bluuebunny/crossref_metadata_2025_split huggingface dataset:
Demographic and Viral-Genetic Analyses of COVID-19 Severity in Bahrain Identify Local Risk Factors and a Protective Effect of Polymerase Mutations
Authors: Koch Evan M. , Du Justin , Dressner Michelle , Alwasti Hashmeya Erahim , Al Taif Zahra , Shehab Fatima , Mohamed Afaf Merza , Ghanem Amjad , Alhajeri Amani , Alawadhi Amna , Almoamen Nabeel , Ashoor Khulood , Hasan Sara , Haghighi Alireza , Sunyaev Shamil , Farhat Maha 
Published: August 2022

AbstractA multitude of demographic, health, and genetic factors are associated with the risk of developing severe COVID-19 following infection by the SARS-CoV-2. There is a need to perform studies across human societies and to investigate the full spectrum of genetic variation of the virus. Using data from 869 COVID-19 patients in Bahrain between March 2020 and March 2021, we analyzed paired viral sequencing and non-genetic host data to understand host and viral determinants of severe COVID-19. We estimated the effects of demographic variables specific to the Bahrain population and found that the impact of health factors are largely consistent with other populations. To extend beyond the common variants of concern in the Spike protein analyzed by previous studies, we used a viral burden approach and detected a protective effect of low-frequency missense viral mutations in the RNA-dependent RNA polymerase (Pol) gene on disease severity. Our results contribute to the survey of severe COVID-19 in diverse populations and highlight the benefits of studying rare viral mutations.
Fear of relapse and quality of life in multiple sclerosis: the mediating role of psychological resilience
Authors: Broche-Pérez Yunier , Jiménez-Morales Rodneys M. , Monasterio-Ramos Laura Ortiz , Vázquez-Gómez Lázaro A. , Bauer Johana , Fernández-Fleites Zoylen 
Published: August 2022

AbstractThe goal of this study was to examine the mediating role of psychological resilience in the relationship between fear of relapse and quality of life in a sample of patients with multiple sclerosis (PwMS). This cross-sectional study was developed online. A total of 240 PwMS were surveyed using the Multiple Sclerosis Quality of Life inventory, the Fear of Relapse Scale and the Connor-Davidson Resilience Scale. To perform the mediation analysis PROCESS macro was used. In our study, fear of relapse was a predictor of psychological resilience and quality of life, and psychological resilience was a predictor of quality of life. Finally, psychological resilience showed a mediating role in the relationship between fear of relapse and quality of life. Considering that resilience is a modifiable variable, the implementation of interventions aimed at enhancing resilience can have a favorable impact on the psychological well-being and quality of life of patients with multiple sclerosis.
Monkeypox virus shows potential to infect a diverse range of native animal species across Europe, indicating high risk of becoming endemic in the region
Authors: Blagrove Marcus SC , Pilgrim Jack , Kotsiri Aurelia , Hui Melody , Baylis Matthew , Wardeh Maya 
Published: August 2022

AbstractBackgroundMonkeypox is a zoonotic virus which persists in animal reservoirs and periodically spills over into humans, causing outbreaks. During the current 2022 outbreak, monkeypox virus has persisted via human-human transmission, across all major continents and for longer than any previous record. This unprecedented spread creates the potential for the virus to ‘spillback’ into local susceptible animal populations. Persistent transmission amongst such animals raises the prospect of monkeypox virus becoming enzootic in new regions. However, the full and specific range of potential animal hosts and reservoirs of monkeypox remains unknown, especially in newly at-risk non-endemic areas.MethodsHere, utilising ensembles of classifiers comprising different class balancing techniques and incorporating instance weights, we identify which animal species are potentially susceptible to monkeypox virus. Subsequently, we generate spatial distribution maps to highlight high-risk geographic areas at high resolution.FindingsWe show that the number of potentially susceptible species is currently underestimated by 2.4 to 4.3-fold, and that a high density of wild susceptible species are native to Europe. We provide lists of these species, and highlight high-risk hosts for spillback and potential long-term reservoirs, which may enable monkeypox virus to become endemic.InterpretationWe highlight the European red fox and brown rat, as they have established interactions with potentially contaminated urban waste and sewage, which provides a mechanism for potential spillback. We anticipate that our results will enable targeted active surveillance of potential spillback event, to minimise risk of the virus becoming endemic in these regions. Our results also indicate the potential of domesticated cats and dogs (latter now confirmed) being susceptible to monkeypox virus, and hence support many health organisations’ advice for infected humans to avoid physical interaction with pets.
Sound localization acuity of the common marmoset (Callithrix jacchus)
Authors: Remington Evan D. , Chen Chenggang , Wang Xiaoqin 
Published: August 2022

