bluuebunny/crossref_metadata_2025_split huggingface dataset:
SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessibility
Authors: Valério Mariana , Borges-Araújo Luís , Melo Manuel N. , Lousa Diana , Soares Cláudio M. 
Published: December 2021

ABSTRACTThe coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has killed over 5 million people and is causing a devastating social and economic impact all over the world. The rise of new variants of concern (VOCs) represents a difficult challenge due to the loss vaccine and natural immunity, and increased transmissibility. All circulating VOCs contain mutations in the spike glycoprotein, which mediates fusion between the viral and host cell membranes, via its receptor binding domain (RBD) that binds to angiotensin-converting enzyme 2 (ACE2). In an attempt to understand the effect of RBD mutations in circulating VOCs, a lot of attention has been given to the RBD-ACE2 interaction. However, this type of analysis is limited, since it ignores more indirect effects, such as the conformational dynamics of the RBD itself. Observing that some VOCs mutations occur in residues that are not in direct contact with ACE2, we hypothesized that they could affect RBD conformational dynamics. To test this, we performed long atomistic (AA) molecular dynamics (MD) simulations to investigate the structural dynamics of wt RBD, and that of three circulating VOCs (alpha, beta, and delta). Our results show that in solution, wt RBD presents two distinct conformations: an “open” conformation where it is free to bind ACE2; and a “closed” conformation, where the RBM ridge blocks the binding surface. The alpha and beta variants significantly impact the open/closed equilibrium, shifting it towards the open conformation by roughly 20%. This shift likely increases ACE2 binding affinity. Simulations of the currently predominant delta variant RBD were extreme in this regard, in that a closed conformation was never observed. Instead, the system alternated between the before mentioned open conformation and an alternative “reversed” one, with a significantly changed orientation of the RBM ridge flanking the RBD. This alternate conformation could potentially provide a fitness advantage not only due to increased availability for ACE2 binding, but also by aiding antibody escape through epitope occlusion. These results support the hypothesis that VOCs, and particularly the delta variant, impact RBD conformational dynamics in a direction that simultaneously promotes efficient binding to ACE2 and antibody escape.
Temporally stable beta sensorimotor oscillations and cortico–muscular coupling underlie force steadiness
Authors: Mongold Scott J. , Piitulainen Harri , Legrand Thomas , Ghinst Marc Vander , Naeije Gilles , Jousmäki Veikko , Bourguignon Mathieu 
Published: December 2021

AbstractAs humans, we seamlessly hold objects in our hands, and may even lose consciousness of these objects. This phenomenon raises the unsettled question of the involvement of the cerebral cortex, the core area for voluntary motor control, in dynamically maintaining steady muscle force. To address this issue, we measured magnetoencephalographic brain activity from healthy adults who maintained a steady pinch grip. Using a novel analysis approach, we uncovered fine-grained temporal modulations in the ∼20-Hz sensorimotor brain rhythm and its coupling with muscle activity, with respect to several aspects of muscle force (rate of increase/decrease or plateauing high/low). These modulations preceded changes in force features by ∼40 ms and possessed behavioral relevance, as less salient or absent modulation predicted a more stable force output. These findings have consequences for the existing theories regarding the functional role of cortico-muscular coupling, and suggest that steady muscle contractions are characterized by a stable rather than fluttering involvement of the sensorimotor cortex.
Multiscale and extended retrieval of associative memory structures in a cortical model of local-global inhibition balance
Authors: Burns Thomas F , Haga Tatsuya , Fukai Tomoki 
Published: December 2021

AbstractInhibitory neurons take on many forms and functions. How this diversity contributes to memory function is not completely known. Previous formal studies indicate inhibition differentiated by local and global connectivity in associative memory networks functions to rescale the level of retrieval of excitatory assemblies. However, such studies lack biological details such as a distinction between types of neurons (excitatory and inhibitory), unrealistic connection schemas, and non-sparse assemblies. In this study, we present a rate-based cortical model where neurons are distinguished (as excitatory, local inhibitory, or global inhibitory), connected more realistically, and where memory items correspond to sparse excitatory assemblies. We use this model to study how local-global inhibition balance can alter memory retrieval in associative memory structures, including naturalistic and artificial structures. Experimental studies have reported inhibitory neurons and their sub-types uniquely respond to specific stimuli and can form sophisticated, joint excitatory-inhibitory assemblies. Our model suggests such joint assemblies, as well as a distribution and rebalancing of overall inhibition between two inhibitory sub-populations – one connected to excitatory assemblies locally and the other connected globally – can quadruple the range of retrieval across related memories. We identify a possible functional role for local-global inhibitory balance to, in the context of choice or preference of relationships, permit and maintain a broader range of memory items when local inhibition is dominant and conversely consolidate and strengthen a smaller range of memory items when global inhibition is dominant. This model therefore highlights a biologically-plausible and behaviourally-useful function of inhibitory diversity in memory.
An experimental test of chronic traffic noise exposure on parental behaviour and reproduction in zebra finches
Authors: Liu Quanxiao , Gelok Esther , Fontein Kiki , Slabbekoorn Hans , Riebel Katharina 
Published: December 2021

