bluuebunny/crossref_metadata_2025_split huggingface dataset:
Learning better by learning together: dyadic visual perceptual learning on orientation discrimination
Authors: Zhang Yifei , Li Jian , Wang Yizhou , Fang Fang 
Published: June 2022

AbstractThe belief that learning can be modulated by social context is mainly supported by high-level value-based learning studies. However, whether social context can even modulate low-level learning such as visual perceptual learning (VPL) is still unknown. Unlike traditional VPL studies in which participants were trained singly, here we developed a novel dyadic VPL paradigm in which paired participants were trained with the same orientation discrimination task and they could monitor each other’s performance. We found that the social context (i.e., dyadic training) led to a greater behavioral performance improvement and a faster learning speed, compared with the single training. Interestingly, the facilitating effects could be modulated by the performance difference between paired participants. Functional magnetic resonance imaging (fMRI) results showed that, compared with the single training, social cognition areas including bilateral parietal cortex and dorsolateral prefrontal cortex displayed a different spatial activity pattern and enhanced functional connectivities to early visual cortex during the dyadic training. Furthermore, the dyadic training resulted in more refined orientation representation in primary visual cortex (V1), which was closely associated with the greater behavioral performance improvement. Taken together, we demonstrate that the social context, learning with a partner, can remarkably augment the plasticity of low-level visual information process by means of reshaping the neural activities in early visual cortex and social cognition areas, as well as their functional interplays.
The Fc-effector function of COVID-19 convalescent plasma contributes to SARS-CoV-2 treatment efficacy in mice
Authors: Ullah Irfan , Beaudoin-Bussières Guillaume , Symmes Kelly , Cloutier Marc , Ducas Eric , Tauzin Alexandra , Laumaea Annemarie , Bégin Philippe , Mothes Walther , Kumar Priti , Bazin Renée , Finzi Andrés , Uchil Pradeep D. 
Published: June 2022

SUMMARYCOVID-19 convalescent plasmas (CCPs) are chosen for plasma therapy based on neutralizing titers and anti-Spike immunoglobulin levels. However, specific CCP characteristics that promote SARS-CoV-2 control in recipients are complex and incompletely defined. Using an in vivo imaging approach, we demonstrate that CCPs with low neutralizing and high Fc-effector activity, in contrast to those with poor Fc-function, afford effective prophylaxis and therapy in K18-hACE2 mice lethally challenged with SARS-CoV-2-nLuc. Macrophages and neutrophils significantly contributed to CCP effects during therapy but to a reduced extent under prophylaxis. Both IgG and Ig(M+A) were required during therapy, but the IgG fraction alone was sufficient during prophylaxis. Finally, despite neutralizing poorly, SARS-CoV-2 Wuhan-elicited CCPs delayed Delta and Beta variants of concern (VOC)-induced mortality in mice illustrating the contribution of polyclonal Fc-effector functions in immunity against VOCs. Thus, in addition to neutralization, Fc-effector activity is a significant criterion for CCP selection for therapeutic applications.
Distinguishing discrete and continuous behavioral variability using warped autoregressive HMMs
Authors: Costacurta Julia C. , Duncker Lea , Sheffer Blue , Gillis Winthrop , Weinreb Caleb , Markowitz Jeffrey E. , Datta Sandeep R. , Williams Alex H. , Linderman Scott W. 
Published: June 2022

