bluuebunny/crossref_metadata_2025_split huggingface dataset:
Priority effects of heritable seed-borne bacteria drive early assembly of the wheat rhizosphere microbiome
Authors: Garrido-Sanz Daniel , Keel Christoph 
Published: October 2024

AbstractMicrobial communities play a critical role in supporting plant health and productivity, making the ability to obtain reproducible plant-associated microbiomes an essential asset for experimentally testing hypotheses related to microbiome manipulation and fundamental principles governing community dynamics. We used a sequential propagation strategy to generate a complex and reproducible wheat rhizosphere microbiome (RhizCom) that was shaped by host selection and periodic habitat resetting. Heritable seed-borne rhizosphere bacteria (SbRB) emerged as the dominant microbiome source after coalescing with the soil community, driven by priority effects and efficient niche exploitation during early habitat development. Functional analyses revealed that niche partitioning through the ability of SbRB to degrade specific saccharides and niche facilitation contributed to the assembly of the RhizCom. Our results advance our understanding of the principles governing microbial community dynamics in early plant development and provide strategies for future microbiome manipulation aimed at improving crop productivity and health.
Towards a unifying phylogenomic framework for tailed phages
Authors: Weinheimer Alaina R. , Ha Anh D. , Aylward Frank O. 
Published: October 2024

AbstractBackgroundClassifying viruses systematically has remained a key challenge of virology due to the absence of universal genes and vast genetic diversity of viruses. In particular, the most dominant and diverse group of viruses, the tailed double-stranded DNA viruses of prokaryotes belonging to the class Caudoviricetes, lack sufficient homology in the genetic machinery that unifies them to reconstruct inclusive, stable phylogenies of these genes. While previous approaches to organize tailed phage diversity have managed to distinguish various taxonomic levels, these methods are limited in scalability and reproducibility, and they do not include modes of evolution, like gene gains and losses.ResultsHere, we present a novel, comprehensive and reproducible framework for examining evolutionary relationships of tailed phages. In this framework, we compare phage genomes based on presences and absences of a fixed set of gene families which is used as binary trait data that is input into maximum likelihood models, which include heterogeneous rates of trait losses and gains. Our resulting phylogeny stably recovers known taxonomic families of tailed phages, with and without the inclusion of metagenomic phages. We also quantify the mosaicism of replication and structural genes among known families. Our results suggest that these exchanges likely underpin the emergence of new families. Additionally, we apply this framework to large phages (>100 kilobases) to map emergences of traits associated with genome expansion.ConclusionTaken together, this evolutionary framework for charting and organizing tailed phage diversity improves the systemization of phage taxonomy, which can unify phage studies and advance our understanding of their evolution.
Transcriptomic landscape identifies two unrecognized ependymoma subtypes and novel pathways in medulloblastoma
Authors: Arora Sonali , Nuechterlein Nicholas , Jensen Matt , Glatzer Gregory , Sievers Philipp , Varadharajan Srinidhi , Korshunov Andrey , Sahm Felix , Mack Stephen C. , Taylor Michael D. , Holland Eric C 
Published: October 2024

AbstractMedulloblastoma and ependymoma are prevalent pediatric central nervous system tumors with significant molecular and clinical heterogeneity. We collected bulk RNA sequencing data from 888 medulloblastoma and 370 ependymoma tumors to establish a comprehensive reference landscape. Following rigorous batch effect correction, normalization, and dimensionality reduction, we constructed a unified landscape to explore gene expression, signaling pathways, gene fusions, and copy number variations. Our analysis revealed distinct clustering patterns, including two primary ependymoma compartments, EPN-E1 and EPN-E2, each with specific gene fusions and molecular signatures. In medulloblastoma, we achieved precise stratification of Group 3/4 tumors by subtype and in SHH tumors by patient age. Our landscape serves as a vital resource for identifying biomarkers, refining diagnoses, and enables the mapping of new patients’ bulk RNA-seq data onto the reference framework to facilitate accurate disease subtype identification. The landscape is accessible via Oncoscape, an interactive platform, empowering global exploration and application.One Sentence SummaryA landscape built using only Transcriptomic analysis for medulloblastoma and ependymoma reveals novel insights about subtype specific biology.
Hearing thresholds in the bat Carollia perspicillata vary by sex but not age
Authors: Molano Olivia , Dale Emily , Portfors Christine , Coffin Allison 
Published: October 2024

