bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep Heterogeneous Dilation of LSTM for Transient-phase Gesture Prediction through High-density Electromyography: Towards Application in Neurorobotics
Authors: Sun Tianyun , Hu Qin , Libby Jacqueline , Atashzar S. Farokh 
Published: October 2021

AbstractDeep networks have been recently proposed to estimate motor intention using conventional bipolar surface electromyography (sEMG) signals for myoelectric control of neurorobots. In this regard, Deepnets are generally challenged by long training times (affecting practicality and calibration), complex model architectures (affecting the predictability of the outcomes), and a large number of trainable parameters (increasing the need for big data). Capitalizing on our recent work on homogeneous temporal dilation in a Recurrent Neural Network (RNN) model, this paper proposes, for the first time, heterogeneous temporal dilation in an LSTM model and applies that to high-density surface electromyography (HD-sEMG), allowing for the decoding of dynamic temporal dependencies with tunable temporal foci. In this paper, a 128-channel HD-sEMG signal space is considered due to the potential for enhancing the spatiotemporal resolution of human-robot interfaces. Accordingly, this paper addresses a challenging motor intention decoding problem of neurorobots, namely, transient intention identification. Our approach uses only the dynamic and transient phase of gesture movements when the signals are not stabilized or plateaued, which can significantly enhance the temporal resolution of human-robot interfaces. This would eventually enhance seamless real-time implementations. Additionally, this paper introduces the concept of “dilation foci” to modulate the modeling of temporal variation in transient phases. In this work a high number (e.g., 65) of gestures is included, which adds to the complexity and significance of the understudied problem. Our results show state-of-the-art performance for gesture prediction in terms of accuracy, training time, and model convergence.
Descriptive analysis of social determinant of mental health factors in an ethnically diverse Black adult population
Authors: Pederson Aderonke Bamgbose , Hawkins Devan , Lartey Lynette 
Published: October 2021

AbstractBackgroundBlack adults are often treated as a homogeneous group in research and health care despite the diversity within the Black population across ethnicity. This study considers ethnicity in assessing the heterogeneity among Black adults across multiple social determinants of mental health. Understanding the diversity within the Black population will help close the gap in mental health disparities by offering a more streamlined approach to meeting unmet mental health needs.MethodsA cross-sectional descriptive study and analysis was conducted among Black adults in the United States (n = 269, ages 18-65) from diverse ethnic backgrounds (African-Americans, African immigrants, Afro-Caribbean immigrants). We calculated mean differences according to ethnicity, citizenship status, age group, and gender in the areas of medical mistrust, use of mental health services, depression symptom severity, mental health knowledge and stigma behavior.ResultsAfrican Americans with moderate to severe depression symptoms had greater stigma behavior (mean = 12.2, SD = 3.2), than African Americans who screened in the minimal to mild depression range (mean = 13.1, SD = 3.5). Black immigrants across the spectrum of depression scores had greater stigma than African Americans (p = 0.037). Participants who identified as male had a prevalence of mild depression (5-9) that was 1.7 times higher than those who identified as female. Whereas, those who identified as female had a prevalence that was 1.2 times higher for moderate to severe depression (10-19) and 4.7 times higher for severe depression (20-27) compared to males (p = 0.021). Non-United States citizens reported higher medical mistrust (mean value difference = 0.16) compared to United States citizens (p = 0.011). We found statistically significant differences in depression symptom severity based on gender, prevalence of depression, medical mistrust and stigma behavior across demographic factors within the sample.ConclusionThis study shows key variations across social determinant of mental health factors within the Black adult population. There is a need to better understand the heterogeneity within the Black population in order to improve the effectiveness of programs that seek to reduce mental health disparities.
Structure Insight into Photosystem I Octamer from Cyanobacteria
Authors: Chen Ming , He Yujie , Liu Dongyang , Tian Lijin , Xu Pengqi , Liu Xuan , Pan Yihang , He Jun , Zhang Ying 
Published: October 2021

ABSTRACTDiversity of photosystem oligomers is essential to understand how photosynthetic organisms adopted to light conditions. Given by the structural and physiological significance, the assemblies of PSI supercomplex is of great interest in both chloroplast and cyanobacteria recently. In this study, two novel photosystem I supercomplexes were isolated for the first time from the low light incubated culture of filamentous cyanobacterium Anabaena sp. PCC 7120. These complexes were defined as PSI hexamers and octamers through biochemical and biophysical characterization. Their 77K emission spectra indicated that the red forms of chlorophylls seemed not to be affected during oligomerization. By cryo-EM single particle analysis, a near-atomic (7.0 Å) resolution structure of PSI octamer was resolved, and the molecular assemblies of stable PSI octamer was revealed.
Sequence dependencies and mutation rates of localized mutational processes in cancer
Authors: Poulsgaard Gustav Alexander , Sørensen Simon Grund , Juul Randi Istrup , Nielsen Morten Muhlig , Pedersen Jakob Skou 
Published: October 2021

