bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selective Functional Connectivity between Ocular Dominance Columns in the Primary Visual Cortex
Authors: Aganj Iman , Nasr Shahin 
Published: May 2024

AbstractThe primary visual cortex (V1) in humans and many animals is comprised of fine-scale neuronal ensembles that respond preferentially to the stimulation of one eye over the other, also known as the ocular dominance columns (ODCs). Despite its importance in shaping our perception, to date, the nature of the functional interactions between ODCs has remained poorly understood. In this work, we aimed to improve our understanding of the interaction mechanisms between fine-scale neuronal structures distributed within V1. To that end, we applied high-resolution functional MRI to study mechanisms of functional connectivity between ODCs. Using this technique, we quantified the level of functional connectivity between ODCs as a function of the ocular preference of ODCs, showing thatalikeODCs are functionally more connected compared tounalikeones. Through these experiments, we aspired to contribute to filling the gap in our knowledge of the functional connectivity of ODCs in humans as compared to animals.
Nitrogen starvation response in hornworts and liverworts provides little evidence for complex priming to the cyanobiont
Authors: Yue Yuling , Sablok Gaurav , Neubauer Anna , Hyvönen Jaakko , Szövényi Péter 
Published: May 2024

AbstractMutualistic plant-microbe symbiotic interactions are thought to have evolved from a loose association between host plants and microbes when nutrients are limited. Therefore, the molecular network enabling intimate mutualistic plant-microbe symbioses may have evolved from a nutrient starvation response shared by all land plants. While the molecular link between nutrient status and symbiotic interaction is well-established, it remains poorly understood in some systems. This is especially true for the symbiotic associations between plants and cyanobacteria.To test the conservation of the starvation network across land plants as well as to investigate the link between nutrient starvation and symbiosis initiation in the plant-cyanobacteria symbiosis, here we explore the transcriptional responses to nutrient starvation in two non-vascular plant species, a hornwortAnthoceros agrestisand a liverwortBlasia pusilla, forming plant-cyanobacteria endophytic symbioses. We observe a deep conservation of the systemic starvation response across land plants. However, very few if any components of the starvation network appear to be specific to cyanobacteria hosting plants, providing little evidence for extensive and specific priming to the cyanobiont. Moreover, we found that some bioactive molecules known to be important in initiating the plant-mycorrhiza and nodule-forming bacteria symbioses, may also have a similar role in plant-cyanobacteria symbioses.HighlightOur results suggest that the most critical step in establishing plant-cyanobacteria interactions using non-host plants is the attraction of the cyanobiont. This finding has significant impact on crop engineering.
Interferon-Induced PARP14-Mediated ADP-Ribosylation in p62 Bodies Requires an Active Ubiquitin-Proteasome System
Authors: Raja Rameez , Biswas Banhi , Abraham Rachy , Liu Hongrui , Chang Che-Yuan , Vu Hien , Leung Anthony K. L. 
Published: May 2024

ABSTRACTBiomolecular condensates are cellular compartments without enveloping membranes, enabling them to dynamically adjust their composition in response to environmental changes through post-translational modifications. A recent study has revealed that interferon-induced ADP-ribosylation (ADPr), which can be reversed by a SARS-CoV-2-encoded hydrolase, is enriched within a condensate. However, the identity of the condensate and responsible host ADP-ribosyltransferase remain elusive. Here, we demonstrate that interferon induces ADPr through transcriptional activation of PARP14, requiring both its physical presence and catalytic activity for condensate formation. Interferon-induced ADPr colocalizes with PARP14, and these PARP14/ADPr condensates contain key components of p62 bodies—including the selective autophagy receptor p62 and its binding partner NBR1, along with K48-linked and K63-linked polyubiquitin chains—but lack the autophagosome marker LC3B. Knockdown of p62 disrupts the formation of these ADPr condensates. Importantly, these structures are unaffected by autophagy inhibition but depend on both ubiquitin activation and proteasome activity. Taken together, these findings demonstrate that interferon triggers PARP14-mediated ADP-ribosylation in p62 bodies, which requires an active ubiquitin-proteasome system.
Diffusion within the synaptonemal complex can account for signal transduction along meiotic chromosomes
Authors: von Diezmann Lexy , Bristow Chloe , Rog Ofer 
Published: May 2024