AbstractBats rely heavily on auditory perception for critical behaviors including navigation (echolocation) and conspecific communication. However, there is little information on the impacts of age and sex on the bat auditory system. Here, we used auditory brainstem response recordings to measure auditory thresholds inCarollia perspicillata(Seba’s short-tailed bat). We did not detect an age-related threshold shift at the age range examined (1-8 years old), suggesting that bats may be relatively resistant to age-related hearing loss. We had considerably more young bats (aged 1-2 years) than older animals (aged 4-8 years) so our results should be interpreted with caution. However, they are consistent with other studies showing that bats exhibit fewer signs of aging relative to other small mammals. In addition, we show significantly lower auditory thresholds among females compared to age-matched males, similar to sex differences reported in other mammals. Finally, we found increased thresholds in a single non-pigmented bat relative to age- and sex-matched conspecifics. While preliminary, this finding suggests that pigmentation may be important for inner ear function in bats, similar to results from other mammals.
The spatio-temporal dynamics of phoneme encoding in aging and aphasia
Authors: Kries Jill , De Clercq Pieter , Vandermosten Maaike , Gwilliams Laura 
Published: October 2024

AbstractDuring successful language comprehension, speech sounds (phonemes) are encoded within a series of neural patterns that evolve over time. Here we tested whether these neural dynamics of speech encoding are altered for individuals with a language disorder. We recorded EEG responses from individuals with post-stroke aphasia and healthy age-matched controls (i.e., older adults) during 25 min of natural story listening. We estimated the duration of phonetic feature encoding, speed of evolution across neural populations, and the spatial location of encoding over EEG sensors. First, we establish that phonetic features are robustly encoded in EEG responses of healthy older adults. Second, when comparing individuals with aphasia to healthy controls, we find significantly decreased phonetic encoding in the aphasic group after shared initial processing pattern (0.08-0.25s after phoneme onset). Phonetic features were less strongly encoded over left-lateralized electrodes in the aphasia group compared to controls, with no difference in speed of neural pattern evolution. Finally, we observed that phonemes with high uncertainty about word identity were encoded longer in controls than in individuals with aphasia. This indicates that encoding phonetic information until word identity is resolved might be a crucial mechanism for successful speech comprehension. Together, our results suggest that aphasia may entail failure to maintain lower-order information long enough to recognize lexical items.Significance statementThis study reveals robust phonetic decoding with EEG recordings in older adults, as well as decreased phonetic processing in individuals with a language disorder (aphasia) compared to healthy controls. This was most prominent over left-sided electrodes. Additionally, we observed that healthy controls, but not individuals with aphasia, encode phonetic features longer when uncertainty about word identity is high, indicating that this mechanism - encoding phonetic information until word identity is resolved - is crucial for successful language processing. These insights deepen our understanding of disrupted mechanisms in a language disorder, and show how the integration between language processing levels works in the healthy aging, neurotypical brain.
Associations between Urinary Pesticide Metabolites and Serum Inflammatory Biomarkers in Adolescents Living in an Agricultural Region
Authors: Hussari Mohammed N. , Chronister Briana N.C. , Yang Kun , Tu Xin , Martinez Danilo , Parajuli Rajendra P , Suarez-Torres Jose , Barr Dana Boyd , Hong Suzi , Suarez-Lopez Jose R. 
Published: October 2024

