Miracle-dz/UniFAR-FTUs huggingface dataset:
Control Modification of Grasp Force Covaries Agency and Performance on Rigid and Compliant Surfaces

This study investigated how modifications in the display of a computer trace under user control of grasp forces can co-modulate agency (perception of control) and performance of grasp on rigid and compliant surfaces. We observed positive correlation (p < 0.01) between implicit agency, measured from time-interval estimation for intentional binding, and grasp performance, measured by force-tracking error, across varying control modes for each surface type. The implications of this work are design directives for cognition-centered device interfaces for rehabilitation of grasp after neurotraumas such as spinal cord and brain injuries while considering if grasp interaction is rigid or compliant. These device interfaces should increase user integration to virtual reality training and powered assistive devices such as exoskeletons and prostheses. The modifications in control modes for this study included changes in force magnitude, addition of mild noise, and a measure of automation. Significant differences (p < 0.001) were observed for each surface type across control modes with metrics for implicit agency, performance, and grasp control efficiency. Explicit agency, measured from user survey responses, did not exhibit significant variations in this study, suggesting implicit measures of agency are needed for identifying co-modulation with grasp performance. Grasp on the compliant surface resulted in greater dependence of performance on agency and increases in agency and performance with the addition of mild noise. Noise in conjunction with perceived freedom at a flexible surface may have amplified visual feedback responses. Introducing automation in control decreased agency and performance for both surfaces, suggesting the value in continuous user control of grasp. In conclusion, agency and performance of grasp can be co-modulated across varying modes of control, especially for compliant grasp actions. Future studies should consider reliable measures of implicit agency, including physiological recordings, to automatically adapt rehabilitation interfaces for better cognitive engagement and to accelerate functional outcomes.
The Utility of Specific Antibodies Against SARS-CoV-2 in Laboratory Diagnosis

The Coronavirus Disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has now become a global pandemic due to its high transmissibility. The unavoidable shortcomings of traditional diagnostic assay, including nucleic acid testing, diverse serological assays characterized by high-throughput and less workload, are playing a more and more crucial role to supplement the nucleic acid test. In this review, we summarize the dynamic change of the specific IgM, IgG, and IgA antibodies against SARS-CoV-2 as well as neutralizing antibodies and discuss the clinical utility and limitations of the different serological assays. SARS-CoV-2, a newly discovered virus, shows some unique pathogenetic and epidemiological characteristics that have not been completely understood so far. Currently, studies about the antibody responses against SARS-CoV-2 and the clinical utility of serological testing are increasing. It’s well suggested that the combination of serological tests and nucleic acid tests can cohesively improve the testing efficiency for identifying COVID-19 suspected patients.
A Novel Insecticidal Spider Peptide that Affects the Mammalian Voltage-Gated Ion Channel hKv1.5

Spider venoms include various peptide toxins that modify the ion currents, mainly of excitable insect cells. Consequently, scientific research on spider venoms has revealed a broad range of peptide toxins with different pharmacological properties, even for mammal species. In this work, thirty animal venoms were screened against hKv1.5, a potential target for atrial fibrillation therapy. The whole venom of the spider Oculicosa supermirabilis, which is also insecticidal to house crickets, caused voltage-gated potassium ion channel modulation in hKv1.5. Therefore, a peptide from the spider O. supermirabilis venom, named Osu1, was identified through HPLC reverse-phase fractionation. Osu1 displayed similar biological properties as the whole venom; so, the primary sequence of Osu1 was elucidated by both of N-terminal degradation and endoproteolytic cleavage. Based on its primary structure, a gene that codifies for Osu1 was constructed de novo from protein to DNA by reverse translation. A recombinant Osu1 was expressed using a pQE30 vector inside the E. coli SHuffle expression system. recombinant Osu1 had voltage-gated potassium ion channel modulation of human hKv1.5, and it was also as insecticidal as the native toxin. Due to its novel primary structure, and hypothesized disulfide pairing motif, Osu1 may represent a new family of spider toxins.
ATACgraph: Profiling Genome-Wide Chromatin Accessibility From ATAC-seq

Assay for transposase-accessible chromatin using sequencing data (ATAC-seq) is an efficient and precise method for revealing chromatin accessibility across the genome. Most of the current ATAC-seq tools follow chromatin immunoprecipitation sequencing (ChIP-seq) strategies that do not consider ATAC-seq-specific properties. To incorporate specific ATAC-seq quality control and the underlying biology of chromatin accessibility, we developed a bioinformatics software named ATACgraph for analyzing and visualizing ATAC-seq data. ATACgraph profiles accessible chromatin regions and provides ATAC-seq-specific information including definitions of nucleosome-free regions (NFRs) and nucleosome-occupied regions. ATACgraph also allows identification of differentially accessible regions between two ATAC-seq datasets. ATACgraph incorporates the docker image with the Galaxy platform to provide an intuitive user experience via the graphical interface. Without tedious installation processes on a local machine or cloud, users can analyze data through activated websites using pre-designed workflows or customized pipelines composed of ATACgraph modules. Overall, ATACgraph is an effective tool designed for ATAC-seq for biologists with minimal bioinformatics knowledge to analyze chromatin accessibility. ATACgraph can be run on any ATAC-seq data with no limit to specific genomes. As validation, we demonstrated ATACgraph on human genome to showcase its functions for ATAC-seq interpretation. This software is publicly accessible and can be downloaded at https://github.com/RitataLU/ATACgraph.
A THP-1 Cell Line-Based Exploration of Immune Responses Toward Heat-Treated BLG