AbstractMeiotic chromosomes efficiently transduce information along their length to regulate the distribution of genetic exchanges within and between chromosomes. However, the mode of signal transduction remains unknown. Recently, a conserved chromosomal interface, the synaptonemal complex, was shown to be a biomolecular condensate, offering an attractive mechanism for signal transduction: diffusion of signaling molecules within the synaptonemal complex to allow transmission of information along each pair of chromosomes. Here, we test the feasibility of this mechanism in liveC. elegansgonads. Single-molecule tracking shows that a component of the synaptonemal complex (SYP-3) and a conserved regulator of exchanges (ZHP-3) both diffuse within the synaptonemal complex. However, ZHP-3 diffuses 4- and 9-fold faster than SYP-3 before and after crossovers formation, respectively. We use these measurements to parameterize a physical model for signal transduction. We find that ZHP-3, but not SYP-3, explores the lengths of chromosomes on the time scale of crossover maturation, consistent with a role in the spatial regulation of exchanges. Given the conservation of ZHP-3 paralogs across eukaryotes, we propose that diffusion within the synaptonemal complex may be a conserved mechanism of meiotic regulation. More broadly, our work explores how diffusion contained within condensates regulates crucial cellular functions.
At the roots of interference control: Conflict task in rats reveals the commonalities of onto- and phylo-genetic development
Authors: Poitreau Julien , Ambroggi Frédéric , Hasbroucq Thierry , Sargolini Francesca , Burle Boris 
Published: May 2024

AbstractResponding to internal goals and filtering irrelevant environmental cues is essential for adapted behavior. To better understand their phylogenetic evolution, we explored the underlying mechanisms in rats, thanks to the adaptation of a well-established conflict task in Humans. Besides mean performance, state of the art data analysis based on distribution analysis and formal modeling (diffusion model adapted to conflict tasks that proved very powerful in Humans) revealed mechanisms similar to the ones observed in human adults, grounding any theoretical explanation into an evolutionary perspective. Besides, the dynamics of the underlying processes in this simple conflict task resembles the ones observed in human children performing a more challenging conflict task, including the tendency to loose goals. The present study bridges the gap between onto- and phylo-genetic development of cognitive control, opening new perspectives to understand both their functional and neural implementation.
Quantifying Population-level Neural Tuning Functions Using Ricker Wavelets and the Bayesian Bootstrap
Authors: Ahumada Laura , Panitz Christian , Traiser Caitlin , Gilbert Faith , Ding Mingzhou , Keil Andreas 
Published: May 2024

AbstractExperience changes the tuning of sensory neurons, including neurons in retinotopic visual cortex, as evident from work in humans and non-human animals. In human observers, visuo-cortical re-tuning has been studied during aversive generalization learning paradigms, in which the similarity of generalization stimuli (GSs) with a conditioned threat cue (CS+) is used to quantify tuning functions. This work utilized pre-defined tuning shapes reflecting prototypical generalization (Gaussian) and sharpening (Difference-of-Gaussians) patterns. This approach may constrain the ways in which re-tuning can be characterized, for example if tuning patterns do not match the prototypical functions or represent a mixture of functions. The present study proposes a flexible and data-driven method for precisely quantifying changes in neural tuning based on the Ricker wavelet function and the Bayesian bootstrap. The method is illustrated using data from a study in which university students (n = 31) performed an aversive generalization learning task. Oriented gray-scale gratings served as CS+ and GSs and a white noise served as the unconditioned stimulus (US). Acquisition and extinction of the aversive contingencies were examined, while steady-state visual event potentials (ssVEP) and alpha-band (8-13 Hz) power were measured from scalp EEG. Results showed that the Ricker wavelet model fitted the ssVEP and alpha-band data well. The pattern of re-tuning in ssVEP amplitude across the stimulus gradient resembled a generalization (Gaussian) shape in acquisition and a sharpening (Difference-of-Gaussian) shape in an extinction phase. As expected, the pattern of re-tuning in alpha-power took the form of a generalization shape in both phases. The Ricker-based approach led to greater Bayes factors and more interpretable results compared to prototypical tuning models. The results highlight the promise of the current method for capturing the precise nature of visuo-cortical tuning functions, unconstrained by the exact implementation of prototypical a-priori models.HighlightsTuning functions are a common way for describing sensory responses, primarily in the visual cortex.The quantification and interpretation of tuning functions has faced computational and conceptual problems.We demonstrated how the Ricker function can be used as a simple and interpretable way for measuring tuning functions.We applied a Ricker function together with a Bayesian Bootstrap approach across a gradient of stimulus features in a generalization conditioning task to characterize visual tuning in the human EEG data.
Functional Activity, Functional Connectivity and Complex Network Biomarkers of Progressive Hyposmia Parkinson’s Disease with No Cognitive Impairment: Evidences from Resting-state fMRI Study
Authors: Geng Lei , Cao Wenfei , Zuo Juan , Yan Hongjie , Wan Jinxin , Sun Yi , Wang Nizhuan 
Published: May 2024