ABSTRACTBackgroundIn-vitro and in-vivo studies have shown evidence for the immuno-modulatory properties of different pesticides. However, few epidemiological studies on inflammation and pesticide exposure exist, with none in children and adolescents. Associations between pesticide metabolites in urine and inflammatory biomarkers in serum were evaluated among children and adolescents (n=512) of rural Ecuador as part of the ESPINA studyMethodsSeventeen urinary biomarkers of insecticide, herbicide and N, N-diethyl-meta-toluamide (DEET) insect repellent exposure were measured. Among them, acetamiprid-N-desmethyl [AND], 3,5,6-Trichloro-2-pyridinol [TCPy],para-nitrophenol [PNP], malathion dicarboxylic acid [MDA], 3-phenoxybenzoic acid [3-PBA], 2,4-Dichlorophenoxyacetic acid [2,4-D], glyphosate and 3-(diethylcarbamoyl) benzoic acid [DCBA] were included in analyses as they were detected in >30% of participants. Serum analysis included c-reactive protein (CRP), interleukin-6 (IL-6), tumor necrosis factor-⍺ (TNF-⍺), soluble intercellular adhesion molecule-1 (sICAM-1), soluble vascular cell adhesion molecule-1 (sVCAM-1), serum amyloid A (SAA), and soluble CD14 (sCD14). Associations were evaluated by generalized estimating equations (GEE) and partial least squares (PLS) regression, adjusting for demographic, anthropometric and socioeconomic variables.ResultsPositive quadratic associations were found between 2,4-D and CRP (β2=0.13, [0.00, 0.27]), IL-6 (β2=0.10, [0.04, 0.15]), SAA (β2=0.13, [0.01, 0.30]), sICAM-1 (β2=53.25, [27.26, 79.24]) and sVCAM-1 (β2=61.11, [30.52, 91.70]). The pesticide metabolites PLS composite variable was positively associated with IL-6 (β=0.09, [0.01. 0.17]), SAA (β=0.43, [0.13, 0.17]), sICAM-1 (β=63.52, [9.92, 117.13]), sVCAM-1 (β=69.03, [8.29, 129.76]) and TNF-⍺ (β=0.08, [0.00, 0.16]), and negatively associated with CRP (β=-0.28, [-0.49, -0.08], Figure 1).ConclusionsOur findings demonstrate a novel pesticide/herbicide-inflammation link in adolescents, which may be an underlying mechanism of the health impacts of pesticides/herbicides.
Robust uncertainty quantification in popular estimators of the instantaneous reproduction number
Authors: Steyn Nicholas , Parag Kris V 
Published: October 2024

AbstractThe instantaneous reproduction number (Rt) is a key measure of the rate of spread of an infectious disease. Correctly quantifying uncertainty inRtestimates is crucial for making well-informed decisions. PopularRtestimators leverage smoothing techniques to distinguish signal from noise. Examples include EpiEstim and EpiFilter, which are both controlled by a “smoothing parameter” that is traditionally selected by users. We demonstrate that the values of these smoothing parameters are unknown, vary markedly with epidemic dynamics, and show that data-driven smoothing is crucial for accurate uncertainty quantification ofRtestimates. We derive model likelihoods for the smoothing parameters in both EpiEstim and EpiFilter and develop a Bayesian framework to automatically marginalise these parameters when fitting to epidemiological time-series data. This yields novel marginal posterior predictive distributions which prove integral to rigorous model evaluation. Applying our methods, we find that default parameterisations of these widely-used estimators can negatively impactRtinference, delaying detection of epidemic growth, and misrepresenting uncertainty (typically producing overconfident estimates), with implications for public health decision-making. Our extensions mitigate these issues, provide a principled approach to uncertainty quantification, improve the robustness of real-timeRtinference, and facilitate model comparison using observable quantities.
Local control of cellular proliferation underlies neuromast regeneration in zebrafish
Authors: Lavalle Natalia G. , Miranda-Rodríguez Jerónimo , Cura Costa Emanuel , Borges Augusto , Viader-Llargués Oriol , López-Schier Hernán , Chara Osvaldo 
Published: October 2024