AbstractA core goal in systems neuroscience and neuroethology is to understand how neural circuits generate naturalistic behavior. One foundational idea is that complex naturalistic behavior may be composed of sequences of stereotyped behavioral syllables, which combine to generate rich sequences of actions. To investigate this, a common approach is to use autoregressive hidden Markov models (ARHMMs) to segment video into discrete behavioral syllables. While these approaches have been successful in extracting syllables that are interpretable, they fail to account for other forms of behavioral variability, such as differences in speed, which may be better described as continuous in nature. To overcome these limitations, we introduce a class of warped ARHMMs (WARHMM). As is the case in the ARHMM, behavior is modeled as a mixture of autoregressive dynamics. However, the dynamics under each discrete latent state (i.e. each behavioral syllable) are additionally modulated by a continuous latent “warping variable.” We present two versions of warped ARHMM in which the warping variable affects the dynamics of each syllable either linearly or nonlinearly. Using depth-camera recordings of freely moving mice, we demonstrate that the failure of ARHMMs to account for continuous behavioral variability results in duplicate cluster assignments. WARHMM achieves similar performance to the standard ARHMM while using fewer behavioral syllables. Further analysis of behavioral measurements in mice demonstrates that WARHMM identifies structure relating to response vigor.
Neuroanatomy of stomatopod central complexes offers putative neural substrate for oriented behaviors in crustaceans
Authors: Chou Alice , Sayre Marcel E. , Lin Chan , Cronin Thomas W. 
Published: June 2022

AbstractAll insects studied to date possess a centrally located group of neuropils, known collectively as the central complex, that has been implicated in sensory integration and motor action selection. Among the functions prescribed to the central complex, none is perhaps as intriguing as its role in orientation and navigation. Neurobiological correlates of both current and desired headings have been described in insect CXs. Despite the diversity of arthropods, understanding of the CX as a navigational center originates entirely from terrestrial insects. Stomatopod crustaceans, commonly referred to as mantis shrimps, form an order of predatory marine crustaceans with intricate and diverse visual systems that maintain the distinction of being the only fully aquatic animal known to utilize the navigational strategy of path integration. They utilize idiothetic, celestial, and landmark cues to orient in the benthos. Here, we investigate the neuroanatomy of adult and developing mantis shrimp central complexes and associated neuropils to begin understanding this brain region in a sensorially and behaviorally complex crustacean.
Can deep learning provide a generalizable model for dynamic sound encoding in auditory cortex?
Authors: Pennington Jacob R. , David Stephen V. 
Published: June 2022

AbstractConvolutional neural networks (CNNs) can provide powerful and flexible models of neural sensory processing. However, the utility of CNNs in studying the auditory system has been limited by their requirement for large datasets and the complex response properties of single auditory neurons. To address these limitations, we developed a population encoding model: a CNN that simultaneously predicts activity of several hundred neurons recorded during presentation of a large set of natural sounds. This approach defines a shared spectro-temporal space and pools statistical power across neurons. Population models of varying architecture performed consistently better than traditional linear-nonlinear models on data from primary and non-primary auditory cortex. Moreover, population models were highly generalizable. The output layer of a model pre-trained on one population of neurons could be fit to novel single units, achieving performance equivalent to that of neurons in the original fit data. This ability to generalize suggests that population encoding models capture a general set of computations performed by auditory cortex.
MetaboDirect: An Analytical Pipeline for the processing of FTICR-MS-based Metabolomics Data
Authors: Ayala-Ortiz Christian , Graf-Grachet Nathalia , Freire-Zapata Viviana , Fudyma Jane , Hildebrand Gina , AminiTabrizi Roya , Howard-Varona Cristina , Corilo Yuri E. , Hess Nancy , Duhaime Melissa , Sullivan Matthew , Tfaily Malak 
Published: June 2022