AbstractBackgroundOlfactory dysfunction stands as one of the most prevalent non-motor symptoms in the initial stage of Parkinson’s disease (PD). Nevertheless, the intricate mechanisms underlying olfactory deficits in Parkinson’s disease still remain elusive.MethodsThis study collected rs-fMRI data from 30 PD patients (15 with severe hyposmia (PD-SH) and 15 with no/mild hyposmia (PD-N/MH)) and 15 healthy controls (HC). To investigate functional segregation, the amplitude of low-frequency fluctuation (ALFF) and regional homogeneity (ReHo) were utilized. Functional connectivity (FC) analysis was performed to explore the functional integration across diverse brain regions. Additionally, the graph theory-based network analysis was employed to assess functional networks in PD patients. Furthermore, Pearson correlation analysis was conducted to delve deeper into the relationship between the severity of olfactory dysfunction and various functional metrics.ResultsFirstly, PD patients showed significantly higher ALFF values in the superior temporal gyrus compared to HC, especially in the PD-SH group versus PD-N/MH. Meanwhile, ALFF values in this region negatively correlated with olfactory testing scores. Secondly, PD patients had higher ReHo in middle temporal gyrus and superior frontal gyrus than HC, especially PD-SH. Meanwhile, olfactory scores negatively correlated with these ReHo values. Thirdly, we observed a negative correlation between superior cerebellar-insula connectivity and olfactory scores, suggesting a neural circuit link to olfactory dysfunction. Lastly, the PD patients’ brain networks consistently showed small-world attributes, with the PD-N/MH group having significantly higher nodal betweenness in the superior cerebellum than the PD-SH group. There’s also a positive link between superior cerebellum’s betweenness and olfactory scores. Additionally, there is a notable difference in the node degree of the superior temporal gyrus when comparing the PD-SH group to the PD-N/MH group.ConclusionUsing fMRI, our study analyzed brain function in PD-SH, PD-N/MH, and HC groups, revealing impaired segregation and integration in PD-SH and PD-N/MH. We hypothesize that changes in temporal, frontal, occipital, and cerebellar activities, along with aberrant cerebellum-insula connectivity and node degree and betweenness disparities, may be linked to olfactory dysfunction in PD patients.
Contribute to balance, wire in accordance: Emergence of backpropagation from a simple, bio-plausible neuroplasticity rule
Authors: Fan Xinhao , Mysore Shreesh P 
Published: May 2024