ABSTRACTChronic traffic noise is increasingly recognised as a potential hazard to wildlife. Several songbird species have been shown to breed poorly in traffic noise exposed habitats. However, identifying whether noise is causal in this requires experimental approaches. We tested whether experimental exposure to chronic traffic noise affected parental behaviour and reproductive success in zebra finches (Taeniopygia guttata). In a counterbalanced repeated-measures design, breeding pairs were exposed to continuous playback of one of two types of highway noise previously shown to be either neutral (control) or aversive. Parental nest attendance positively correlated with feeding effort and was higher for the aversive than the control sound and this effect was more pronounced for parents attending larger broods. However, neither noise condition affected offspring number, growth or body mass. The absence of an effect held when we combined our data with data from two other comparable studies into a meta-analysis. We discuss whether the increased nest attendance could be a compensatory strategy that alleviated detrimental noise effects on the chicks, and whether it could be caused by impaired parent-offspring or within-pair communication. Future work should test these hypotheses and investigate potential long-term costs of increased parental engagement.
Broad human and animal coronavirus neutralisation by SARS-CoV-2 S2-targeted vaccination
Authors: Ng Kevin W. , Faulkner Nikhil , Finsterbusch Katja , Wu Mary , Harvey Ruth , Hussain Saira , Greco Maria , Liu Yafei , Kjaer Svend , Swanton Charles , Gandhi Sonia , Beale Rupert , Gamblin Steve J. , Cherepanov Peter , McCauley John , Daniels Rodney , Howell Michael , Arase Hisashi , Wack Andeas , Bauer David L.V. , Kassiotis George 
Published: December 2021

AbstractSeveral common-cold coronaviruses (HCoVs) are endemic in humans and several variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have emerged during the current Coronavirus disease 2019 (COVID-19) pandemic. Whilst antibody cross-reactivity with the Spike glycoproteins (S) of diverse coronaviruses has been documented, it remains unclear whether such antibody responses, typically targeting the conserved S2 subunit, contribute to or mediate protection, when induced naturally or through vaccination. Using a mouse model, we show that prior HCoV-OC43 S immunity primes neutralising antibody responses to otherwise subimmunogenic SARS-CoV-2 S exposure and promotes S2-targeting antibody responses. Moreover, mouse vaccination with SARS-CoV-2 S2 elicits antibodies that neutralise diverse animal and human alphacoronaviruses and betacoronaviruses in vitro, and protects against SARS-CoV-2 challenge in vivo. Lastly, in mice with a history of SARS-CoV-2 Wuhan-based S vaccination, further S2 vaccination induces stronger and broader neutralising antibody response than booster Wuhan S vaccination, suggesting it may prevent repertoire focusing caused by repeated homologous vaccination. The data presented here establish the protective value of an S2-targeting vaccine and support the notion that S2 vaccination may better prepare the immune system to respond to the changing nature of the S1 subunit in SARS-CoV-2 variants of concern (VOCs), as well as to unpredictable, yet inevitable future coronavirus zoonoses.
The effects of probabilistic context inference on motor adaptation
Authors: Dario Cuevas Rivera , Stefan Kiebel 
Published: December 2021

AbstractHumans have been shown to adapt their movements when a sudden or gradual change to the dynamics of the environment are introduced, a phenomenon called motor adaptation. If the change is reverted, the adaptation is also quickly reverted. Humans are also able to adapt to multiple changes in dynamics presented separately, and to be able to switch between adapted movements on the fly. Such switching relies on contextual information which is often noisy or misleading, affecting the switch between known adaptations. Recently, computational models for motor adaptation and context inference have been introduced, which contain components for context inference and Bayesian motor adaptation. These models were used to show the effects of context inference on learning rates across different experiments. We expanded on these works by using a simplified version of the recently-introduced COIN model to show that the effects of context inference on motor adaptation and control go even further than previously shown. Here, we used this model to simulate classical motor adaptation experiments from previous works and showed that context inference, and how it is affected by the presence and reliability of feedback, effect a host of behavioral phenomena that had so far required multiple hypothesized mechanisms, lacking a unified explanation. Concretely, we show that the reliability of direct contextual information, as well as noisy sensory feedback, typical of many experiments, effect measurable changes in switching-task behavior, as well as in action selection, that stem directly from probabilistic context inference.
Dynamic Resting State Motor Network Connectivity of Neurotypical Children, the Groundwork for Network-Guided Therapy in Childhood Movement Disorders
Authors: Sussman Bethany L. , Wyckoff Sarah N. , Fine Justin M. , Heim Jennifer , Wilfong Angus A. , Adelson P. David , Kruer Michael C. , Boerwinkle Varina L. 
Published: December 2021

