bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling the effects of COVID-19 mobility disruptions on RSV transmission in Seattle, Washington
Authors: Srinivas Duddu Atchuta , Elgamal Islam , Camacho-Mateu José , Holubowska Olena , Rella Simon A. , Bents Samantha J. , Viboud Cécile , Hansen Chelsea L. , Pullano Giulia , Perofsky Amanda C. 
Published: September 2024

AbstractIntroductionRespiratory Syncytial Virus (RSV) infection is a major cause of acute respiratory hospitalizations in young children and older adults. In early 2020 most countries implemented non-pharmaceutical interventions (NPIs) to slow the spread of SARS-CoV-2. COVID-19 NPIs disrupted the transmission of RSV on a global scale, and many locations did not experience widespread re-circulation until late 2020 or 2021. Here, we use a mechanistic transmission model informed by cellphone mobility data to determine which aspects of population behavior had the greatest influence on post-pandemic RSV rebound in Seattle, Washington.MethodsWe used aggregated mobile device location data to characterize within-city mixing, visitor in-flows, and foot traffic to points of interest in Seattle. We fit an age-structured epidemiological model to data on weekly RSV hospitalizations, allowing for reductions in transmission due to declines in mobility during the pandemic. We compared model fits to observed data to assess which mobility behaviors best capture RSV dynamics during the first two post-pandemic waves in Seattle.ResultsIn Seattle, COVID-19 NPIs perturbed RSV seasonality from 2020 to 2022. Seattle experienced a small out-of-season outbreak in Summer 2021 and an atypically large and early wave in Fall 2022. RSV transmission models incorporating mobility network connectivity (measured as the average shortest path length between Seattle neighborhoods) or the inflow of visitors from outside of Seattle best captured the timing and magnitude of the first two post-pandemic waves. Models including foot traffic to schools or child daycares or within-neighborhood movement produced poor fits to observed data.ConclusionsOur results suggest that case importations from other regions and local spread between neighborhoods had the greatest influence on the timing of RSV reemergence in Seattle. These findings contribute to the understanding of behavioral factors underlying RSV epidemic spread and can inform the timing of preventative measures, such as the administration of immunoprophylaxis.
Prevalence and determinants of modern contraception use among persons with disabilities in low- and middle-income countries: a systematic review and meta-analysis
Authors: Chowdhury Atika Rahman , Khanam Shimlin Jahan , Islam Mohammad Zahidul , Khandaker Gulam , Khan Md Nuruzzaman 
Published: September 2024

BackgroundPersons with disabilities should require the same level of access to contraception as the general population. However, the extent of contraception use among this group is underexplored in low- and middle-income countries (LMICs).ObjectiveThis study aimed to determine the prevalence of modern contraception use among persons with disabilities in LMICs and identify the key determinants.MethodsIn June 2024, we conducted a systematic search across six databases to identify studies on disability and modern contraception in LMICs. The primary outcomes were the prevalence of modern contraception use and its determinants among persons with disabilities. Summary estimates were calculated using fixed or random-effects meta-analysis, depending on the level of heterogeneity.ResultsA total of 19 studies were identified, with 11 included in the meta-analysis. The pooled prevalence of modern contraception use among persons with disabilities was 31.4% (95% CI: 26.5, 36.2), with significant heterogeneity across respondent characteristics. Five factors were significantly associated with higher contraception use: age over 25 years, having some level of education, being in a higher wealth quintile, adequate knowledge of family planning, and being in a formal marital relationship.ConclusionThis study reveals a significantly lower prevalence of modern contraception use among persons with disabilities in LMICs. Improving access to education, addressing social norms, and strengthening healthcare systems may contribute to increase contraception access and uptake among persons with disabilities in LMICs.
Deep learning for classifying neuronal morphologies: combining topological data analysis and graph neural networks
Authors: Kanari Lida , Schmidt Stanislav , Casalegno Francesco , Delattre Emilie , Banjac Jelena , Negrello Thomas , Shi Ying , Meystre Julie , Defferrard Michaël , Schürmann Felix , Markram Henry 
Published: September 2024