AbstractThe common marmoset (Callithrix jacchus) is a small arboreal New World primate which has emerged as a promising model in auditory neuroscience. One potentially useful application of this model system is in the study of the neural mechanism underlying spatial hearing in primate species, as the marmoset’s visually occluded natural habitat in the forest would make sound localization an essential behavior for survival. However, interpretation of neurophysiological data on sound localization requires an understanding of perceptual abilities, and the sound localization behavior of marmosets has not been well studied. The present experiment measured sound localization acuity using an operant conditioning procedure in which marmosets were trained to discriminate changes in sound location in the horizontal (azimuth) or vertical (elevation) dimension. Our results showed that the minimum audible angle (MAA) for horizontal discrimination was on average 15° for band-passed Gaussian noise and 13° for Random Spectral Shape (RSS) stimuli, whereas the MAA for vertical locations was at 17° and 22° for band-passed Gaussian noises containing more and less high frequency energy, respectively.
Factors associated with low school readiness, a linked health and education data study in Wales, UK
Authors: Bandyopadhyay Amrita , Marchant Emily , Jones Hope , Parker Michael , Evans Julie , Brophy Sinead 
Published: August 2022

AbstractBackgroundSchool readiness is a measure of a child’s cognitive, social, and emotional readiness to begin formal schooling. Children with low school readiness need additional support from schools for learning, developing required social and academic skills, and catching-up with their school-ready peers. This study aims to identify the modifiable risk factors associated with low school readiness using linked routine data for children in Wales.MethodThis was a longitudinal data linkage cohort study. The cohort comprises of children who completed the Foundation Phase assessment between 2012 and 2018. Individuals were identified by linking Welsh Demographic Service and Pre16 Education Attainment datasets. School readiness was assessed via the binary outcome of the Foundation Phase assessment (achieved/not achieved). This study used multivariable logistic regression model and decision tree to identify and weight the most important risk factors associated with low school readiness.ResultsIn order of importance, logistic regression identified maternal learning difficulties (adjusted odds ratio 5.35(95% confidence interval 3.97-7.22)), childhood epilepsy (2.95(2.39-3.66)), very low birth weight (2.24(1.86-2.70), being a boy (2.11(2.04-2.19)), being on free school meals (1.85(1.78–1.93)), living in most deprived area (1.67(1.57–1.77)), maternal death (1.47(1.09-1.98)), and maternal diabetes (1.46(1.23 - 1.78)) as factors associated with low school readiness. Using a decision tree, eligibility for free school meals, being a boy, absence/low attendance at school, being a younger child (e.g., August born), being born low birth weight, and not being breastfed were factors found to be associated with low school readinessConclusionThis work suggests that public health interventions focusing on children who are: boys, living in deprived areas, have poor early years attendance, have parents with learning difficulties, have parents with an illness or have illnesses themselves, would make the most difference to school readiness in the population.
The COVID HOME study research protocol: Prospective cohort study of non-hospitalised COVID-19 patients
Authors: Tami A. , van der Gun B.T.F. , Wold K.I. , Vincenti-González M.F. , Veloo A.C.M. , Knoester M. , Harmsma V.P.R. , de Boer G.C. , Huckriede A.L.W. , Pantano D. , Gard L. , Rodenhuis-Zybert I. , Upasani V. , Smit J. , Dijkstra A. , de Haan J. , van Elst J. , van den Boogaard J. , O’ Boyle S. , Nacul L. , Niesters H.G.M. , Friedrich A.W. 
Published: August 2022