ABSTRACTBackgroundMicrobiomes are now recognized as main drivers of ecosystem function ranging from the oceans and soils to humans and bioreactors. However, a grand challenge in microbiome science is to characterize and quantify the chemical currencies of organic matter (i.e. metabolites) that microbes respond to and alter. Critical to this has been the development of Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), which has drastically increased molecular characterization of complex organic matter samples, but challenges users with hundreds of millions of data points where readily available, user-friendly, and customizable software tools are lacking.ResultsHere, we build on years of analytical experience with diverse sample types to develop MetaboDirect, an open-source, command-line based pipeline for the analysis, visualization, and presentation of metabolomics data by direct injection FTICR-MS after molecular formula assignment has been performed. When compared to all other available FTICR software, MetaboDirect is superior with respect to its compute time as it only requires a single line of code that launches a fully automated framework for the generation and visualization of a wide range of plots, with minimal coding experience required. Among the tools evaluated, MetaboDirect is also uniquely able to automatically generate biochemical transformation networks (ab initio) based on mass differences that provide a comprehensive experimental assessment of metabolite connectives within a given sample or a complex metabolic system, thereby providing important information about the nature of the samples and the set of the microbial reactions or pathways that gave rise to them. Finally, for more experienced users, MetaboDirect allows users to customize plots, outputs, and analyses.ConclusionApplication of MetaboDirect to FTICR-MS-based metabolomics datasets from a marine phage-bacterial infection experiment and aSphagnumleachate microbiome incubation experiment showcase the exploration capabilities of the pipeline that will enable the FTICR-MS research community to evaluate and interpret their data in greater depth and in less time. It will further advance our knowledge of how microbial communities influence and are influenced by the chemical makeup of the surrounding system. Source code and User’s guide of MetaboDirect are freely available through (https://github.com/Coayala/MetaboDirect) and (https://metabodirect.readthedocs.io/en/latest/) respectively.
Edge-based growth control inArabidopsisinvolves two cell wall-associated Receptor-Like Proteins
Authors: Elliott Liam , Kalde Monika , Schuerholz Ann-Kathrin , Wolf Sebastian , Moore Ian , Kirchhelle Charlotte 
Published: June 2022

SummaryMorphogenesis of multicellular organs requires coordination of cellular growth. In plants, 3D growth is driven by undirected turgor pressure, whereas growth directionality is controlled by cell wall mechanical properties at 2D cell faces. Their shared cell wall also fixes cells in their position, and plants thus have to integrate tissue-scale mechanical stresses arising due to growth in a fixed tissue topology. This implies a need to monitor cell wall mechanical and biochemical status and to adapt growth accordingly. Here, we propose that plant cells use their 1D cell edges to monitor cell wall status. We describe two Receptor-Like Proteins, RLP4 and RLP4-L1, which occupy a unique polarity domain at cell edges established through a targeted secretory transport pathway. We show that at cell edges, RLP4s associate with the cell wall via their extracellular domain, and contribute to directional growth control inArabidopsis.
Multiple memory systems for efficient temporal order memory
Authors: Jafarpour Anna , Lin Jack J. , Knight Robert T. , Buffalo Elizabeth A. 
Published: June 2022

AbstractWe report the distinct contribution of multiple memory systems to retrieval of the temporal order of events. The neural dynamics related to retrieval of movie scenes revealed that recalling the temporal order of close events elevates hippocampal theta power, like that observed for recalling close spatial relationships. In contrast, recalling far events elevates beta power in the orbitofrontal cortex, reflecting recall based on the overall movie structure.
Asymmetric retinal direction tuning predicts optokinetic eye movements across stimulus conditions
Authors: Harris Scott C. , Dunn Felice A. 
Published: June 2022

ABSTRACTAcross species, the optokinetic reflex (OKR) stabilizes vision during self-motion. OKR occurs when ON direction-selective retinal ganglion cells (oDSGCs) detect slow, global image motion on the retina. How oDSGC activity is integrated centrally to generate behavior remains unknown. Here, we discover mechanisms that contribute to motion encoding in vertically-tuned oDSGCs, and leverage these findings to empirically define signal transformation between retinal output and vertical OKR behavior. We demonstrate that motion encoding in vertically-tuned oDSGCs is contrast-sensitive and asymmetric for oDSGC types that prefer opposite directions. These phenomena arise from the interplay between spike threshold nonlinearities and differences in synaptic input weights, including shifts in the balance of excitation and inhibition. In behaving mice, these neurophysiological observations, along with a central subtraction of oDSGC outputs, accurately predict the trajectories of vertical OKR across stimulus conditions. Thus, asymmetric tuning across competing sensory channels can critically shape behavior.
Adaptation shapes local cortical reactivity: from bifurcation diagram and simulations to human physiological and pathological responses
Authors: Cattani Anna , Galluzzi Andrea , Fecchio Matteo , Pigorini Andrea , Mattia Maurizio , Massimini Marcello 
Published: June 2022