AbstractThe shape of neuronal morphologies plays a critical role in determining their dynamical properties and the functionality of the brain. With an abundance of neuronal morphology reconstructions, a robust definition of cell types is important to understand their role in brain functionality. However, an objective morphology classification scheme is hard to establish due to disagreements on the definition of cell types, on which subjective views of field experts show significant differences. The robust grouping of neurons based on their morphological shapes is important for generative models and for establishing a link between anatomical properties and other modalities, such as biophysical and transcriptomic information. We combine deep learning techniques with a variety of mathematical descriptions of neurons and evaluate the classification accuracy of different methods. We demonstrate that various methodologies, including graph neural networks, topological morphology descriptors, and morphometrics, consistently perform with the highest accuracy for a variety of datasets. Based on these methods, we present a robust classification of both inhibitory and excitatory cell types in the rodent cortex and propose a generalized scheme for a consistent classification of neurons into classes.
Variant Evolution Graph: Can We Infer How SARS-CoV-2 Variants are Evolving?
Authors: Das Badhan , Heath Lenwood S. 
Published: September 2024

AbstractThe SARS-CoV-2 virus has undergone mutations over time, leading to genetic diversity among circulating viral strains. This genetic diversity can affect the characteristics of the virus, including its transmissibility and the severity of symptoms in infected individuals. During the pandemic, this frequent mutation creates an enormous cloud of variants known as viral quasispecies. Most variation is lost due to the tight bottlenecks imposed by transmission and survival. Advancements in next-generation sequencing have facilitated the rapid and cost-effective production of complete viral genomes, enabling the ongoing monitoring of the evolution of the SARS-CoV-2 genome. However, inferring a reliable phylogeny from GISAID (the Global Initiative on Sharing All Influenza Data) is daunting due to the vast number of sequences. In the face of this complexity, this research proposes a new method of representing the evolutionary and epidemiological relationships among the SARS-CoV-2 variants inspired by quasispecies theory. We aim to build a Variant Evolution Graph (VEG), a novel way to model viral evolution in a local pandemic region based on the mutational distance of the genotypes of the variants. VEG is a directed acyclic graph and not necessarily a tree because a variant can evolve from more than one variant; here, the vertices represent the genotypes of the variants associated with their human hosts, and the edges represent the evolutionary relationships among these variants. A disease transmission network, DTN, which represents the transmission relationships among the hosts, is also proposed and derived from the VEG. We downloaded the genotypes of the variants recorded in GISAID, which are complete, have high coverage, and have a complete collection date from five countries: Somalia (22), Bhutan (102), Hungary (581), Iran (1334), and Nepal (1719). We ran our algorithm on these datasets to get the evolution history of the variants, build the variant evolution graph represented by the adjacency matrix, and infer the disease transmission network. Our research represents a novel and unprecedented contribution to the field of viral evolution, offering new insights and approaches not explored in prior studies.
Multifaceted roles of H2B mono-ubiquitylation in D-loop metabolism during homologous recombination repair
Authors: Hung Shih-Hsun , Liang Yuan , Heyer Wolf-Dietrich 
Published: September 2024

