bluuebunny/crossref_metadata_2025_split huggingface dataset:
PDG-Arena: An ecophysiological model for characterizing tree-tree interactions in heterogeneous and mixed stands
Authors: Rouet Camille , Davi Hendrik , Druel Arsène , Fady Bruno , Morin Xavier 
Published: February 2024

AbstractIn the context of the ongoing climate and biodiversity crises, mixed forest stands are increasingly considered as a sustainable management alternative to monocultures. We developed a new individual-based and process-based forest growth model, PDG-Arena, to simulate mixed forest functioning and test ecophysiological interactions among trees in mixed stands. The model builds upon the validated ecophysiological stand-scale model CASTANEA and integrates tree competition for light and water. We evaluated the performance of PDG-Arena by comparing the simulated growth with annual dendrochronological growth data from 37 common beech and silver fir monospecific and mixed plots in the French Alps. PDG-Arena showed a slightly better performance than CASTANEA when simulating even-age and monospecific forests (r2of 32.1 versus 29.5%). When using structure-diverse and species-diverse inventories, PDG-Arena performed better than CASTANEA in pure beech (38.3 versus 22.9%) and mixed stands (40.5 versus 36.3%), but not in pure fir stands (39.8 versus 42.0%). The new model also showed a significant positive effect of species mixing on gross primary production (+5.5%), canopy absorbance (+11.1%) and transpiration (+15.8%). Our results thus show that tree-level process-based models such as PDG-Arena, formally simulating interspecific interactions, can serve as a valuable tool to understand and simulate the carbon, light and water dynamics of mixed stands.
Identification of novel genes regulating the development of the palate
Authors: Bhaskar Ashwin , Astrof Sophie 
Published: February 2024

AbstractThe International Mouse Phenotyping Consortium (IMPC) has generated thousands of knockout mouse lines, many of which exhibit embryonic or perinatal lethality. Using micro-computed tomography (micro-CT), the IMPC has created and publicly released 3D image datasets of embryos from these lethal and subviable lines. In this study, we leveraged this dataset to screen homozygous null mutants for anomalies in secondary palate development. We analyzed optical sections from 2,987 embryos at embryonic days E15.5 and E18.5, representing 484 homozygous mutant lines. Our analysis identified 45 novel genes implicated in palatogenesis. Gene set enrichment analysis highlighted biological processes and pathways relevant to palate development and uncovered 18 genes jointly regulating the development of the eye and the palate. These findings present a valuable resource for further research, offer novel insights into the molecular mechanisms underlying palatogenesis, and provide important context for understanding the etiology of rare human congenital disorders involving simultaneous malformations of the palate and other organs, including the eyes, ears, kidneys, and lungs.
Microbial responses to stress cryptically alter natural selection on plants
Authors: Bolin Lana G. , Lau Jennifer A. 
Published: February 2024

SUMMARYMicrobial communities can rapidly respond to stress, meaning plants may encounter altered soil microbial communities in stressful environments. These altered microbial communities may then affect natural selection on plants. Because stress can cause lasting changes to microbial communities, microbes may also cause legacy effects on plant selection that persist even after the stress ceases.To explore how microbial responses to stress and persistent microbial legacy effects of stress affect natural selection, we grewChamaecrista fasciculataplants in stressful (salt, herbicide, or herbivory) or non-stressful conditions with microbes that had experienced each of these environments in the previous generation.Microbial community responses to stress generally counteracted the effects of stress itself on plant selection, thereby weakening the strength of stress as a selective agent. Microbial legacy effects of stress altered plant selection in non-stressful environments, suggesting that stress-induced changes to microbes may continue to affect selection after stress is lifted.These results suggest that soil microbes may play a cryptic role in plant adaptation to stress, potentially reducing the strength of stress as a selective agent and altering the evolutionary trajectory of plant populations.
Myosin-I Synergizes with Arp2/3 Complex to Enhance Pushing Forces of Branched Actin Networks
Authors: Xu Mengqi , Rutkowski David M. , Rebowski Grzegorz , Boczkowska Malgorzata , Pollard Luther W. , Dominguez Roberto , Vavylonis Dimitrios , Ostap E. Michael 
Published: February 2024