Allergen recognition and processing by antigen presenting cells is essential for the sensitization step of food allergy. Macrophages and dendritic cells are both phagocytic antigen presenting cells and play important roles in innate immune responses and signaling between the innate and adaptive immune system. To obtain a model system with a homogeneous genetic background, we derived macrophages and dendritic cells from THP-1 monocytes. The difference between macrophages and dendritic cells was clearly shown by differences in their transcription response (microarray) and protein expression levels. Their resemblance to primary cells was analyzed by comparison to properties as described in literature. The uptake of β-lactoglobulin after wet-heating (60°C in solution) by THP-1 derived macrophages was earlier reported to be significantly increased. To analyse the subsequent immune response, we incubated THP-1 derived macrophages and dendritic cells with native and differently processed β-lactoglobulin and determined the transcription and cytokine expression levels of the cells. A stronger transcriptional response was found in macrophages than in dendritic cells, while severely structurally modified β-lactoglobulin induced a more limited transcriptional response, especially when compared to native and limitedly modified β-lactoglobulin. These results show that processing is relevant for the transcriptional response toward β-lactoglobulin of innate immune cells.
Reactivity of Ag+ ion with thiol ligands in the presence of iron sulfide

Dissolved silver (Ag) in the presence of amorphous iron sulfide(FeS) rapidly equilibrates to ultra‐trace levels ( ∼5 ng/L), which agrees with equilibrium calculations based on Ag2S solubility. This finding, along with the authors' discovery that crystalline Ag2S (acanthite) precipitates rapidly under supersaturated conditions, suggests that a discrete Ag‐S phase is formed. Furthermore, potential interferences (Cl−, Cu2+, and dissolved organic carbon) show no effect on the Ag‐FeS system. Only the presence of organosulfur (thiol) ligands at 10−3 to 10−4 M result in increased dissolved silver. Agreement between calculations and measured values were good for 1.8 × 10−4 M 3‐mercaptopropanoic acid; however, calculations predicted higher dissolved silver than measured values for higher thiol levels, possibly due to Ag‐thiol binding to FeS.
Effects of a Trans-Theoretical Model-Based Health Education Program on the Management of Cognitive Dysfunction in Older Adults With Mild Cognitive Impairment: Study Rationale and Protocol Design for a Randomized Controlled Trial

Introduction: Recent studies have confirmed that the management of cognitive dysfunction produces considerable positive effects in individuals with mild cognitive impairment (MCI), however, compliance with participation in various cognitive dysfunction management strategies remains scant in older adults with MCI. Health education programs can improve the level of knowledge of the disease effectively, though it remains unclear as to whether health education programs are sufficient to promote behavior changes of older adults with MCI in the community. Objective: The study aims to provide insight into the effect of a trans-theoretical Model (TTM)-based health education program on increasing knowledge about mild cognitive impairment (MCI), compliance in cognitive dysfunction management, and other cognition-related health outcomes (general cognitive function, sleep quality, depression symptoms, apathy symptoms) for older adults with MCI. Methods: This study is a single-blinded, randomized, prospective clinical trial. We will recruit 132 participants with MCI who will be randomly assigned to a TTM-based health education group and a standard health education group in a ratio of 1:1. The intervention group will receive a TTM-based health education program (1 session/week, 4–560 min/session for 8 weeks), while the control group will receive standard health education. Assessors blinded to participant allocation will conduct baseline, post-intervention, and 3-month follow-up assessments. Statistical analyses will consist of the Wilcoxon test, the Chi-square test, the T-test, and 2 (group) × 3 (time) ANOVA with a 5% cut-off for significance. Discussion: Supposing the TTM-based health education program will provide validated community-based cognitive dysfunction management strategies for older adults with MCI, this would be a feasible approach to improve the compliance of participation in cognitive dysfunction management and the cognition-related health outcomes. Clinical Trial Registration: ChiCTR1900028351. Registered on December 19, 2019. http://www.chictr. org.cn/edit.aspx? pid=47223&htm=4.
Rethinking Biological Invasions as a Metacommunity Problem