SUMMARYRepairing DNA double-strand breaks is crucial for maintaining genome integrity, which occurs primarily through homologous recombination (HR) inS. cerevisiae.Nucleosomes, composed of DNA wrapped around a histone octamer, present a natural barrier to end-resection to initiate HR, but the impact on the downstream HR steps of homology search, DNA strand invasion and repair synthesis remain to be determined. Displacement loops (D-loops) play a pivotal role in HR, yet the influence of chromatin dynamics on D-loop metabolism remains unclear. Using the physical D-loop capture (DLC) and D-loop extension (DLE) assays to track HR intermediates, we employed genetic analysis to reveal that H2B mono-ubiquitylation (H2Bubi) affects multiple steps during HR repair. We infer that H2Bubi modulates chromatin structure, not only promoting histone degradation for nascent D-loop formation but also stabilizing extended D-loops through nucleosome assembly. Furthermore, H2Bubi regulates DNA resectionviaRad9 recruitment to suppress a feedback control mechanism that dampens D-loop formation and extension at hyper-resected ends. Through physical and genetic assays to determine repair outcomes, we demonstrate that H2Bubi plays a crucial role in preventing break-induced replication and thus promoting genomic stability.Graphical AbstractHighlightsH2Bubi is epistatic to H2A.Z and INO80 in promoting homology search and D-loop formationH2Bubi stabilizes extended D-loopExcessive resection counteracts D-loop formation and extensionH2Bubi promotes crossover events and limits the frequency of break-induced replication outcomes in HR repair
Purkinje cells in Crus I and II encode the visual stimulus and the impending choice as monkeys learn a reinforcement based visuomotor association task
Authors: Ipata Anna E. , Fascianelli Valeria , De Zeeuw Chris I. , Sendhilnathan Naveen , Fusi Stefano , Goldberg Michael E. 
Published: September 2024

AbstractVisuomotor association involves linking an arbitrary visual cue to a well-learned movement. Transient inactivation of Crus I/II impairs primates’ ability to learn new associations and delays motor responses without affecting the kinematics of the movement. The simple spikes of Purkinje cells in the Crus regions signal cognitive errors as monkeys learn to associate specific fractal stimuli with movements of the left or right hand. Here we show that as learning progresses, the simple spike activity of individual neurons becomes more selective for stimulus-response associations, with selectivity developing closer to the appearance of visual stimuli. Initially, most neurons respond to both associations, irrespective of the identity of the stimulus and the associated movement, but as learning advances, more neurons distinguish between specific stimulus-hand associations. Using a linear decoder, it was found that in early learning stages, the visual stimulus can be decoded only when the choice can also be decoded. As learning improves, the visual stimulus is decoded earlier than the choice. A simple model can replicate the observed simple spike signals and the monkeys’ behavior in both the early and late learning stages.
Surface-mediated Bacteriophage Defense Incurs Fitness Tradeoffs for Interbacterial Antagonism
Authors: Tsai Chia-En , Wang Feng-Qi , Yang Chih-Wen , Yang Ling-Li , Nguyen Thao V. , Chen Yung-Chih , Chen Po-Yin , Hwang Ing-Shouh , Ting See-Yeun 
Published: September 2024

ABSTRACTBacteria in polymicrobial habitats are constantly exposed to biotic threats from bacteriophages (or “phages”), antagonistic bacteria, and predatory eukaryotes. These antagonistic interactions play crucial roles in shaping the evolution and physiology of bacteria. To survive, bacteria have evolved mechanisms to protect themselves from such attacks, but the fitness costs of resisting one threat and rendering bacteria susceptible to others remain unappreciated. Here, we examined the fitness consequences of phage resistance inSalmonella enterica, revealing that phage-resistant variants exhibited significant fitness loss upon co-culture with competitor bacteria. These phage-resistant strains display varying degrees of lipopolysaccharide (LPS) deficiency and increased susceptibility to contact-dependent interbacterial antagonism, such as the type VI secretion system (T6SS). Utilizing mutational analyses and atomic force microscopy, we show that the long-modal length O-antigen of LPS serves as a protective barrier against T6SS-mediated intoxication. Notably, this competitive disadvantage can also be triggered independently by phages possessing LPS-targeting endoglycosidase in their tail spike proteins, which actively cleave the O- antigen upon infection. Our findings reveal two distinct mechanisms of phage-mediated LPS modifications that modulate interbacterial competition, shedding light on the dynamic microbial interplay within mixed populations.
Spatiotemporal Patterns of Gene Expression During Development of a Complex Colony Morphology
Authors: Cromie Gareth A. , Tan Zhihao , Hays Michelle , Sirr Amy , Dudley Aimée M. 
Published: September 2024

