liu Siqin , Birnbaum Stephanie S.L. , Williams Alissa M. , Prakash Arun , Tate Ann T. 
Published: August 2024

AbstractEnergetic resources fuel immune responses and parasite growth within organisms, but it is unclear whether energy allocation is sufficient to explain changes in infection outcomes under the threat of multiple parasites. We manipulated diet in flour beetles (Tribolium confusum) infected with two natural parasites to investigate the role of resources in shifting metabolic and immune responses after single and co-infection. Our results suggest that gregarine parasites alter the within-host energetic environment, and by extension juvenile development time, in a diet- dependent manner. Gregarines do not affect host resistance to acute bacterial infection but do stimulate the expression of an alternative set of immune genes and promote damage to the gut, ultimately contributing to reduced survival regardless of diet. Thus, energy allocation is not sufficient to explain the immunological contribution to coinfection outcomes, emphasizing the importance of mechanistic insight for predicting the impact of coinfection across levels of biological organization.
Per- and Poly-fluoroalkyl Substances (PFAS) in Circulation in a Canadian Population: Their Association with Serum Liver Enzyme Biomarkers and Piloting a Novel Method to Reduce Serum PFAS
Authors: Schlezinger Jennifer J. , Bello Anila , Mangano Kelsey M. , Biswas Kushal , Patel Paridhiben P. , Pennoyer Emily H. , Wolever Thomas M.S. , Heiger-Bernays Wendy J. , Bello Dhimiter 
Published: August 2024

AbstractExtensive use of per- and polyfluoroalkyl substances (PFAS) has resulted in their ubiquitous presence in human blood. PFAS exposures have been associated with multiple adverse human health effects including increased risk of liver damage, elevated serum lipids, impaired vaccine response, adverse birth outcomes and cancer. Biomonitoring studies have focused on measuring long-chain PFAS, but these are being replaced by shorter chain PFAS and PFAS with alternative structures, resulting in incomplete understanding of human exposures. Here, we take advantage of serum samples collected as part of a clinical trial testing the efficacy of a dietary fiber intervention to reduce serum cholesterol to investigate exposure to legacy and replacement PFAS chemicals in Canadian participants. Serum samples were collected from 72 participants in 2019-2020 at baseline and after 4 weeks of the intervention and were analyzed for 17 PFAS species. The highest geometric mean concentrations of PFAS measured at baseline corresponded to PFOSA (7.1 ng/ml), PFOS (4.2, ng/ml), PFOA (1.8 ng/ml) and PFHxS (1.3 ng/ml). Short chain PFAS including PFBuA, PFHxS and/or PFHpA were detected in 100% of participants and GenX was detected in 70% of participants. Analyses of associations between PFAS serum concentrations and biomarkers of adverse health outcomes showed the PFBuA, PFHxA, PFDA and PFOSA were associated with higher serum gamma-glutamyl transferase concentrations but not with measures of serum total or low-density lipoprotein cholesterol. Comparison of PFAS concentrations at baseline and after a 4-week follow-up showed that total PFAS concentrations decreased in both the control and cholesterol intervention groups. However, the suite of PFAS of concern identified by the United States National Academies of Sciences, Engineering, and Medicine, significantly decreased only in the cholesterol intervention group. This observation suggests that a dietary fiber intervention may reduce PFAS body burden, but future intervention studies need to control for PFAS exposure sources and extend beyond 4 weeks. Overall, the results show that exposures to short-chain and alternative PFAS are common in this Canadian population.
Improving Tuberculosis Detection in Chest X-ray Images through Transfer Learning and Deep Learning: A Comparative Study of CNN Architectures
Authors: Mirugwe Alex , Tamale Lillian , Nyirenda Juwa 
Published: August 2024

AbstractIntroductionTuberculosis remains a significant global health challenge, necessitating more efficient and accurate diagnostic methods.MethodsThis study evaluates the performance of various convolutional neural network (CNN) architectures— VGG16, VGG19, ResNet50, ResNet101, ResNet152, and Inception-ResNet-V2—in classifying chest X-ray (CXR) images as either normal or TB-positive. The dataset comprised 4,200 CXR images, with 700 labeled as TB-positive and 3,500 as normal. We also examined the impact of data augmentation on model performance and analyzed the training times and the number of parameters for each architecture.ResultsOur results showed that VGG16 outperformed the other models across all evaluation metrics, achieving an accuracy of 99.4%, precision of 97.9%, recall of 98.6%, F1-score of 98.3%, and AUC-ROC of 98.25%. Surprisingly, data augmentation did not improve performance, suggesting that the original dataset’s diversity was sufficient. Furthermore, models with large numbers of parameters, such as ResNet152 and Inception-ResNet-V2, required longer training times without yielding proportionally better performance.DiscussionThese findings highlight the importance of selecting the appropriate model architecture based on task-specific requirements. While more complex models with larger parameter counts may seem advantageous, they do not necessarily offer superior performance and often come with increased computational costs.ConclusionThe study demonstrates the potential of simpler models such as VGG16 to effectively diagnose TB from CXR images, providing a balance between performance and computational efficiency. This insight can guide future research and practical implementations in medical image classification.
Relative income and its relationship with mental health in UK employees: a conceptual and methodological review
Authors: Croak Bethany , Grover Laura E. , Wessely Simon , Kharicha Kalpa , Lamb Danielle , Stevelink Sharon A.M. 
Published: August 2024

AbstractThe relative income hypothesis theorises that one’s earnings relative to others exert a greater influence on subjective wellbeing than absolute income. Understanding the relationship between relative income and mental health could contribute to employee wellbeing. This review narratively synthesised the defining features and measurement of relative income, and its impact on mental health among UK employees. Systematic searches of qualitative and quantitative research evidence identified 13 studies. A conceptualisation of relative income revealed that an income comparison is either researcher-defined using averages or self-assessed based on a person’s perception. Having a lower income than the reference group was commonly associated with diminished wellbeing, though moderating factors (gender, income inequality and composition of reference group) are discussed.Implications for practice and policy are considered amidst the UK’s ‘cost of living crisis’ and ongoing pay disputes in various sectors.