AbstractHuman studies employing intracerebral and transcranial perturbations suggest that the input-output properties of cortical circuits are dramatically affected during sleep in healthy subjects as well as in awake patients with multifocal and focal brain injury. In all these conditions, cortical circuits react to direct stimulation with an initial activation followed by suppression of activity (Off-period) that disrupts the build-up of sustained causal interactions typically observed in healthy wakefulness. The transition to this stereotypical response is of clinical relevance, being associated with loss of consciousness or loss of function. Here, we provide a mechanistic explanation of these findings by means of mean-field theory and simulations of a cortical-like module endowed with activity-dependent adaptation. First, we show that fundamental aspects of the local responses elicited in humans by direct cortical stimulation can be replicated by systematically varying the relationships between adaptation strength and excitation level in the network. Then, we reveal a region in the adaptation-excitation parameter space of key relevance for both physiological and pathological conditions, where spontaneous activity and responses to perturbation diverge in their ability to reveal Off-periods. Finally, we substantiate through simulations of connected cortical-like modules the role of adaptation mechanisms in preventing cortical neurons from engaging in reciprocal causal interactions, as suggested by empirical studies. These modeling results provide a general theoretical framework and a mechanistic interpretation for a body of neurophysiological measurements that bears key relevance for physiological states as well as for the assessment and rehabilitation of brain-injured patients.Significance StatementSuppression of cortical activity following an initial activation is a defining feature of deep sleep in healthy subjects and wakefulness in patients affected by focal and multifocal brain injuries. Experimental findings suggest that these bimodal responses disrupt the emergence of complex interactions among cortical regions, leading to loss of consciousness or functional impairments. Given their practical implications, it is important to study the mechanisms involved within a general theoretical framework. Using a neuronal network model, we provide evidence for a key role of activity-dependent adaptation mechanisms in shaping the responses to perturbation and in affecting the build-up of complex cortical interactions. Overall, this work provides a mechanistic interpretation relevant for the stratification, follow-up, and rehabilitation of brain-injured patients.
Zinc binding inhibits cellular uptake and antifungal activity of Histatin-5 in Candida albicans
Authors: Campbell Joanna X. , Gao Sean , Anand Keerthi S. , Franz Katherine J. 
Published: June 2022

AbstractHistatin-5 (Hist-5) is a polycationic, histidine-rich antimicrobial peptide with potent antifungal activity against the opportunistic fungal pathogen Candida albicans. Hist-5 has the ability to bind metals in vitro and metals have been shown to alter the fungicidal activity of the peptide. Previous reports on the effect of Zn2+ on Hist-5 activity have been varied and seemingly contradictory. Here we present data elucidating the dynamic role Zn2+ plays as an inhibitory switch to regulate Hist-5 fungicidal activity. A novel fluorescently labeled Hist-5 peptide (Hist-5*) was developed to visualize changes in internalization and localization of the peptide as a function of metal availability in the growth medium. Hist-5* was verified for use as a model peptide and retained antifungal activity and mode of action similar to native Hist-5. Cellular growth assays showed that Zn2+ had a concentration-dependent inhibitory effect on Hist-5 antifungal activity. Imaging by confocal microscopy revealed that equimolar concentrations of Zn2+ kept the peptide localized along the cell periphery rather than internalizing, thus preventing cytotoxicity and membrane disruption. However, the Zn-induced decrease in Hist-5 activity and uptake was rescued by decreasing Zn2+ availability upon addition of a metal chelator EDTA or S100A12, a Zn-binding protein involved in the innate immune response. These results lead us to suggest a model wherein commensal C. albicans may exist in harmony with Hist-5 at concentrations of Zn2+ that inhibit peptide internalization and antifungal activity. Activation of host immune processes that initiate Zn-sequestering mechanisms of nutritional immunity could trigger Hist-5 internalization and cell killing.
Effect of entomopathogenic fungus Metarhizium robertsii on disease incidence of Faba beans (Vicia faba L.) in field conditions
Authors: Ashmarina Lyudmila F. , Sadokhina Tatiana A. , Tyurin Maxim , Danilovb Victor P. , Glupov Victor 
Published: June 2022