AbstractClonal communities of single celled organisms, such as bacterial or fungal colonies and biofilms, are spatially structured, with subdomains of cells experiencing differing environmental conditions. In the development of such communities, cell specialization is not only important to respond and adapt to the local environment but has the potential to increase the fitness of the clonal community through division of labor. Here, we examine colony development in a yeast strain (F13) that produces colonies with a highly structured “ruffled” phenotype in the colony periphery and an unstructured “smooth” phenotype in the colony center. We demonstrate that in the F13 genetic background deletions of transcription factors can either increase(dig1Δ,sfl1Δ) or decrease(tec1Δ) the degree of colony structure. To investigate the development of colony structure, we carried out gene expression analysis on F13 and the three deletion strains using RNA-seq. Samples were taken early in colony growth (day2), which precedes ruffled phenotype development in F13, and from the peripheral and central regions of colonies later in development (day5), at which time these regions are structured and unstructured (respectively) in F13. We identify genes responding additively and non-additively to the genotype and spatiotemporal factors and cluster these genes into a number of different expression patterns. We identify clusters whose expression correlates closely with the degree of colony structure in each sample and include genes with known roles in the development of colony structure. Individual deletion of 26 genes sampled from different clusters identified 5 with strong effects on colony morphology (BUD8,CIS3,FLO11,MSB2andSFG1), all of which eliminated or greatly reduced the structure of the F13 outer region.
Connectomic analysis of taste circuits inDrosophila
Authors: Walker Sydney R. , Peña-Garcia Marco , Devineni Anita V. 
Published: September 2024

SUMMARYOur sense of taste is critical for regulating food consumption. The fruit flyDrosophilarepresents a highly tractable model to investigate mechanisms of taste processing, but taste circuits beyond sensory neurons are largely unidentified. Here, we use a whole-brain connectome to investigate the organization ofDrosophilataste circuits. We trace pathways from four populations of sensory neurons that detect different taste modalities and project to the subesophageal zone (SEZ). We find that second-order taste neurons are primarily located within the SEZ and largely segregated by taste modality, whereas third-order neurons have more projections outside the SEZ and more overlap between modalities. Taste projections out of the SEZ innervate regions implicated in feeding, olfactory processing, and learning. We characterize interconnections between taste pathways, identify modality-dependent differences in taste neuron properties, and use computational simulations to relate connectivity to predicted activity. These studies provide insight into the architecture ofDrosophilataste circuits.
Magnetic excitation in the hyperkagome antiferromagnet
Mn3RhSi
Authors: Shamoto Shin-ichi , Yamauchi Hiroki , Iida Kazuki , Ikeuchi Kazuhiko , Kaneko Koji , Chen Yu-Sheng , Yano Shin-ichiro , Hsu Pai-Tse , Lee Min Kai , Hall Amelia Elisabeth , Balakrishnan Geetha , Chang Lieh-Jeng 
Published: September 2024

In a paramagnetic state of a hyperkagome lattice antiferromagnet Mn3RhSi, magnetic diffuse scattering by magnetic short-range order is observed over a wide temperature range of approximately 500 K above the Néel temperature of 190 K. We have studied the magnetic excitation with a single crystal in a wide energy range from 0.3 to 140 meV by inelastic neutron scattering, where the prominent inelastic neutron-scattering signal is observed at Q=(2,0,0). The inelastic scattering intensity integrated for two of twelve magnon modes leads to a localized magnetic moment of about 5 μB per Mn site, although the long-range ordered magnetic moment is only 2.61 μB at 4 K. The result suggests that a large part of the magnetic moment does not order in Mn3RhSi, possibly due to the geometrical spin frustration of the hyperkagome lattice.