AbstractBackgroundCancer mutations accumulate through replication errors and DNA damage coupled with incomplete repair. Individual mutational processes often show strong sequence and regional preferences. As a result, some sequence contexts mutate at much higher rates than others. Mutational hotspots, with recurrent mutations across cancer samples, represent genomic positions with elevated mutation rates, often caused by highly localized mutational processes.ResultsWe analyze the mutation rates of all 11-mer genomic sequence contexts using the PCAWG set of 2,583 pan-cancer whole genomes. We further associate individual mutations and contexts to mutational signatures and estimate their relative mutation rates. We show that hotspots generally identify highly mutable sequence contexts. Using these, we show that some mutational signatures are enriched in hotspot sequence contexts, corresponding to well-defined sequence preferences for the underlying localized mutational processes. This includes signature 17b (of unknown etiology) and signatures 62 (POLE), 7a (UV), and 72 (linked to lymphomas). In some cases, the mutation rate increases further when focusing on certain genomic regions, such as signature 62 in poised promoters, where the mutation is increased several thousand folds over the overall data set average.ConclusionWe summarize our findings in a catalog of localized mutational processes, their sequence preferences, and their estimated mutation rates.
Brain macrophages acquire distinct transcriptomes prior to demyelination in multiple sclerosis
Authors: Miedema Anneke , Gerrits Emma , Brouwer Nieske , Jiang Qiong , Kracht Laura , Meijer Michel , Nutma Erik , Peferoen-Baert Regina , Pijnacker Anna T.E. , Wesseling Evelyn M. , Wijering Marion H.C. , Gabius Hans-Joachim , Amor Sandra , Eggen Bart J.L. , Kooistra Susanne M. 
Published: October 2021

AbstractMultiple sclerosis (MS) is a disease of the central nervous system (CNS) that is characterized by inflammation and focal areas of demyelination, ultimately resulting in axonal degradation and neuronal loss. Several lines of evidence point towards a role for microglia and other brain macrophages in disease initiation and progression, but exactly how lesion formation is triggered is currently unknown. Here, we characterized early changes in MS brain tissue through transcriptomic analysis of normal appearing white matter (NAWM). We found that NAWM was characterized by enriched expression of genes associated with inflammation and cellular stress derived from brain macrophages. Single cell RNA sequencing confirmed an early stress response in brain macrophages in NAWM and identified specific macrophage subsets that associate with different stages of demyelinating lesions. These early changes associated with lesion development in MS brain tissue may provide therapeutic targets to limit lesion progression and demyelination.
Long-term stability of single neuron activity in the motor system
Authors: Jensen Kristopher T. , Harpaz Naama Kadmon , Dhawale Ashesh K. , Wolff Steffen B. E. , Ölveczky Bence P. 
Published: October 2021

AbstractHow an established behavior is retained and stably produced by a nervous system in constant flux remains a mystery. One possible solution is to fix the activity patterns of single neurons in the relevant circuits. Alternatively, activity in single cells could drift over time provided that the population dynamics are constrained to produce stable behavior. To arbitrate between these possibilities, we recorded single unit activity in motor cortex and striatum continuously for several weeks as rats performed stereotyped motor behaviors – both learned and innate. We found long-term stability in single neuron activity patterns across both brain regions. A small amount of drift in neural activity, observed over weeks of recording, could be explained by concomitant changes in task-irrelevant behavioral output. These results suggest that stereotyped behaviors are generated by stable single neuron activity patterns.
Neurons in human pre-supplementary motor area encode key computations for value-based choice
Authors: Aquino Tomas G. , Cockburn Jeffrey , Mamelak Adam N. , Rutishauser Ueli , O’Doherty John P. 
Published: October 2021

AbstractAdaptive behavior in real-world environments demands that choices integrate over several variables, including the novelty of the options under consideration, their expected value, and uncertainty in value estimation. We recorded neurons from the human pre-supplementary motor area (preSMA), ventromedial prefrontal cortex (vmPFC) and dorsal anterior cingulate to probe how integration over decision variables occurs during decision-making. In contrast to the other areas, preSMA neurons not only represented separate pre-decision variables for each choice option, but also encoded an integrated utility signal and, subsequently, the decision itself. Conversely, post-decision related encoding of variables for the chosen option was more widely distributed and especially prominent in vmPFC. Our findings position the human preSMA as central to the implementation of value-based decisions.
Dendritic cell ICAM-1 strengthens immune synapses but is dispensable for effector and memory responses
Authors: Sapoznikov Anita , Kozlovski Stav , Feigelson Sara W , Davidzohn Natalia , Wigoda Noa , Feldmesser Ester , Petrovich-Kopitman Ekaterina , Grafen Anika , Biton Moshe , Alon Ronen 
Published: October 2021

