Miracle-dz/UniFAR-FTUs huggingface dataset:
Predicting Factors of Professional Behavior of Indonesian Nurses, West Java Province, Indonesia

Background: The understanding of how nurses perceive the concept of professionalism has always been fundamental in terms of creating appropriate policy. However, Indonesia managed to pass the updated Nursing Act in 2014 and has been struggling to create proper policy regarding nurses so far. It is apparent that the main problem is due to the lack of clarity in giving meaning towards the perception of professionalism. As a result, there is an immediate need to properly describe and analyze several factors that may be significantly related to nurse professionalism in general. This study aims to examine and identify the predicting factors of professional behavior of Indonesian nurses, in West Java, Indonesia. Methods: A descriptive predictive study was conducted at three type A hospitals in West Java. A total of 160 participants were recruited for the study. The personal factor questionnaire, General Self-Efficacy scale (GSE), Survey of Perceived Organizational Support (SPOS), Psychological Empowerment Questionnaire, and Registered Nurses’ Association of Ontario (RNAO) professionalism questionnaire were used to collect the data. Descriptive statistics, Pearson’s r correlation, Chi-square test, and Stepwise multiple regression were used to analyze the data. Results: Study results indicate that perceived organizational supports had a low relation with professional behavior in nursing (r = .210; p = .008). Both self-efficacy and psychological empowerment showed a moderate relation to professional behavior (r = .576; p = < .001; r = .558; p = <001, respectively). Furthermore, personal factors which consist of level of education (X² = 20.363) and years of experience (r = .499; p = <.001) also showed moderate relationships. The overall perception of professional behavior by Indonesian nurses had a good ranking score (M= 3.81-4.26) for each component of professional behaviors. The Stepwise multiple regression resulted in four variables being selected for the model: self-efficacy, psychological empowerment, years of experience and education explained 49.1 % of the variance of professional behavior, (R² = .478). Conclusion: The conclusion for this study indicates that self-efficacy, psychological empowerment, years of experience and education together can statistically predict professional behavior of Indonesian nurses in West Java. Greater effort, however, is required to improve self-efficacy and psychological empowerment due to such average results. Notably, the weakest relationship variable found in this study was organizational support, which implies an immediate need to construct a policy to improve and maintain various forms of institutional support channels for nurses in West Java.
Smarter Crowdsourcing for Zika and Other Mosquito-Borne Diseases: A Handbook of Innovative Legal, Technical, and Policy Proposals and a Guide to their Implementation

The Inter-American Development Bank and New York University’s GovLab have convened ministries of health from four countries, including Argentina, Colombia, Panama and the City of Rio de Janeiro, Brazil, for a pilot initiative to quickly generate responses to the Zika epidemic in the Latin American and Caribbean Region. This collaboration, known as “Smarter Crowdsourcing for Zika” convened over 100 subject-matter experts and public health practitioners from around the world via online conferences to discuss viable areas for preventing and responding to mosquito-borne diseases (MBDs). This investigative process identified innovative solutions across several areas, including public awareness, behavioral change, long-term care for complications secondary to the Zika infection, as well as data governance and predictive analytics. This document provides a detailed set of recommendations for guiding the implementation of the discussed solutions.
Monoclonal antibodies for the S2 subunit of spike of SARS-CoV cross-react with the newly-emerged SARS-CoV-2

The emergence of a novel coronavirus, SARS-CoV-2, at the end of 2019 has resulted in widespread human infections across the globe. While genetically distinct from SARS-CoV, the etiological agent that caused an outbreak of severe acute respiratory syndrome (SARS) in 2003, both coronaviruses exhibit receptor binding domain (RBD) conservation and utilize the same host cell receptor, angiotensin-converting enzyme 2 (ACE2), for virus entry. Therefore, it will be important to test the cross-reactivity of antibodies that have been previously generated against the surface spike (S) glycoprotein of SARS-CoV in order to aid research on the newly emerged SARS-CoV-2. Here, we show that an immunogenic domain in the S2 subunit of SARS-CoV S is highly conserved in multiple strains of SARS-CoV-2. Consistently, four murine monoclonal antibodies (mAbs) raised against this immunogenic SARS-CoV fragment were able to recognise the S protein of SARS-CoV-2 expressed in a mammalian cell line. Importantly, one of them (mAb 1A9) was demonstrated to detect S in SARS-CoV-2-infected cells. To our knowledge, this is the first study showing that mAbs targeting the S2 domain of SARS-CoV can cross-react with SARS-CoV-2 and this observation is consistent with the high sequence conservation in the S2 subunit. These cross-reactive mAbs may serve as tools useful for SARS-CoV-2 research as well as for the development of diagnostic assays for its associated coronavirus disease COVID-19.
Identification and characterization of long noncoding RNAs and their association with acquisition of blood meal in Culex quinquefasciatus