Published by the American Physical Society
2024
Determinants of tweens’ saving intentions: a cross-sectional study
Authors: Lučić Andrea , Erceg Nikola , Barbić Dajana 
Published: September 2024

PurposeChildren are beginning to socialize as consumers earlier than ever, highlighting the importance of their saving behavior as an effective form of consumer protection. The paper explored the influence of parents, peers, attitudes, knowledge, past behavior, allowance and self-efficacy on saving intention.Design/methodology/approachWith the aim to explore a range of determinants of adolescent saving and to specify the potential mechanisms through which different determinants operate, we adopted a multitheoretical approach based on theories of planned behavior, consumer and financial socialization, and self-efficacy. The paper investigates the formation of the saving intentions on a sample of 1,476 children 10–15 years old in Croatia.FindingsThe results indicate strong importance of parental influence and self-efficacy, implying that saving intention among tweens requires a supportive family structure as well as beliefs in the tweens themselves that they are able to save money and face difficulties.Originality/valueThis paper investigates the very nature of saving intention formation at a crucial developmental stage; it investigates the interplay of mechanisms through which determinants of savings operate at that developmental stage; and it explores the age-variance of the mechanism and the interplay of relevant variables, shedding light on the nature of the mechanism of development.
“What do you mean by that?”: solidarity in Canadian development practice
Authors: Boutilier Sophia 
Published: September 2024

PurposeWith the launch of the Feminist International Assistance Policy (FIAP), the Canadian government named solidarity as a shared value and a driving motivation behind the FIAP. This paper explores how development workers understand and apply solidarity to their work, uncovering the opportunities and constraints they face.Design/methodology/approachIn-depth, semi-structured interviews were conducted with 42 development workers from Canada’s federal development agency between 2019 and 2020. Transcribed data were coded by the author to identify how workers made sense of solidarity within the development industry.FindingsThe majority of workers were unsure of how to define or operationalize solidarity, demonstrating confusion. Commonality was routinely mentioned as a facet of solidarity, but workers understood this term in diverse ways, with some considering commonality as a precondition that inhibited a sense of solidarity with development partners in the global South due to differences in living conditions. About a quarter identified power and privilege as necessary considerations in the process of building solidarity, showing potential for bonds across the inequalities that define development. About 40% of workers identified the institutional structure of the organization as an obstacle to solidarity.Originality/valueThis paper presents original data from Canadian development workers, providing the first study of their understanding of solidarity as a development ethic. It shows the gaps between rhetoric and practice while recommending ways for development organizations to meaningfully engage with solidarity in their work.
Model optimization and acceleration method based on meta-learning and model pruning for laser vision weld tracking system
Authors: Zou Yanbiao , Yang Jianhui 
Published: September 2024

Purpose
This paper aims to propose a lightweight, high-accuracy object detection model designed to enhance seam tracking quality under strong arcs and splashes condition. Simultaneously, the model aims to reduce computational costs.

Design/methodology/approach
The lightweight model is constructed based on Single Shot Multibox Detector (SSD). First, a neural architecture search method based on meta-learning and genetic algorithm is introduced to optimize pruning strategy, reducing human intervention and improving efficiency. Additionally, the Alternating Direction Method of Multipliers (ADMM) is used to perform structural pruning on SSD, effectively compressing the model with minimal loss of accuracy.

Findings
Compared to state-of-the-art models, this method better balances feature extraction accuracy and inference speed. Furthermore, seam tracking experiments on this welding robot experimental platform demonstrate that the proposed method exhibits excellent accuracy and robustness in practical applications.

Originality/value
This paper presents an innovative approach that combines ADMM structural pruning and meta-learning-based neural architecture search to significantly enhance the efficiency and performance of the SSD network. This method reduces computational cost while ensuring high detection accuracy, providing a reliable solution for welding robot laser vision systems in practical applications.