AbstractMyosin-Is colocalize with Arp2/3 complex-nucleated actin networks at sites of membrane protrusion and invagination, but the mechanisms by which myosin-I motor activity coordinates with branched actin assembly to generate force are unknown. We mimicked the interplay of these proteins using the “comet tail” bead motility assay, where branched actin networks are nucleated by Arp2/3 complex on the surface of beads coated with myosin-I and the WCA domain of N-WASP. We observed that myosin-I increased bead movement efficiency by thinning actin networks without affecting growth rates. Remarkably, myosin-I triggered symmetry breaking and comet-tail formation in dense networks resistant to spontaneous fracturing. Even with arrested actin assembly, myosin-I alone could break the network. Computational modeling recapitulated these observations suggesting myosin-I acts as a repulsive force shaping the network’s architecture and boosting its force-generating capacity. We propose that myosin-I leverages its power stroke to amplify the forces generated by Arp2/3 complex-nucleated actin networks.
Processing-bias correction with DEBIAS-M improves cross-study generalization of microbiome-based prediction models
Authors: Austin George I. , Kav Aya Brown , Park Heekuk , Biermann Jana , Uhlemann Anne-Catrin , Korem Tal 
Published: February 2024

AbstractEvery step in common microbiome profiling protocols has variable efficiency for each microbe. For example, different DNA extraction kits may have different efficiency for Gram-positive and -negative bacteria. These variable efficiencies, combined with technical variation, create strong processing biases, which impede the identification of signals that are reproducible across studies and the development of generalizable and biologically interpretable prediction models. “Batch-correction” methods have been used to alleviate these issues computationally with some success. However, many make strong parametric assumptions which do not necessarily apply to microbiome data or processing biases, or require the use of an outcome variable, which risks overfitting. Lastly and importantly, existing transformations used to correct microbiome data are largely non-interpretable, and could, for example, introduce values to features that were initially mostly zeros. Altogether, processing bias currently compromises our ability to glean robust and generalizable biological insights from microbiome data. Here, we present DEBIAS-M (Domain adaptation with phenotypeEstimation andBatchIntegrationAcrossStudies of theMicrobiome), an interpretable framework for inference and correction of processing bias, which facilitates domain adaptation in microbiome studies. DEBIAS-M learns bias-correction factors for each microbe in each batch that simultaneously minimize batch effects and maximize cross-study associations with phenotypes. Using benchmarks of HIV and colorectal cancer classification from gut microbiome data, and cervical neoplasia prediction from cervical microbiome data, we demonstrate that DEBIAS-M outperforms batch-correction methods commonly used in the field. Notably, we show that the inferred bias-correction factors are stable, interpretable, and strongly associated with specific experimental protocols. Overall, we show that DEBIAS-M allows for better modeling of microbiome data and identification of interpretable signals that are reproducible across studies.
Discovery of Phenyl-β-D-glucuronide Medical Function for in Vivo Producing Handheld Gas Sensor Detectable Phenol-like Breath Marker: The Future of Induced Volatolomics in Cancer Risk Pre-warning
Authors: Xue Cuili , Yan Yufei , Ni Huiyan , Yi Chenghan , Xu Yuli , Xiang Siyi , Wu Yuejun , Jin Han , Cui Daxiang 
Published: February 2024

ABSTRACTInduced volatolomics provides a promising approach for cancer risk pre-warning. Nevertheless, continues to be questioned bio-compatibility of the synthetic exogenous agents and sophisticated instrument solely detectable isotopes labeled volatile compounds restrained induced volatolomics in clinic application. Here, we report phenyl-β-D-glucuronide as a potential exogenous agent of induced volatolomics. As a nature product, phenyl-β-D-glucuronide demonstrates satisfactory bio-compatibility in pilot study and metabolizes into volatile phenol under the action of tumor micro-environment highly accumulated β-glucuronidase. For conveniently recording breath signal, handheld breath-analyzer based on electrochemical phenol sensor is developed. After administrating healthy or tumor bearing mice with phenyl-β-D-glucuronide, breath signal given by breath-analyzer is verified to be capable of not only predicting various tumor risk with specificity/sensitivity/accuracy above 94.3% in 10 min, but also speculating tumor stage.
The Impact of Gender on Pediatric Surgical Access and Outcomes in Africa
Authors: Williams Sacha , Serhan Olivia , Wang Jenny , Guindi Christian , Guadagno Elena , Trudeau Maeve , Ameh Emannuel , Lakhoo Kokila , Poenaru Dan 
Published: February 2024