AbstractBackgroundNormative childhood motor network resting-state fMRI effective connectivity is undefined, yet necessary for translatable dynamic resting-state network informed treatments in pediatric movement disorders.MethodCross-spectral dynamic causal modelling of resting-state fMRI was investigated in 19 neurotypically developing 5-7-year-old children. Fully connected six-node motor network models were created for each hemisphere including primary motor cortex, striatum, subthalamic nucleus, globus pallidus internus, thalamus, and contralateral cerebellum. Parametric Empirical Bayes with exhaustive Bayesian model reduction and Bayesian modeling averaging were used to create a group model for each hemisphere; Purdue Pegboard Test (PPBT) scores for relevant hand motor behavior were also entered as a covariate at the group level to determine the brain-behavior relationship.ResultsOverall, the resting-state functional MRI effective connectivity of motor cortico-basal ganglia-cerebellar networks was similar across hemispheres, with greater connectivity in the left hemisphere. The motor network effective connectivity relationships between the nodes were consistent and robust across subjects. Additionally, the PPBT score for each hand was positively correlated with the thalamus to contralateral cerebellum connection.DiscussionThe normative effective connectivity from resting-state functional MRI in children largely reflect the direction of inter-nodal signal predicted by other prior modalities and was consistent and robust across subjects, with differences from these prior task-dependent modalities that likely reflect the motor rest-action state during acquisition. Effective connectivity of the motor network was correlated with motor behavior, indicating effective connectivity brain-behavior relationship has physiological meaning in the normally developing. Thus, it may be helpful for future studies in children with movement disorders, wherein comparison to normative effective connectivity will be critical for network-targeted intervention.Impact StatementThis is the first study to use pediatric resting-state functional MRI to create a normative effective connectivity model of the motor network and to also show correlation with behavior, which may have therapeutic implications for children with movement disorders.
T cell receptor repertoire signatures associated with COVID-19 severity
Authors: Park Jonathan J. , Lee Kyoung A V. , Lam Stanley Z. , Chen Sidi 
Published: December 2021

AbstractT cell receptor (TCR) repertoires are critical for antiviral immunity. Determining the TCR repertoires composition, diversity, and dynamics and how they change during viral infection can inform the molecular specificity of viral infection such as SARS-CoV-2. To determine signatures associated with COVID-19 disease severity, here we performed a large-scale analysis of over 4.7 billion sequences across 2,130 TCR repertoires from COVID-19 patients and healthy donors. TCR repertoire analyses from these data identified and characterized convergent COVID-19 associated CDR3 gene usages, specificity groups, and sequence patterns. T cell clonal expansion was found to be associated with upregulation of T cell effector function, TCR signaling, NF-kB signaling, and Interferon-gamma signaling pathways. Machine learning approaches accurately predicted disease severity for patients based on TCR sequence features, with certain high-power models reaching near-perfect AUROC scores across various predictor permutations. These analyses provided an integrative, systems immunology view of T cell adaptive immune responses to COVID-19.
Variance in Variants: Propagating Genome Sequence Uncertainty into Phylogenetic Lineage Assignment
Authors: Champredon David , Becker Devan , Chato Connor , Gugan Gopi , Poon Art 
Published: December 2021

AbstractGenetic sequencing is subject to many different types of errors, but most analyses treat the resultant sequences as if they are known without error. Next generation sequencing methods rely on significantly larger numbers of reads than previous sequencing methods in exchange for a loss of accuracy in each individual read. Still, the coverage of such machines is imperfect and leaves uncertainty in many of the base calls. On top of this machine-level uncertainty, there is uncertainty induced by human error, such as errors in data entry or incorrect parameter settings. In this work, we demonstrate that the uncertainty in sequencing techniques will affect downstream analysis and propose a straightforward method to propagate the uncertainty.Our method uses a probabilistic matrix representation of individual sequences which incorporates base quality scores as a measure of uncertainty that naturally lead to resampling and replication as a framework for uncertainty propagation. With the matrix representation, resampling possible base calls according to quality scores provides a bootstrap- or prior distribution-like first step towards genetic analysis. Analyses based on these re-sampled sequences will include a more complete evaluation of the error involved in such analyses.We demonstrate our resampling method on SARS-CoV-2 data. The resampling procedures adds a linear computational cost to the analyses, but the large impact on the variance in downstream estimates makes it clear that ignoring this uncertainty may lead to overly confident conclusions. We show that SARS-CoV-2 lineage designations via Pangolin are much less certain than the bootstrap support reported by Pangolin would imply and the clock rate estimates for SARS-CoV-2 are much more variable than reported.
The enteric nervous system of C. elegans is specified by the Sine Oculis-like homeobox gene ceh-34
Authors: Vidal Berta , Gulez Burcu , Cao Wen Xi , Leyva-Diaz Eduardo , Tekieli Tessa , Hobert Oliver 
Published: December 2021