AbstractLymphocyte priming in lymph nodes (LNs) depends on the formation of functional TCR specific immune synapses (ISs) with antigen (Ag) presenting dendritic cells. The high affinity LFA-1 ligand ICAM-1 has been implicated in different ISs studiedin vitro. The in vivo roles of DC ICAM-1 in Ag stimulated T cell differentiation have been unclear. In newly generated DC conditional ICAM-1 knockout mice, we report that under Th1 polarizing conditions, ICAM-1 deficient DCs could not engage in stable conjugates with newly generated CD8 blasts. Nevertheless, these DCs triggered normal lymphocyte priming, proliferation and differentiation into functional cytotoxic T cells (CTLs) and central memory lymphocytes (Tcm) in both vaccinated and virus infected skin. Single cell RNAseq analysis confirmed that Tcm were normally generated in these mice and gave rise to normal T effectors during a recall skin response. Our results suggest that although CD8 T cell blasts tightly bind DC-ICAM-1, strongly adhesive DC-T ISs are not necessary for functional TCR dependent DC mediated CD8 T cell proliferation and differentiation into productive effector and memory lymphocytes.SummarySapoznikov et al generated a new genetic murine model deficient in dendritic cell expression of the key adhesion molecule ICAM-1 and found that CD8 lymphocytes do not require strong adhesion to dendritic cells for antigen-dependent differentiation into effector and memory T cells.
Phylogenetic analysis and in silico studies link spike Q675H mutation to SARS-CoV-2 adaptive evolution
Authors: Anna Bertelli , Pasqualina D’Ursi , Giovanni Campisi , Serena Messali , Maria Milanesi , Marta Giovanetti , Massimo Ciccozzi , Francesca Caccuri , Arnaldo Caruso 
Published: October 2021

AbstractGenotype screening was implemented in Italy and showed a significant prevalence of new SARS-CoV-2 mutants carrying Q675H mutation, near the furin cleavage site of spike protein. Currently, this mutation, which is expressed on different SARS-CoV-2 lineages circulating worldwide, has not been thoughtfully investigated. Therefore, we performed phylogenetic and biocomputational analysis to better understand SARS-CoV-2 Q675H mutants’ evolutionary relationships with other circulating lineages and Q675H function in its molecular context. Our studies reveal that Q675H spike mutation is the result of parallel evolution because it arose independently in separate evolutionary clades. In silico data show that the Q675H mutation gives rise to a hydrogen-bonds network in the spike polar region delimiting the conformational space of the highly flexible loop containing the furin cleavage site. This results in an optimized directionality of arginine residues involved in interaction of spike with the furin binding pocket, thus improving proteolytic exposure of the viral protein. Furin was found to have a greater affinity for Q675H than Q675 substrate conformations. As a consequence, Q675H mutation is likely to confer a fitness advantage to SARS-CoV-2 by promoting a more efficient viral entry. Interestingly, here we show an ongoing increase in the occurrence of Q675H spike mutation in the most common SARS-CoV-2 variants of concern (VOC). This finding highlights that, VOC are still evolving and start acquiring the Q675H mutation. At the same time, it suggests that our hypothesis of fitness advantage prompted by Q675H could be concrete.
Neural network models for spinal implementation of muscle synergies
Authors: Song Yunqing , Hirashima Masaya , Takei Tomohiko 
Published: October 2021

AbstractMuscle synergies have been proposed as functional modules to simplify the complexity of body motor control; however, their neural implementation is still unclear. Converging evidence suggests that output projections of the spinal premotor interneurons (PreM-INs) underlie the formation of muscle synergies, but they exhibit a substantial variation across neurons and exclude standard models assuming a small number of unitary “modules” in the spinal cord. Here we compared neural network models for muscle synergies to seek a biologically plausible model that reconciles previous clinical and electrophysiological findings. We examined three neural network models: one with random connections (non-synergy model), one with a small number of spinal synergies (simple synergy model), and one with a large number of spinal neurons representing muscle synergies with a certain variation (population synergy model). We found that the simple and population synergy models emulate the robustness of muscle synergies against cortical stroke observed in human stroke patients. Furthermore, the size of the spinal variation of the population synergy matched well with the variation in spinal PreM-INs recorded in monkeys. These results suggest that a spinal population with moderate variation is a biologically plausible model for the neural implementation of muscle synergies.
Spindle - slow oscillation coupling correlates with memory performance and connectivity changes in a hippocampal network after sleep
Authors: Bastian Lisa , Samanta Anumita , de Paula Demetrius Ribeiro , Weber Frederik , Schoenfeld Robby , Dresler Martin , Genzel Lisa 
Published: October 2021