Perhaps more than any other ecological discipline, invasion biology has married the practices of basic science and the application of that science. The conceptual frameworks of population regulation, metapopulations, supply-side ecology, and community assembly have all to some degree informed the regulation, management, and prevention of biological invasions. Invasion biology needs to continue to adopt emerging frameworks and paradigms to progress as both a basic and applied science. This need is urgent as the biological invasion problem continues to worsen. The development of metacommunity theory in the last two decades represents a paradigm-shifting approach to community ecology that emphasizes the multi-scale nature of community assembly and biodiversity regulation. Work on metacommunities has demonstrated that even relatively simple processes at local scales are often heavily influenced by regional-scale processes driven primarily by the dispersal of organisms. Often the influence of dispersal interacts with, or even swamps, the influence of local-scale drivers like environmental conditions and species interactions. An emphasis on dispersal and a focus on multi-scale processes enable metacommunity theory to contribute strongly to the advancement of invasion biology. Propagule pressure of invaders has been identified as one of the most important drivers facilitating invasion, so the metacommunity concept, designed to address how dispersal-driven dynamics affect community structure, can directly address many of the central questions of invasion biology. Here we revisit many of the important concepts and paradigms of biological invasions—propagule pressure, biotic resistance, enemy release, functional traits, neonative species, human-assisted transport,—and view those concepts through the lens of metacommunity theory. In doing so, we accomplish several goals. First, we show that work on metacommunities has generated multiple predictions, models, and the tools that can be directly applied to invasion scenarios. Among these predictions is that invasibility of a community should decrease with both local controls on community assembly, and the dispersal rates of native species. Second, we demonstrate that framing biological invasions in metacommunity terms actually unifies several seemingly disparate concepts central to invasion biology. Finally, we recommend several courses of action for the control and management of invasive species that emerge from applying the concepts of metacommunity theory.
Nicotine Increases Spontaneous Glutamate Release in the Rostromedial Tegmental Nucleus

The rostromedial tegmental nucleus (RMTg) is a bilateral structure localized in the brainstem and comprise of mainly GABAergic neurons. One of the main functions of the RMTg is to regulate the activity of dopamine neurons of the mesoaccumbens pathway. Therefore, the RMTg has been proposed as a modulator of the reward system and adaptive behaviors associated to reward learning. The RMTg receives an important glutamatergic input from the lateral habenula. Also, it receives cholinergic inputs from the laterodorsal and pedunculopontine tegmental nuclei. Previously, it was reported that nicotine increases glutamate release, evoked by electric stimulation, in the RMTg nucleus. However, the mechanisms by which nicotine induces this effect were not explored. In the present work, we performed electrophysiological experiments in brainstem slices to study the effect of nicotine on spontaneous excitatory postsynaptic currents recorded from immunocytochemically identified RMTg neurons. Also, we used calcium imaging techniques to explore the effects of nicotine on multiple RMTg neurons simultaneously. We found that nicotine promotes the persistent release of glutamate through the activation of α7 nicotinic acetylcholine receptors present on glutamatergic afferents and by a mechanism involving calcium release from intracellular stores. Through these mechanisms, nicotine increases the excitability and synchronizes the activity of RMTg neurons. Our results suggest that the RMTg nucleus mediates the noxious effects of the nicotine, and it could be a potential therapeutic target against tobacco addiction.
Global Imperative of Suicidal Ideation in 10 Countries Amid the COVID-19 Pandemic

Background: The novel coronavirus (COVID-19) has had a detrimental impact on individuals' psychological well-being; however, a multi-country comparison on the prevalence of suicidal ideation due to the virus is still lacking. Objectives: To examine the prevalence and correlates of suicidal ideation among the general population across 10 countries during the COVID-19 pandemic. Materials and methods: This was a cross-sectional study which used convenience sampling and collected data by conducting an online survey. Participants were sourced from 10 Eastern and Western countries. The Patient Health Questionnaire (PHQ-9) was used to measure the outcome variable of suicidal ideation. Ordinal regression analysis was used to identify significant predictors associated with suicidal ideation. Results: A total of 25,053 participants (22.7% male) were recruited. Results from the analysis showed that the UK and Brazil had the lowest odds of suicidal ideation compared to Macau (p < 0.05). Furthermore, younger age, male, married, and differences in health beliefs were significantly associated with suicidal ideation (p < 0.05). Conclusions: The findings highlight the need for joint international collaboration to formulate effective suicide prevention strategies in a timely manner and the need to implement online mental health promotion platforms. In doing so, the potential global rising death rates by suicide during the pandemic can be reduced.
Teacher Practices, Peer Dynamics, and Academic Enablers: A Pilot Study Exploring Direct and Indirect Effects Among Children at Risk for ADHD and Their Classmates