The Southern house mosquito, Culex quinquefasciatus (Cx. quinquefasciatus) is an important vector that transmit multiple diseases including West Nile encephalitis, Japanese encephalitis, St. Louis encephalitis and lymphatic filariasis. Long noncoding RNAs (lncRNAs) involve in many biological processes such development, infection, and virus-host interaction. However, there is no systematic identification and characterization of lncRNAs in Cx. quinquefasciatus. Here, we report the first ever lncRNA identification in Cx. quinquefasciatus. By using 31 public RNA-seq datasets, a total of 4,763 novel lncRNA transcripts were identified, of which 3,591, 569, and 603 were intergenic, intronic, and antisense respectively. Examination of genomic features revealed that Cx. quinquefasciatus shared similar characteristics with other species such as short in length, low GC content, low sequence conservation, and low coding potential. Furthermore, compared to protein-coding genes, Cx. quinquefasciatus lncRNAs had lower expression values, and tended to be expressed in temporally-specific fashion. In addition, weighted correlation network and functional annotation analyses showed that lncRNAs may have roles in blood meal acquisition of adult female Cx. quinquefasciatus mosquitoes. This study presents the first systematic identification and analysis of Cx. quinquefasciatus lncRNAs and their association with blood feeding. Results generated from this study will facilitate future investigation on the function of Cx. quinquefasciatus lncRNAs.
Population structure and dispersal across small and large spatial scales in a direct developing marine isopod

Marine organisms generally exhibit one of two developmental modes: biphasic, with distinct adult and larval morphology, and direct development, in which larvae resemble adults. Developmental mode is thought to significantly influence dispersal, with direct developers expected to have much lower dispersal potential. However, in contrast to our relatively good understanding of dispersal and population connectivity for biphasic species, comparatively little is known about direct developers. In this study, we use a panel of 8,020 SNPs to investigate population structure and gene flow for a direct developing species, the New Zealand endemic marine isopod Isocladus armatus. On a small spatial scale (20 kms), gene flow between locations is extremely high and suggests an island model of migration. However, over larger spatial scales (600km), populations exhibit a clear pattern of isolation-by-distance. Because our sampling range is intersected by two well-known biogeographic barriers (the East Cape and the Cook Strait), our study provides an opportunity to understand how such barriers influence dispersal in direct developers. Our results indicate that I. armatus exhibits significant migration across these barriers, and suggests that ocean currents associated with these locations do not present a barrier to dispersal. Interestingly, we do find evidence of a north-south population genetic break occurring between Māhia and Wellington, two locations where there are no obvious biogeographic barriers between them. We conclude that developmental life history largely predicts dispersal in intertidal marine isopods. However, localised biogeographic processes can disrupt this expectation.
The Role of Potassium and Host Calcium Signaling in Toxoplasma gondii egress

Toxoplasma gondii, an obligate intracellular parasite, is capable of invading virtually any nucleated cell. Ca2+ signaling is universal and both T. gondii and its mammalian host cell will utilize Ca2+ signaling to stimulate diverse cellular functions. Egress of T. gondii from the host cell is an essential step for the infection cycle of T. gondii and a cytosolic Ca2+ increase initiates the Ca2+ signaling cascade that culminates in stimulation of motility and egress. In this work we demonstrate that intracellular T. gondii is capable of taking up Ca2+ from the host cytoplasm when this concentration is increased during host signaling events. Both intracellular and extracellular Ca2+ sources are important to reach a threshold of cytosolic Ca2+ needed for a successful egress. Two peaks of Ca2+ were observed in single parasites that egressed with the second peak resulting from Ca2+ influx. We patched infected host cells to allow a precise delivery of exact concentrations of Ca2+ for stimulating motility and egress. Using this approach, we found that low potassium concentration modulates but do not trigger host cell egress. This is the first study using whole-cell patches to study the role of ions such as K+ and Ca2+ in T. gondii egress.
Genomic islands of differentiation in a rapid avian radiation have been driven by recent selective sweeps