ABSTRACTOverarching themes in the terminal differentiation of the enteric nervous system, an autonomously acting unit of animal nervous systems, have so far eluded discovery. We describe here the overall regulatory logic of enteric nervous system differentiation of the nematode C. elegans that resides within the foregut (pharynx) of the worm. A Caenorhabditis elegans homolog of the Drosophila Sine Oculis homeobox gene, ceh-34, is expressed in all 14 classes of interconnected pharyngeal neurons from their birth throughout their life time, but in no other neuron type of the entire animal. Constitutive and temporally controlled ceh-34 removal shows that ceh-34 is required to initiate and maintain the neuron type-specific terminal differentiation program of all pharyngeal neuron classes, including their circuit assembly, without affecting panneuronal features. Through additional genetic loss of function analysis, we show that within each pharyngeal neuron class, ceh-34 cooperates with different homeodomain transcription factors to individuate distinct pharyngeal neuron classes. Our analysis underscores the critical role of homeobox genes in neuronal identity specification and links them to the control of neuronal circuit assembly of the enteric nervous system. Together with the pharyngeal nervous system simplicity as well as its specification by a Sine Oculis homolog, our findings invite speculations about the early evolution of nervous systems.
Effect of spatiotemporally changing environment on serial dependence in ensemble representations
Authors: Son Sangkyu , Lee Joonyeol , Kwon Oh-Sang , Kim Yee-Joon 
Published: December 2021

SummaryThe recent visual past has a strong impact on our current perception. Recent studies of serial dependence in perception show that low-level adaptation repels our current perception away from previous stimuli1–5 whereas post-perceptual decision attracts perceptual report toward the immediate past6–12. In their studies, these repulsive and attractive biases were observed with different task demands perturbing ongoing sequential process. Therefore, it is unclear whether the opposite biases arise naturally in navigating complex real-life environments. Here we only manipulated the environmental statistics to characterize how serially dependent perceptual decisions unfold in spatiotemporally changing visual environments. During sequential mean orientation adjustment task on the array of Gabor patches, we found that the repulsion effect dominated only when ensemble variance increased across consecutive trials whereas the attraction effect prevailed when ensemble variance decreased or remained the same. The observed attractive bias by high- to-low-variance stimuli and repulsive bias by low-to-high-variance stimuli were reinforced by the repeated exposure to the low and the high ensemble variance, respectively. Further, this variance-dependent differential pattern of serial dependence in ensemble representation remained the same regardless of whether observers had a prior knowledge of environmental statistics or not. We used a Bayesian observer model constrained by visual adaptation13,14 to provide a unifying account of both attractive and repulsive bias in perception. Our results establish that the temporal integration and segregation of visual information is flexibly adjusted through variance adaptation.
Chitin-induced systemic disease resistance in rice requires both OsCERK1 and OsCEBiP and is mediated via perturbation of cell-wall biogenesis in leaves
Authors: Takagi Momoko , Hotamori Kei , Naito Keigo , Matsukawa Sumire , Egusa Mayumi , Nishizawa Yoko , Kanno Yuri , Seo Mitsunori , Ifuku Shinsuke , Mine Akira , Kaminaka Hironori 
Published: December 2021

SummaryChitin is a well-known elicitor of disease resistance whose recognition by plants is crucial to perceive fungal infections. Chitin can induce both a local immune response and a systemic disease resistance when provided as a supplement in soils. Unlike local immune responses, how chitin-induced systemic disease resistance is deployed has not been studied in detail.In this study, we evaluated systemic disease resistance against the fungal pathogen Bipolaris oryzae by performing a transcriptome analysis and monitoring cell-wall composition in rice plants grown in chitin-supplemented soils. We also examined the local immune response to chitin by measuring the production of reactive oxygen species in leaves.Chitins induced both local immune response and systemic disease resistance with differing requirements for the receptors OsCERK1 and OsCEBiP. Transcriptome analysis suggested that a perturbation in cell-wall biogenesis is involved in the induction of systemic disease resistance, an idea which was supported by the induction of disease resistance by treatment with a cellulose biosynthesis inhibitor and alterations of cell-wall composition.These findings suggest that chitin-induced systemic disease resistance in rice is caused by a perturbation of cell-wall biogenesis in leaves through long-distance signalling after recognition of chitins by OsCERK1 and OsCEBiP.