AbstractIntroductionGirls, whose care is often affected by barriers steeped in gender inequity, may be at higher risk of poor surgical outcomes. This study explored the impact of gender on pediatric surgical care in Africa.MethodsDifferences in access to care and clinical outcomes for boys and girls were examined for pediatric surgical conditions that do not differ by physiological sex. A systematic review of African pediatric surgical studies ensued, followed by a random effects meta-analysis, and risk of bias assessment.ResultsOf the 12281 records retrieved, 54 were selected for review. Most studies were retrospective (57.4%), single-site (94.4%), from Egypt, Nigeria, Ghana, or Ethiopia (55.6%), focussed on gastrointestinal conditions (63.0%), published in 2010 or sooner (85.1%), had study durations of 5 years or less (68.5%), and cohorts of less than 200 children (57.4%). Sixty percent reported the outcome of mortality. Meta-analysis odds ratios revealed surgery was performed 3.6 times more often on boys (95% CI: 2.6, 4.9); and mortality was 1.6 times greater for girls (95% CI: 1.3, 2.0).ConclusionAfrican girls appear to face gender inequities in pediatric surgical care. Findings will be further explored in a mixed-methods study.Level of evidenceIHighlightsGender disparities in global surgical care have been documented in the African adult population. However gender specific differentials in surgical access and outcomes have yet to be documented for African pediatric populations.This study provides first-time evidence of gender inequity in pediatric surgical care in Africa.
Cell non-autonomous signaling through the conservedC. elegansglycopeptide hormone receptor FSHR-1 regulates cholinergic neurotransmission
Authors: Buckley Morgan , Jacob William P. , Bortey Letitia , McClain Makenzi , Ritter Alyssa L. , Godfrey Amy , Munneke Allyson S. , Ramachandran Shankar , Kenis Signe , Kolnik Julie C. , Olofsson Sarah , Adkins Ryan , Kutoloski Tanner , Rademacher Lillian , Heinecke Olivia , Alva Alexandra , Beets Isabel , Francis Michael M. , Kowalski Jennifer R. 
Published: February 2024

AbstractModulation of neurotransmission is key for organismal responses to varying physiological contexts such as during infection, injury, or other stresses, as well as in learning and memory and for sensory adaptation. Roles for cell autonomous neuromodulatory mechanisms in these processes have been well described. The importance of cell non-autonomous pathways for inter-tissue signaling, such as gut-to-brain or glia-to-neuron, has emerged more recently, but the cellular mechanisms mediating such regulation remain comparatively unexplored. Glycoproteins and their G protein-coupled receptors (GPCRs) are well-established orchestrators of multi-tissue signaling events that govern diverse physiological processes through both cell-autonomous and cell non-autonomous regulation. Here, we show that follicle stimulating hormone receptor, FSHR-1, the soleCaenorhabditis elegansortholog of mammalian glycoprotein hormone GPCRs, is important for cell non-autonomous modulation of synaptic transmission. Inhibition offshr-1expression reduces muscle contraction and leads to synaptic vesicle accumulation in cholinergic motor neurons. The neuromuscular and locomotor defects infshr-1loss-of-function mutants are associated with an underlying accumulation of synaptic vesicles, build-up of the synaptic vesicle priming factor UNC-10/RIM, and decreased synaptic vesicle release from cholinergic motor neurons. Restoration of FSHR-1 to the intestine is sufficient to restore neuromuscular activity and synaptic vesicle localization tofshr-1-deficient animals. Intestine-specific knockdown of FSHR-1 reduces neuromuscular function, indicating FSHR-1 is both necessary and sufficient in the intestine for its neuromuscular effects. Re-expression of FSHR-1 in other sites of endogenous expression, including glial cells and neurons, also restored some neuromuscular deficits, indicating potential cross-tissue regulation from these tissues as well. Genetic interaction studies provide evidence that downstream effectorsgsa-1/GαS,acy-1/adenylyl cyclase andsphk-1/sphingosine kinase and glycoprotein hormone subunit orthologs, GPLA-1/GPA2 and GPLB-1/GPB5, are important for FSHR-1 modulation of the NMJ. Together, our results demonstrate that FSHR-1 modulation directs inter-tissue signaling systems, which promote synaptic vesicle release at neuromuscular synapses.
Natural variation in infection specificity ofCaenorhabditis briggsaeisolates by two RNA viruses
Authors: Alkan Cigdem , Brésard Gautier , Frézal Lise , Richaud Aurélien , Ruaud Albane , Zhang Gaotian , Félix Marie-Anne 
Published: February 2024