AbstractBackgroundGuidelines on COVID-19 management are developed as we learn from this pandemic. However, most research has been done on hospitalised patients and the impact of the disease on non-hospitalised and their role in transmission are not yet well understood.The COVID HOME study conducts research among COVID-19 patients and their family members who were not hospitalised during acute disease, to guide patient care and inform public health guidelines for infection prevention and control in the community and household.MethodsAn ongoing prospective longitudinal observational study of COVID-19 outpatients was established in March 2020 in the Netherlands. Laboratory confirmed SARS-CoV-2 infected individuals of all ages that did not merit hospitalisation, and their household (HH) members, were enrolled after written informed consent. Enrolled participants were visited at home within 48 hours after initial diagnosis, and then weekly on days 7, 14 and 21 to obtain clinical data, a blood sample for biochemical parameters/cytokines and serological determination; and a nasopharyngeal/throat swab plus urine, stool and sperm or vaginal secretion (if consenting) to test for SARS-CoV-2 by RT-PCR (viral shedding) and for viral culturing. Weekly nasopharyngeal/throat swabs and stool samples, plus a blood sample on days 0 and 21 were also taken from HH members to determine whether and when they became infected. All participants were invited to continue follow-up at 3-, 6-, 12- and 18-months post-infection to assess long-term sequelae and immunological status.Preliminary ResultsA total of 256 participants belonging to 103 HH were included of which, 190 (74.2%) were positive for SARS-CoV-2 infection. Most individuals (183/190, 96.3%) developed mild to moderate disease. At the time of writing, all participants had reached the 3 and 6 month time-points of the long-term follow-up, while approximately 78% reached 12 month and 23% the 18 month time-point. Preliminary analysis showed that 43% (52/121) positive individuals reported having complaints at 3 months post-infection, while 42.7% (61/143) had complaints at 6 months.
The Protein Common Assembly Database (ProtCAD) – A comprehensive structural resource of protein complexes
Authors: Xu Qifang , Dunbrack Roland L. 
Published: August 2022

ABSTRACTProteins often act through oligomeric interactions with other proteins. X-ray crystallography and cryo-electron microscopy provide detailed information on the structures of biological assemblies, defined as the most likely biologically relevant structures derived from experimental data. In crystal structures, the most relevant assembly may be ambiguously determined, since multiple assemblies observed in the crystal lattice may be plausible. It is estimated that 10-15% of PDB entries may have incorrect or ambiguous assembly annotations. Accurate assemblies are required for understanding functional data and training of deep learning methods for predicting assembly structures. As with any other kind of biological data, replication via multiple independent experiments provides important validation for the determination of biological assembly structures. Here we present the Protein Common Assembly Database (ProtCAD), which presents clusters of protein assembly structures observed in independent structure determinations of homologous proteins in the Protein Data Bank (PDB). ProtCAD is searchable by PDB entry, UniProt identifiers, or Pfam domain designations and provides downloads of coordinate files, PyMol scripts, and publicly available assembly annotations for each cluster of assemblies. About 60% of PDB entries contain assemblies in clusters of at least 2 independent experiments. All clusters and coordinates are available on ProtCAD web site (http://dunbrack2.fccc.edu/protcad).
Disentangling the Neural Correlates of Agency, Ownership and Multisensory Processing
Authors: Harduf Amir , Shaked Ariel , Yaniv Adi Ulmer , Salomon Roy 
Published: August 2022