AbstractFaba beans (Vicia faba L.) are affected by a large number of pathogens. Studies carried out in western Siberia revealed the influence of the entomopathogenic fungus Metarhizium robertsii on reducing the development and prevalence of a complex of diseases in faba bean in the field. There was a decreasing tendency of the level of phytopathogen infection of seed material and fragments of underground organs during presowing treatment of the bean seeds with M. robertsii. Treatment with M. robertsii significantly reduced the development of root rot by 2.9 and 9.5 times in 2019 and 2020, respectively, and the prevalence of the disease decreased by 2.9-3.0 times. It also resulted in reduction of the severity of diseases of aerial organs during the growing season on average for the plant: the disease development index (DDI) of powdery mildew by 3.8 times and chocolate spot by 3.5 times. There was a significant increase in the number of active nodules on the roots of plants during the treatment with M. robertsii. The results obtained indicate that the treatment of bean seeds with the entomopathogenic fungus M. robertsii improved the phytosanitary situation of the sowing of the crop, and in the future, this technique can be used in agricultural practice.
The effects of background noise on a biophysical model of olfactory bulb mitral cells
Authors: Craft Michelle , Ly Cheng 
Published: June 2022

AbstractThe spiking activity of mitral cells (MC) in the olfactory bulb is a key attribute in olfactory sensory information processing to downstream cortical areas. A more detailed understanding of the modulation of MC spike statistics could shed light on mechanistic studies of olfactory bulb circuits, and olfactory coding. We study the spike response of a recently developed single-compartment biophysical MC model containing 7 known ionic currents and calcium dynamics subject to constant current input with background white noise. We observe rich spiking dynamics even with constant current input, including multimodal peaks in the interspike interval distribution (ISI). Although weak to moderate background noise for a fixed current input does not change the firing rate much, the spike dynamics can change dramatically, exhibiting non-monotonic spike variability not commonly observed in standard neuron models. We explain these dynamics with a phenomenological model of the ISI probability density function. Our study clarifies some of the complexities of MC spiking dynamics.
Assessment of models for calculating the hydrodynamic radius of intrinsically disordered proteins
Authors: Pesce Francesco , Newcombe Estella A. , Seiffert Pernille , Tranchant Emil E. , Olsen Johan G. , Grace Christy R. , Kragelund Birthe B. , Lindorff-Larsen Kresten 
Published: June 2022

ABSTRACTDiffusion measurements by pulsed field gradient NMR and fluorescence correlation spectroscopy can be used to probe the hydrodynamic radius of proteins, which contains information about the overall dimension of a protein in solution. The comparison of this value with structural models of intrinsically disordered proteins is nonetheless impaired by the uncertainty of the accuracy of the methods for computing the hydrodynamic radius from atomic coordinates. To tackle this issue, we here build conformational ensembles of 11 intrinsically disordered proteins that we ensure are in agreement with measurements of compaction by small-angle X-ray scattering. We then use these ensembles to identify the forward model that more closely fits the radii derived from pulsed field gradient NMR diffusion experiments. Of the models we examined, we find that the Kirkwood-Riseman equation provides the best description of the hydrodynamic radius probed by pulsed field gradient NMR experiments. While some minor discrepancies remain, our results enable better use of measurements of the hydrodynamic radius in integrative modelling and for force field benchmarking and parameterization.SIGNIFICANCEAccurate models of the conformational properties of intrinsically disordered proteins rely on our ability to interpret experimental data that reports on the conformational ensembles of these proteins in solution. Methods to calculate experimental observables from conformational ensembles are central to link experiments and computation, for example in integrative modelling or the assessment of molecular force fields. Benchmarking such methods is, however, difficult for disordered proteins because it is difficult to construct accurate ensembles without using the data. We here circumvent this problem by combining independent measures of protein compaction to test several methods to calculate the hydrodynamic radius of a disordered protein, as measured by pulsed field gradient NMR diffusion experiments, and find the Kirkwood-Riseman model to be most accurate.