AbstractAntagonistic relationships such as host-virus interactions potentially lead to rapid evolution and specificity in interactions. The Orsay virus is so far the only horizontal virus naturally infecting the nematodeC. elegans. In contrast, several related RNA viruses infect its congenerC. briggsae, including Santeuil (SANTV) and Le Blanc (LEBV) viruses. Here we focus on the host’s intraspecific variation in sensitivity to these two intestinal viruses. Many temperate-originC. briggsaestrains, including JU1264 and JU1498, are sensitive to both, while many tropical strains, such as AF16, are resistant to both. Interestingly, someC. briggsaestrains exhibit a specific resistance, such as the HK104 strain, specifically resistant to LEBV. The viral sensitivity pattern matches the strains’ geographic and genomic relationships. The heavily infected strains mount a seemingly normal small RNA response that is insufficient to suppress viral infection, while the resistant strains show no small RNA response, suggesting an early block in viral entry or replication. We use a genetic approach from the host side to map genomic regions participating in viral resistance polymorphisms. Using Advanced Intercrossed Recombinant Inbred Lines (RILs) between virus-resistant AF16 and SANTV-sensitive HK104, we detect Quantitative Trait Loci (QTLs) on chromosomes IV and III. Building RILs between virus-sensitive JU1498 and LEBV-resistant HK104 followed by bulk segregant analysis, we identify a chromosome II QTL. In both cases, further introgressions of the regions confirmed the QTLs. This diversity provides an avenue for studying virus entry, replication, and exit mechanisms, as well as host-virus specificity and the host response to a specific virus infection.
Key unprotected areas for carnivore conservation in Mexico
Authors: Gonzalez Germar , Harris Nyeema C. 
Published: February 2024

AbstractArea-based conservation remains a pivotal component of global wildlife protection efforts. Mexico hosts a diverse array of area-based approaches, encompassing protected areas (PAs) and other effective area-based conservation measures (OECMs) such as voluntary conservation areas (VCAs) and wildlife management units (UMAs). Indigenous Territories (ITs) also provide heightened conservation potential through traditional ecological knowledge systems. These conservation spaces exhibit significant variations in community involvement, national coverage, and governance. Here, we evaluate the conservation potential of these land management types for 29 terrestrial carnivores, focusing on spatial co-occurrence. We determine areas in Mexico lacking area-based protection and calculate carnivore richness per land management type. Analyzing overlap between land management types and carnivore ranges, we employ heat maps to visualize overlap occurrence and key unprotected areas. We found that across all carnivore ranges, 87% of the area remains unprotected under designated protection areas (PAs & VCAs), decreasing to 65.2% after including non-designated types (ITs and UMAs). We identified several key gaps in the protection estate for Mexican carnivores, most notably on the eastern Mexican coast in the state of Veracruz. Our findings corroborate the importance of including Indigenous Peoples and Local Communities in conservation efforts, emphasizing their contributions to the stewardship of Mexican ecosystems. As the global protected area estate continues to expand under the post-2020 global biodiversity targets, and the importance of a well-designed and diverse portfolio of practices for conservation is recognized, the need for collective action, increased collaboration and inclusivity, and effective communication amongst stakeholders becomes necessary for carnivore conservation.
Unifying approaches from statistical genetics and phylogenetics for mapping phenotypes in structured populations
Authors: Schraiber Joshua G. , Edge Michael D. , Pennell Matt 
Published: February 2024