AbstractThe experience of the self as an embodied agent in the world is an essential aspect of human consciousness. This experience arises from the feeling of control over one’s bodily actions, termed the Sense of Agency (SoA), and the feeling that the body belongs to the self, Body Ownership (BO). Despite long-standing philosophical and scientific interest in the relationship between the body and brain, the neural systems involved in SoA and BO and especially their interactions, are not yet understood. In this preregistered study using the Moving Rubber Hand Illusion inside an MR-scanner, we aimed to uncover the relationship between BO & SoA in the human brain. Importantly, by using both visuomotor and visuotactile stimulations and measuring online trial-by-trial fluctuations in the illusion magnitude, we were able to disentangle brain systems related to objective sensory stimulation and subjective judgments of the bodily-self. Our results indicate that at both the behavioral and neural levels, BO and SoA are strongly interrelated. Multisensory regions in the occipital and fronto-parietal regions encoded convergence of sensory stimulation conditions. However, the subjective judgments of bodily-self were also related to BOLD fluctuations in regions not activated by the sensory conditions such as the insular cortex and precuneus. Our results highlight the convergence of multisensory processing in specific neural systems for both BO and SoA with partially dissociable regions for subjective judgments in regions of the default mode network.
Recombination between heterologous human acrocentric chromosomes
Authors: Guarracino Andrea , Buonaiuto Silvia , de Lima Leonardo Gomes , Potapova Tamara , Rhie Arang , Koren Sergey , Rubinstein Boris , Fischer Christian ,   Human Pangenome Reference Consortium, Gerton Jennifer L. , Phillippy Adam M. , Colonna Vincenza , Garrison Erik 
Published: August 2022

AbstractThe short arms of the human acrocentric chromosomes 13, 14, 15, 21, and 22 share large homologous regions, including the ribosomal DNA repeats and extended segmental duplications (Floutsakou et al. 2013; van Sluis et al. 2019). While the complete assembly of these regions in the Telomere-to-Telomere consortium’s CHM13 provided a model of their homology (Nurk et al. 2022), it remained unclear if these patterns were ancestral or maintained by ongoing recombination exchange. Here, we show that acrocentric chromosomes contain pseudo-homologous regions (PHRs) indicative of recombination between non-homologs. Considering an all-to-all comparison of the high-quality human pangenome from the Human Pangenome Reference Consortium (HPRC) (Liao et al. 2022), we find that contigs from all of the acrocentric short arms form a community similar to those formed by single chromosomes or the sex chromosome pair. A variation graph (Garrison et al. 2018) constructed from centromere-spanning acrocentric contigs indicates the presence of regions where most contigs appear nearly identical between heterologous CHM13 acrocentrics. Except on chromosome 15, we observe faster decay of linkage disequilibrium in the PHRs than in the corresponding short and long arms, indicating higher rates of recombination (N. Li and Stephens 2003; Huttley et al. 1999). The PHRs include sequences previously shown to lie at the breakpoint of Robertsonian translocations (Jarmuz-Szymczak et al. 2014), and we show that their arrangement is compatible with crossover in inverted duplications on chromosomes 13, 14, and 21. The ubiquity of signals of recombination between heterologous chromosomes seen in the HPRC draft pangenome’s acrocentric assemblies suggests that these shared sequences form the basis for recurrent Robertsonian translocations, providing sequence and population-based confirmation of hypotheses first developed cytogenetically fifty years ago (Hamerton et al. 1975).
The evolution of behavioral cues and signaling in displaced communication
Authors: Bernard Arthur , Wischmann Steffen , Floreano Dario , Keller Laurent 
Published: August 2022