AbstractAfter experiences are encoded, post-encoding reactivations during sleep have been proposed to mediate long-term memory consolidation. Spindle-slow oscillation coupling during NREM sleep is a candidate mechanism through which a hippocampal-cortical dialogue may strengthen a newly formed memory engram. Here, we investigated the role of fast spindle- and slow spindle-slow oscillation coupling in the consolidation of spatial memory in humans with a virtual water maze task involving allocentric and egocentric learning strategies. Furthermore, we analyzed how resting-state functional connectivity evolved across learning, consolidation, and retrieval of this task using a data-driven approach. Our results show task-related connectivity changes in the executive control network, the default mode network, and the hippocampal network at post-task rest. The hippocampal network could further be divided into two subnetworks of which only one showed modulation by sleep. Decreased functional connectivity in this subnetwork was associated with higher spindle-slow oscillation coupling power, which was also related to better memory performance at test. Overall, this study contributes to a more holistic understanding of the functional resting-state networks and the mechanisms during sleep associated to spatial memory consolidation.
Parameter and model recovery of reinforcement learning models for restless bandit problems
Authors: Danwitz Ludwig , Mathar David , Smith Elke , Tuzsus Deniz , Peters Jan 
Published: October 2021

AbstractMulti-armed restless bandit tasks are regularly applied in psychology and cognitive neuroscience to assess exploration and exploitation behavior in structured environments. These models are also readily applied to examine effects of (virtual) brain lesions on performance, and to infer neurocomputational mechanisms using neuroimaging or pharmacological approaches. However, to infer individual, psychologically meaningful parameters from such data, computational cognitive modeling is typically applied. Recent studies indicate that softmax (SM) decision rule models that include a representation of environmental dynamics (e.g. the Kalman Filter) and additional parameters for modeling exploration and perseveration (Kalman SMEP) fit human bandit task data better than competing models. Parameter and model recovery are two central requirements for computational models: parameter recovery refers to the ability to recover true data-generating parameters; model recovery refers to the ability to correctly identify the true data generating model using model comparison techniques. Here we comprehensively examined parameter and model recovery of the Kalman SMEP model as well as nested model versions, i.e. models without the additional parameters, using simulation and Bayesian inference. Parameter recovery improved with increasing trial numbers, from around .8 for 100 trials to around .93 for 300 trials. Model recovery analyses likewise confirmed acceptable recovery of the Kalman SMEP model. Model recovery was lower for nested Kalman filter models as well as delta rule models with fixed learning rates.Exploratory analyses examined associations of model parameters with model-free performance metrics. Random exploration, captured by the inverse softmax temperature, was associated with lower accuracy and more switches. For the exploration bonus parameter modeling directed exploration, we confirmed an inverse-U-shaped association with accuracy, such that both an excess and a lack of directed exploration reduced accuracy. Taken together, these analyses underline that the Kalman SMEP model fulfills basic requirements of a cognitive model.
Inhibiting adult neurogenesis differentially affects spatial learning in females and males
Authors: O’Leary Timothy P , Askari Baran , Lee Bonnie , Darby Kathryn , Knudson Cypress , Ash Alyssa M , Seib Desiree R , Espinueva Delane F , Snyder Jason S 
Published: October 2021

ABSTRACTAdult hippocampal neurogenesis has been implicated in the spatial processing functions of the hippocampus but ablating neurogenesis does not consistently lead to behavioral deficits in spatial tasks. Parallel studies have shown that adult-born neurons also regulate behavioral responses to stressful and aversive stimuli. We therefore hypothesized that spatial functions of adult-born neurons may be more prominent under conditions of stress, and may differ between males and females given established sex differences in stress responding. To test this we trained intact and neurogenesis-deficient rats in the spatial water maze at temperatures that vary in their degree of aversiveness. At standard temperatures (25°C) ablating neurogenesis did not alter learning and memory in either sex, consistent with prior work. However, in cold water (16°C), ablating neurogenesis had divergent sex-dependent effects: relative to intact rats, male neurogenesis-deficient rats were slower to escape and female neurogenesis-deficient rats were faster. Neurogenesis promoted temperature-related changes in search strategy in females, but it promoted search strategy stability in males. Females displayed greater recruitment of the dorsal hippocampus than males, particularly at 16°C. However, blocking neurogenesis did not alter activity-dependent immediate-early gene expression in either sex. Finally, morphological analyses of retrovirally-labelled neurons revealed greater experience-dependent plasticity in new neurons in males. Neurons had comparable morphology in untrained rats but 16°C training increased spine density, and 25°C training caused shrinkage of mossy fiber presynaptic terminals, specifically in males. Collectively, these findings indicate that neurogenesis functions in memory are prominent under conditions of stress, they provide the first evidence for sex differences in the behavioral function of newborn neurons, and they suggest possibly distinct roles for neurogenesis in cognition and mental health in males and females.