AbstractOver the past several decades, backpropagation (BP) has played a critical role in the advancement of machine learning and remains a core method in numerous computational applications. It is also utilized extensively in comparative studies of biological and artificial neural network representations. Despite its widespread use, the implementation of BP in the brain remains elusive, and its biological plausibility is often questioned due to inherent issues such as the need for symmetry of weights between forward and backward connections, and the requirement of distinct forward and backward phases of computation. Here, we introduce a novel neuroplasticity rule that offers a potential mechanism for implementing BP in the brain. Similar in general form to the classical Hebbian rule, this rule is based on the core principles of maintaining the balance of excitatory and inhibitory inputs as well as on retrograde signaling, and operates over three progressively slower timescales: neural firing, retrograde signaling, and neural plasticity. We hypothesize that each neuron possesses an internal state, termed credit, in addition to its firing rate. After achieving equilibrium in firing rates, neurons receive credits based on their contribution to the E-I balance of postsynaptic neurons through retrograde signaling. As the network’s credit distribution stabilizes, connections from those presynaptic neurons are strengthened that significantly contribute to the balance of postsynaptic neurons. We demonstrate mathematically that our learning rule precisely replicates BP in layered neural networks without any approximations. Simulations on artificial neural networks reveal that this rule induces varying community structures in networks, depending on the learning rate. This simple theoretical framework presents a biologically plausible implementation of BP, with testable assumptions and predictions that may be evaluated through biological experiments.
EHR-based Case Identification of Pediatric Long COVID: A Report from the RECOVER EHR Cohort
Authors: Botdorf Morgan , Dickinson Kimberley , Lorman Vitaly , Razzaghi Hanieh , Marchesani Nicole , Rao Suchitra , Rogerson Colin , Higginbotham Miranda , Mejias Asuncion , Salyakina Daria , Thacker Deepika , Dandachi Dima , Christakis Dimitri A , Taylor Emily , Schwenk Hayden , Morizono Hiroki , Cogen Jonathan , Pajor Nathan M , Jhaveri Ravi , Forrest Christopher B. , Bailey L. Charles 
Published: May 2024

AbstractObjectiveLong COVID, marked by persistent, recurring, or new symptoms post-COVID-19 infection, impacts children’s well-being yet lacks a unified clinical definition. This study evaluates the performance of an empirically derived Long COVID case identification algorithm, or computable phenotype, with manual chart review in a pediatric sample. This approach aims to facilitate large-scale research efforts to understand this condition better.MethodsThe algorithm, composed of diagnostic codes empirically associated with Long COVID, was applied to a cohort of pediatric patients with SARS-CoV-2 infection in the RECOVER PCORnet EHR database. The algorithm classified 31,781 patients with conclusive, probable, or possible Long COVID and 307,686 patients without evidence of Long COVID. A chart review was performed on a subset of patients (n=651) to determine the overlap between the two methods. Instances of discordance were reviewed to understand the reasons for differences.ResultsThe sample comprised 651 pediatric patients (339 females,Mage= 10.10 years) across 16 hospital systems. Results showed moderate overlap between phenotype and chart review Long COVID identification (accuracy = 0.62, PPV = 0.49, NPV = 0.75); however, there were also numerous cases of disagreement. No notable differences were found when the analyses were stratified by age at infection or era of infection. Further examination of the discordant cases revealed that the most common cause of disagreement was the clinician reviewers’ tendency to attribute Long COVID-like symptoms to prior medical conditions. The performance of the phenotype improved when prior medical conditions were considered (accuracy = 0.71, PPV = 0.65, NPV = 0.74).ConclusionsAlthough there was moderate overlap between the two methods, the discrepancies between the two sources are likely attributed to the lack of consensus on a Long COVID clinical definition. It is essential to consider the strengths and limitations of each method when developing Long COVID classification algorithms.
Menstrual hygiene management among reproductive-aged women with disabilities in Bangladesh
Authors: Khan Md Nuruzzaman , Khanam Shimlin Jahan , Chowdhury Atika Rahman , Hossain Rashed , Kabir Md Awal , Alam Md Badsha 
Published: May 2024