AbstractIn both statistical genetics and phylogenetics, a major goal is to identify correlations between genetic loci or other aspects of the phenotype or environment and a focal trait. In these two fields, there are sophisticated but disparate statistical traditions aimed at these tasks. The disconnect between their respective approaches is becoming untenable as questions in medicine, conservation biology, and evolutionary biology increasingly rely on integrating data from within and among species, and once-clear conceptual divisions are becoming increasingly blurred. To help bridge this divide, we derive a general model describing the covariance between the genetic contributions to the quantitative phenotypes of different individuals. Taking this approach shows that standard models in both statistical genetics (e.g., Genome-Wide Association Studies; GWAS) and phylogenetic comparative biology (e.g., phylogenetic regression) can be interpreted as special cases of this more general quantitative-genetic model. The fact that these models share the same core architecture means that we can build a unified understanding of the strengths and limitations of different methods for controlling for genetic structure when testing for associations. We develop intuition for why and when spurious correlations may occur using analytical theory and conduct population-genetic and phylogenetic simulations of quantitative traits. The structural similarity of problems in statistical genetics and phylogenetics enables us to take methodological advances from one field and apply them in the other. We demonstrate this by showing how a standard GWAS technique—including both the genetic relatedness matrix (GRM) as well as its leading eigenvectors, corresponding to the principal components of the genotype matrix, in a regression model—can mitigate spurious correlations in phylogenetic analyses. As a case study of this, we re-examine an analysis testing for co-evolution of expression levels between genes across a fungal phylogeny, and show that including covariance matrix eigenvectors as covariates decreases the false positive rate while simultaneously increasing the true positive rate. More generally, this work provides a foundation for more integrative approaches for understanding the genetic architecture of phenotypes and how evolutionary processes shape it.
Proteus: Exploring Protein Structure Generation for Enhanced Designability and Efficiency
Authors: Wang Chentong , Qu Yannan , Peng Zhangzhi , Wang Yukai , Zhu Hongli , Chen Dachuan , Cao Longxing 
Published: February 2024

AbstractDiffusion-based generative models have been successfully employed to create proteins with novel structures and functions. However, the construction of such models typically depends on large, pre-trained structure prediction networks, like RFdiffusion. In contrast, alternative models that are trained from scratch, such as FrameDiff, still fall short in performance. In this context, we introduce Proteus, an innovative deep diffusion network that incorporates graph-based triangle methods and a multi-track interaction network, eliminating the dependency on structure prediction pre-training with superior efficiency. We have validated our model’s performance onde novoprotein backbone generation through comprehensive in silico evaluations and experimental characterizations, which demonstrate a remarkable success rate. These promising results underscore Proteus’s ability to generate highly designable protein backbones efficiently. This capability, achieved without reliance on pre-training techniques, has the potential to significantly advance the field of protein design. Codes are available athttps://github.com/Wangchentong/Proteus.
Carbon nanoparticle exposure strengthens water-relation parameters by stimulating abscisic acid pathway and aquaporins genes in rice
Authors: Kumar Aman , Lekshmi Manasa S , Kashyap Jyotiprabha , Mandal Sikha , Mishra Gayatri , Rath Jnanendra , Rout Gyana Ranjan , Panigrahi Kishore CS , Panigrahy Madhusmita 
Published: February 2024

ABSTRACTMechanism of action and molecular basis of positive growth effects including yield increase due to carbon nanoparticle (CNP) treatment in rice plants is dissected here. CNP at 500 -750 µg/mL were found to be the optimum dosages showing best seedling growth. CNP treatment resulted increase in stomata size, gaseous exchange and water use efficiency along with decrease in stomata frequency, relative humidity, internal CO2concentration. CNP treatment exerted cold tolerance in seedlings and water stress tolerance in reproductive stage. CNP-coupled with water uptake was found to be endocytosis mediated, although CNP uptake was not affected by endocytosis inhibitor application in roots. Genomic analysis resulted major involvement of ABA pathway and stomata size and frequency genes inArabidopsisand rice. Elevated endogenous ABA in rice seedlings and flag leaves along with increased expression of ABA biosynthetic genes inArabidopsisand riceAtNCED3,AtNCED6,OsNCED1confirmed increased ABA synthesis. Negative regulators of ABA pathway,OsSNRK2down-regulation and up-regulation of stomagen (OsEPFL9) reconfirmed ABA’s involvement. CNP treatment resulted water stress tolerance by maintaining lower stomatal conductance, transpiration rate and higher relative water content. Increased ABA (OsSNRK1,OsSNRK2) and aquaporin (OsPIP2-5) genes’ expressions could explain the better water stress tolerance in rice plants treated with CNP. Altogether, due to thermomorphogenesis, down-regulation of Phytochrome B resulted altered the ABA pathway and stomatal distribution with size. These changes resulted improved water relation parameters and WUE showing improvement in yield. Detailed mechanism of action of CNP in abiotic stress tolerance can be exploited in in nano-agriculture.