Establishing a positive peer climate in elementary school classrooms is an important goal for educators because peer dynamics are thought to affect academic learning. Thus, it is important to (a) understand the relationship between children's peer dynamics and academic functioning, and (b) identify teacher practices that influence both peer processes and academic outcomes. In this pilot study, we explored whether specific teacher strategies that promote positive behaviors in children and positive peer dynamics influence children's better academic enablers, as well as whether they do so indirectly via improving peer sociometric ratings. Such teacher strategies may be particularly relevant for supporting children who demonstrate impairment in both social and academic domains, such as children at risk for attention-deficit/hyperactivity disorder (ADHD). Thus, we also examined whether these relationships differ for children with elevated ADHD symptoms and peer problems (i.e., target students), relative to classmates (i.e., non-target students). Participants were 194 children in the classrooms of 12 teachers (grades K-4) who participated in an open-trial pilot study of the school-based version of the Making Socially Accepting Inclusive Classrooms (MOSAIC) program. In the fall and spring of a school year, we assessed children's sociometric ratings received from peers, and academic enabler skills as rated by teachers. Throughout one academic year, we obtained assessments of teachers' use of MOSAIC strategies (observed and self-reported). Results showed that, after accounting for fall academic enablers, the teacher strategy of CARE time (involving one-on-one interaction with the student to build the teacher-student relationship) was positively associated with spring academic enablers. However, findings did not support the hypothesized indirect effect of peer sociometric ratings on the relationship between teacher strategy use and academic enablers, or the moderated indirect effect by target student status. Implications for future research and classroom interventions are discussed.
Comparative Decomposition of Humans and Pigs: Soil Biogeochemistry, Microbial Activity and Metabolomic Profiles

Vertebrate decomposition processes have important ecological implications and, in the case of human decomposition, forensic applications. Animals, especially domestic pigs (Sus scrofa), are frequently used as human analogs in forensic decomposition studies. However, recent research shows that humans and pigs do not necessarily decompose in the same manner, with differences in decomposition rates, patterns, and scavenging. The objective of our study was to extend these observations and determine if human and pig decomposition in terrestrial settings have different local impacts on soil biogeochemistry and microbial activity. In two seasonal trials (summer and winter), we simultaneously placed replicate human donors and pig carcasses on the soil surface and allowed them to decompose. In both human and pig decomposition-impacted soils, we observed elevated microbial respiration, protease activity, and ammonium, indicative of enhanced microbial ammonification and limited nitrification in soil during soft tissue decomposition. Soil respiration was comparable between summer and winter, indicating similar microbial activity; however, the magnitude of the pulse of decomposition products was greater in the summer. Using untargeted metabolomics and lipidomics approaches, we identified 38 metabolites and 54 lipids that were elevated in both human and pig decomposition-impacted soils. The most frequently detected metabolites were anthranilate, creatine, 5-hydroxyindoleacetic acid, taurine, xanthine, N-acetylglutamine, acetyllysine, and sedoheptulose 1/7-phosphate; the most frequently detected lipids were phosphatidylethanolamine and monogalactosyldiacylglycerol. Decomposition soils were also significantly enriched in metabolites belonging to amino acid metabolic pathways and the TCA cycle. Comparing humans and pigs, we noted several differences in soil biogeochemical responses. Soils under humans decreased in pH as decomposition progressed, while under pigs, soil pH increased. Additionally, under pigs we observed significantly higher ammonium and protease activities compared to humans. We identified several metabolites that were elevated in human decomposition soil compared to pig decomposition soil, including 2-oxo-4-methylthiobutanoate, sn-glycerol 3-phosphate, and tryptophan, suggesting different decomposition chemistries and timing between the two species. Together, our work shows that human and pig decomposition differ in terms of their impacts on soil biogeochemistry and microbial decomposer activities, adding to our understanding of decomposition ecology and informing the use of non-human models in forensic research.
Genome-Wide Association Study of Maize Aboveground Dry Matter Accumulation at Seedling Stage

Dry matter accumulation and partitioning during the early phases of development could significantly affect crop growth and productivity. In this study, the aboveground dry matter (DM), the DM of different organs, and partition coefficients of a maize association mapping panel of 412 inbred lines were evaluated at the third and sixth leaf stages (V3 and V6). Further, the properties of these phenotypic traits were analyzed. Genome-wide association studies (GWAS) were conducted on the total aboveground biomass and the DM of different organs. Analysis of GWAS results identified a total of 1,103 unique candidate genes annotated by 678 significant SNPs (P value < 1.28e–6). A total of 224 genes annotated by SNPs at the top five of each GWAS method and detected by multiple GWAS methods were regarded as having high reliability. Pathway enrichment analysis was also performed to explore the biological significance and functions of these candidate genes. Several biological pathways related to the regulation of seed growth, gibberellin-mediated signaling pathway, and long-day photoperiodism were enriched. The results of our study could provide new perspectives on breeding high-yielding maize varieties.