AbstractBackgroundWomen with disabilities in low- and middle-income countries face unique challenges in managing menstruation, affecting their health, dignity, and quality of life.ObjectiveThis study explored menstrual hygiene management (MHM) practices among reproductive-aged women with disabilities in Bangladesh and its impact on social participation.MethodsWe analyzed data from 51,535 women from the 2019 Multiple Indicator Cluster Survey (MICS). The outcome variables were: (i) material used to manage blood flow while menstruating (appropriate, inappropriate), (ii) availability of a private place for washing and changing menstruation rags (yes, no), and (iii) impacted in attendance of social activities, school, or work during menstruation (yes, no). Disability status was considered as major explanatory variable and categorized as no disabilities, moderate disabilities, and severe disabilities. Associations of outcome variables with explanatory variable were determined using a multilevel multinomial logistic regression model adjusted for individual-level factors, household-level factors, and community-level factors.ResultsAmong the sample, 2.7% reported severe disability and 19.2% moderate disabilities, with vision-related disabilities (12.2%) being the most prevalent, followed by cognitive (9.5%) and walking disabilities (8.2%). Overall, 4% reported using inappropriate materials for menstrual flow, rising to 8.0% among those with severe disabilities and 5.8% for moderate disabilities. Women with moderate to severe disabilities had 33-47% lower odds of using appropriate materials and 34-44% lower odds of having a private place to change at home. Additionally, women with severe disabilities were 1.66 times more likely to report that menstruation impacted their social activities.ConclusionWomen with disabilities in Bangladesh face significant barriers to effective MHM. Addressing these issues requires targeted interventions, including disability-inclusive menstrual health education, improved access to menstrual products and sanitation facilities, and community initiatives to reduce stigma.
LagaEcosystem, Species Entanglements and the Risk of Zoonotic Disease Transmission: A Multi-Site, Multi-Method Ethnographic Study
Authors: Omia Dalmas , Oketch Dismas , Njoroge Ruth , Ngere Isaac , Gachohi John , Waiguru Samuel , Magarre Abdulai G. , Khamadi Samoel Ashimosi , Nuismer Scott L , Njeru John Mwaniki , Bodha Boku , Nyaga Nazaria , Njaanake Humphrey , Jaoko Walter , Njenga Kariuki , Osoro Eric 
Published: May 2024

AbstractDry riverbeds, also calledIaga, are a complex ecosystem of multispecies interactions between livestock, humans, microorganisms, and their environment. Despitelaga’sOne Health entanglement of species and environment, few studies have explored the risks of transmission of diseases through direct herd-herd or herd-human contact or indirect contact with fomites surrounding thelaga. This study focuses on ethnographic and epidemiological investigations onlagaswithin Kenya. The study deploys qualitative multimethod-walking interviews, in-depth interviews, key informant interviews, focus group discussions and observations to collect the data from Marsabit and Kajiado Counties in Kenya. Results point to the comingling of infected and healthy herds, cross-livestock species mixing, sharing of watering troughs, and feeding dogs placental and parturition materials at the herd level. The human transmission risks include non-protective parturition assistance, the use of camel urine as an antiseptic substance, humans sharing animal-watering troughs, and consuming non-processed milk. Further, the fomites comprise contaminated excreta, infected placental materials onlagastones, deposition of infected aborted fetuses on thelagabody, and bacteria in the sand that end up ingested or inhaled as dust during dry seasons. The study concludes that intensified water insecurity due to climate variability will deepen multispecies interactions at thelagagiven that it holds a lifeline in drylands for pastoralists, hence, heightening brucellosis transmission risks. The study’s results recommend a reinvention of brucellosis preventive measures that consider the pathogen flux withinlagasystems and multispecies interactions. Such an approach should consider the multidimensional-clinical, environmental, and cultural co-production of solutions where preventive behaviors are prioritized.
Genal: A Python Toolkit for Genetic Risk Scoring and Mendelian Randomization
Authors: Rivier Cyprien A. , Clocchiatti-Tuozzo Santiago , Huo Shufan , Torres-Lopez Victor , Renedo Daniela , Sheth Kevin , Falcone Guido J. , Acosta Julian N. 
Published: May 2024

AbstractSummaryHere we present Genal, a python module for population genetic analyses. It includes functionalities for cleaning and formatting Single Nucleotide Polymorphism (SNP)-level data, clumping, lifting, SNP association testing, polygenic risk scoring, and mendelian randomization analyses, all within a single module. It was designed with user-friendliness in mind, aiming to reduce the programming skills threshold required for medical scientists to perform genetic epidemiology studies. Genal eliminates the need to interact with the command line and switch between multiple R packages with different requirements, making it considerably more accessible to a wide range of researchers. Genal draws on concepts from several well-established tools, ensuring that users have access to rigorous statistical techniques in the intuitive Python environment.