AbstractDisplaced communication, whereby individuals communicate regarding a subject that is not immediately present (spatially or temporally), is one of the key innovations of human language. It also occurs in a few animal species, most notably the honeybee, where the waggle dance is used to communicate the location and quality of a patch of flowers. However, it is difficult to study how it emerged given the paucity of species displaying this capacity and the fact that it often occurs via complex multimodal signals. To address this issue, we developed a novel paradigm in which we conducted experimental evolution with foraging agents endowed with neural networks that regulate their movement and the production of signals. Displaced communication readily evolved but, surprisingly, agents did not use signal amplitude to convey information on food location. Instead, they used signal onset-delay and duration-based mode of communication, which depends on the motion of the agent within a communication area. When agents were experimentally prevented from using these modes of communication, they evolved to use signal amplitude instead. Interestingly, this mode of communication was more efficient and led to higher performance. Subsequent controlled experiments suggested that this more efficient mode of communication failed to evolve because it took more generations to emerge than communication grounded on the onset-delay and length of signaling. These results reveal that displaced communication is likely to initially evolve from non-communicative behavioral cues providing incidental information with evolution later leading to more efficient communication systems through a ritualization process.Author SummaryThe evolution of displaced communication, the process through which individuals share information about a remote object (in space or time), is a key innovation in language. By conducting experimental evolution we found that displaced communication is more likely to leverage and evolve from behavioural cues, such as the agent’s movement, rather than from dedicated communication modes, such as the amplitude of emitted signals. This phenomenon is shown to happen because communication via signal amplitude -although more efficient-is slower to evolve. The simple behaviors and neural networks of the agents studied here, also suggest that communication may evolve more frequently than expected via ritualization, a process whereby an action or behavior pattern in an animal loses its original function but is retained for its role in display or other social interactions.
SWIP mediates retromer-independent membrane recruitment of the WASH complex
Authors: Dostál V. , Humhalová T. , Beránková P. , Pácalt O. , Libusová L. 
Published: August 2022

AbstractThe pentameric WASH complex facilitates endosomal protein sorting by activating Arp2/3, which in turn leads to the formation of F-actin patches specifically on the endosomal surface. It is generally accepted that WASH complex attaches to the endosomal membrane via the interaction of its subunit FAM21 with the retromer subunit VPS35. However, we observe the WASH complex and F-actin present on endosomes even in the absence of VPS35. We show that the WASH complex binds to the endosomal surface in both a retromer-dependent and a retromer-independent manner. The retromer-independent membrane anchor is directly mediated by the subunit SWIP. Furthermore, SWIP can interact with a number of phosphoinositide species. Of those, our data suggest that the interaction with phosphatidylinositol-3,5-bisphosphate (PI(3,5)P2) is crucial to the endosomal binding of SWIP. Overall, this study reveals a new role of the WASH complex subunit SWIP and highlights the WASH complex as an independent, self-sufficient trafficking regulator.SummaryDostál et al. contradict the prevailing concept that WASH complex is principally recruited to the endosome via its interaction with the retromer. They show that the WASH complex binds to the endosomal membrane via its subunit SWIP, and this interaction can be prevented by removing phosphatidylinositol-3,5-bisphosphate from cells.
L-type calcium channels link oxidative stress to calcium signaling pathway and membrane excitability: Insights from computational modeling of dopaminergic neurons
Authors: Andres M.A. , Karratti-Abordo S. , Bryan C. , Shoji A. , Zaporteza M. , Castelfranco A.M. 
Published: August 2022

ABSTRACTDopamine neurons, which are critical in movement, cognition, and reward learning, are vulnerable to oxidative stress during aging, drugs of abuse, and viral infection and can lead to neurodegeneration. Previous work used computational modeling to study dopamine neuron function based on experimental findings from rodent brain slices containing dopamine neurons. Here we show for the first time the feasibility and utility of applying such computational models of DA neurons to the analysis of experimental findings from in-vitro cultured cells. We used DCFH-DA (and DHE) and time-lapse, Fura-2 ratiometric imaging to measure changes in ROS levels and changes in intracellular calcium (Ca2+) levels, respectively, in two dopaminergic cell models: differentiated SH-SY5Y and differentiated human neural progenitor cells. We investigated how peroxide-dependent changes in the behavior of the L-type channel might alter the excitability of the dopaminergic cell. We found that L-type channels mediated clusters of calcium spikes (or oscillations) and that our model suggested that such increased excitability could be explained by changes in the voltage-dependence of activation of the L-type channels in response to exogenous peroxide. Our findings suggested that L-type channels link oxidative stress responses to modulation of excitability. We conclude that the Ca2+channel blocker nicardipine may help disrupt this link by reducing oxidative stress and preventing channel activation at more hyperpolarized potentials, thus reducing plasma membrane excitability.