AbstractBiological systems are never at equilibrium but maintain stability despite perennial external disturbance. A prime example is organ regeneration, whereby despite intrinsically stochastic damage, organs are rebuilt via controlled cellular proliferation. Here, we use a mathematical approach to understand how a cell decides to re-enter and exit mitosis during organ repair. Using empirical data from regenerating neuromasts in larval zebrafish, we identify a minimal model based on ordinary differential equations (ODEs). Remarkably, the ODEs model reproduces the regeneration kinetics by assuming a cell-proliferation switch that depends on the type and the number of the neuromast cells. Additionally, a two-dimensional Cellular Potts Model (CPM) predicts that cell proliferation is a delayed response to injury. The CPM recapitulates the experimental results qualitatively and quantitatively, showing that cell proliferation is locally controlled by a switch, where each cell division stops when the type-dependent number of neighbouring cells exceeds a deterministic critical value. An intriguing corollary of our results is that a local negative feedback loop among identical cells may be a general property of organ-level proportional homeostasis.
Temperature-dependent and sex-specific phenotypic plasticity inHeliconius charithonia
Authors: Seixas Fernando , Guerrero Sammy , Xiong Tianzhu , Mallet James 
Published: October 2024

AbstractExternal environmental cues can influence the development trajectory of organisms and lead to the formation of distinct phenotypes from the same genotype. Phenotypic plasticity is common in Lepidoptera, with temperature frequently playing a key role. The zebra-longwing (Heliconius charithonia) gets its name from its characteristic black wings with yellow stripes. In some populations, yellow scales are sometimes partially replaced by orange (‘rusty’) scales. The proportion of individuals with rusty scales varies geographically and individuals within the same population can vary drastically for this phenotype. Whether such variation is genetically encoded, or environment-dependent is not known. Here we test the influence of temperature in producing the rusty scales phenotype, as well as on the developmental rates, weight, and mortality in this species. Only female butterflies reared in warm controlled conditions develop rusty scales on the yellow parts of their wings. However, under more extreme (warmer) conditions, both males and females exhibit pronounced rusty scale phenotypes, indicating a sexually dimorphic response to temperature that affects both sexes. This temperature-sensitive trait can be triggered during both larval and pupal stages. Temperature also affects life-history traits, and we observed a trade-off between developmental rate and mortality. Individuals raised in warmer conditions develop more rapidly than those in cooler environments, but this accelerated growth is accompanied by higher mortality across all developmental stages.
AnimalMotionViz: an interactive software tool for tracking and visualizing animal motion patterns using computer vision
Authors: De Castro Angelo L. , Wang Jin , Bonney-King Jessica G. , Morota Gota , Miller-Cushon Emily K. , Yu Haipeng 
Published: October 2024

AbstractMonitoring the movement patterns of dairy cattle can provide important insight into space utilization or space occupancy in a barn. Although several precision livestock technologies have been developed to record dairy cattle movements, there is a lack of open source tools to track and visualize cattle movement patterns. Therefore, we developed an open-source computer vision software tool, AnimalMotionViz, that allows users to track and visualize dairy cattle movement patterns using a motion heatmap. The software comes with an easy-to-use web-based graphical user interface built with the Python Dash package. It implements a set of background subtraction algorithms in the OpenCV package to track animal motion patterns in real time. The software processes each frame of the input video and identifies the background and foreground using these algorithms. Foreground objects are then subtracted from the background across all frames and cumulatively overlaid on an empty mask image created with the first frame of the input video to visualize the intensity or frequency of motion across different regions. The user can generate motion heatmaps in an image and video, and also track specific regional motion with a custom mask. The software also returns the top three peak intensity locations, the total percentage of regions used, and the within-quadrant percentage of regions used. In four 5 min sample videos, quadrants with peak intensity of space use, as identified using the software, aligned with quadrants where calves spent the greatest duration of time, according to continuous recording of behavior from video. The motion heatmaps generated by AnimalMotionViz can be used to understand space utilization or space occupation by animals, as well as to assess how space allocation affects dairy cow movement. We conclude that the newly developed AnimalMotionViz is a user-friendly and efficient tool to support research developments in precision livestock farming towards enhancing cattle management practices and improving pen designs.
Do metaverse implementation announcements enhance firms’ stock market value in China? A signaling theory perspective
Authors: Wang Shichao , Shao Jinan , Zhang Yueyue , Shangguan Wuyue 
Published: October 2024

PurposeThe metaverse has garnered increasing attention from researchers and practitioners, yet numerous firms remain hesitant to invest in it due to ongoing debates about its potential financial benefits. Therefore, it is crucial to analyze how the implementation of metaverse initiatives affects firms’ stock market value – an area that remains underexplored in the existing literature. Additionally, there is a significant lack of research on the contingency factors that shape the stock market reaction, leaving a noticeable gap in managerial guidance on the timing and benefits of investments in the metaverse. To narrow these gaps, we examine whether and when the implementation of metaverse initiatives enhances firms’ stock market value.Design/methodology/approachBased on 73 metaverse implementation announcements disclosed by Chinese listed firms during January 2021–August 2023, we employ an event study approach to test the hypotheses.FindingsWe find that metaverse implementation announcements elicit a positive stock market reaction. Moreover, the stock market reaction is stronger for technology-focused announcements and smaller firms, or when public attention to the metaverse is higher. Nevertheless, firms’ growth prospects do not significantly alter the stock market reaction.Originality/valueThis study extends the nascent literature on the metaverse by applying signaling theory to offer novel insights into the signaling effect of metaverse implementation announcements on stock market value and the boundary conditions under which the effectiveness of the signal varies. Besides, it provides managers with important implications regarding how to tailor the investment and information disclosure strategies of the metaverse to more effectively enhance firms’ stock market value.
Reshoring concepts: definitions and a structured bibliometric review
Authors: Siddiqui Muhammad Farooq , Khalid Warda , Arsalan Muhammad 
Published: October 2024

PurposeThe aim of this paper is to clearly mark the clusters in the related literature using bibliometric analysis and draw useful implications for the academic research purposes especially in the stream of Supply Chain Management (SCM).Design/methodology/approachBy employing rigorous selection criteria, sample articles were selected for synthesizing and conducting a bibliometric analysis. This paper tries to identify the significance of the concept of reshoring with the aspect of SCM, operations, logistics etc. Starting from sample selection, systematic selection criteria has been used to generate the database, using Scopus. The sample size was 184. Using VOSViewer, statistical and graphical representations were generated for clusters in the literature that will be useful for judging the trends of research under shoring concepts.FindingsFindings show that unclear difference compared to other supply chain concepts obstructs further theory development within reshoring concepts. To address this challenge, the review categorizes themes and defines boundaries. Based on the analysis findings, this paper advocates for additional research in areas that are crucial but have received limited or no attention. Specifically, there is a need for action research on motivations, governance modes, and location selection concerning reshoring decisions.Research limitations/implicationsThis review has a few limitations. The absence of publications in other language, than English, may result in a significant loss of knowledge. This research paper cited a few relevant publications in the form of conference papers, industry reports, books, and book chapters. Nonetheless, they were excluded from the organized bibliometric audit. To further advance the knowledge in this field, exploratory longitudinal case studies will bring to focus the changes on manufacturing strategies using the shoring and reshoring stages.Practical implicationsA current example of this is a French company named Stil (Terzian, 2020) which brought its glass thermometer production back to its home after the unexpected closure of its suppliers from China. Another Italian firm has restarted production of disposal bio-degradable face masks after 15 years to compete with low-cost alternatives from China (Greco, 2020). Reshoring concepts are now under consideration of organizations including Boeing, Bosch, Phillips and more.Originality/valueTo the best of our knowledge, this represents one of the earliest efforts to conceptualize and define reshoring concepts, aiming to distinguish them from one another appropriately. To accomplish this, the earlier demarcated clusters precede this section’s classification of reshoring concepts illustrated in Table 8. Based on the synthesis of definitions and thematic clusters above, we have concluded the literature review in this emerging field. It is intended to contribute to theory development and practitioner support in reshoring decisions by clarifying the dimensions.