Significance Genome-wide scans can identify differentiated loci between species that may have promoted speciation. So-called “islands of differentiation” have generally been identified and characterized using standard population genetic summary statistics (e.g., FST and dxy), which are limited in distinguishing among possible causes of differentiation, such as selection against gene flow and selective sweeps. We introduce a powerful strategy for analyzing such islands, combining new methods for inferring the full ancestral recombination graph and machine learning methods for identifying selective sweeps. We applied our methods to genomic sequences from closely related southern capuchino seedeaters (Neotropical tanagers) and found signatures of recent selective sweeps around pigmentation genes, including many soft sweeps that acted on standing variation. Numerous studies of emerging species have identified genomic “islands” of elevated differentiation against a background of relative homogeneity. The causes of these islands remain unclear, however, with some signs pointing toward “speciation genes” that locally restrict gene flow and others suggesting selective sweeps that have occurred within nascent species after speciation. Here, we examine this question through the lens of genome sequence data for five species of southern capuchino seedeaters, finch-like birds from South America that have undergone a species radiation during the last ∼50,000 generations. By applying newly developed statistical methods for ancestral recombination graph inference and machine-learning methods for the prediction of selective sweeps, we show that previously identified islands of differentiation in these birds appear to be generally associated with relatively recent, species-specific selective sweeps, most of which are predicted to be soft sweeps acting on standing genetic variation. Many of these sweeps coincide with genes associated with melanin-based variation in plumage, suggesting a prominent role for sexual selection. At the same time, a few loci also exhibit indications of possible selection against gene flow. These observations shed light on the complex manner in which natural selection shapes genome sequences during speciation.
Combining tensor decomposition and time warping models for multi-neuronal spike train analysis

Recordings from large neural populations are becoming an increasingly popular and accessible method in experimental neuroscience. While the activity of individual neurons is often too stochastic to interrogate circuit function on a moment-by-moment basis, multi-neuronal recordings enable us to do so by pooling statistical power across many cells. For example, groups of neurons often exhibit correlated gain or amplitude modulation across trials, which can be statistically formalized in a tensor decomposition framework (Williams et al. 2018). Additionally, the time course of neural population dynamics can be shifted or stretched/compressed, which can be modeled by time warping methods (Williams et al. 2020). Here, I describe how these two modeling frameworks can be combined, and show some evidence that doing so can be highly advantageous for practical neural data analysis—for example, the presence of random time shifts hampers the performance and interpretability of tensor decomposition, while a time-shifted variant of this model corrects for these disruptions and uncovers ground truth structure in simulated data.
HisTrader: A Tool to Identify Nucleosome Free Regions from ChIP-Seq of Histone Post-Translational Modifications

Motivation Chromatin immuno-precipitation sequencing (ChIP-Seq) of histone post-translational modifications coupled with de novo motif elucidation and enrichment analyses can identify transcription factors responsible for orchestrating transitions between cell-and disease-states. However, the identified regulatory elements can span several kilobases (kb) in length, which complicates motif-based analyses. Restricting the length of the target DNA sequence(s) can reduce false positives. Therefore, we present HisTrader, a computational tool to identify the regions accessible to transcription factors, nucleosome free regions (NFRs), within histone modification peaks to reduce the DNA sequence length required for motif analyses. Results HisTrader accurately identifies NFRs from H3K27Ac ChIP-seq profiles of the lung cancer cell line A549, which are validated by the presence of DNaseI hypersensitivity. In addition, HisTrader reveals that multiple NFRs are common within individual regulatory elements; an easily overlooked feature that should be considered to improve sensitivity of motif analyses using histone modification ChIP-seq data. Availability and implementation The HisTrader script is open-source and available on GitHub (https://github.com/SvenBaileyLab/Histrader) under a GNU general public license (GPLv3). HisTrader is written in PERL and can be run on any platform with PERL installed.
Response patterns and mechanisms of plants to water stress

Plants are key to the functionality of many ecosystem processes. The duration and intensity of water stress are anticipated to increase in the future; however, an elucidation of the responses of plants to water stress remains incomplete. For this study, we present a global meta-analysis derived from 1301 paired observations from 84 studies to evaluate the response patterns and mechanisms of plants to water stress. The results revealed that while water stress inhibited plant growth and photosynthesis, reactive oxygen species (ROS), plasma membrane permeability, enzymatic antioxidants, and non-enzymatic antioxidants increased. These responses generally increased with the intensity of water stress but were mitigated with experimental duration. Our findings suggested that the overproduction of ROS was the primary mechanism of plants in response to water stress and that plants tend to acclimate to water stress over time to some extent. Our synthesis provides a framework for understanding the responses and mechanisms of plants under drought conditions. One senence summary The overproduction of ROS was the primary mechanism of plants in response to water stress and that plants tend to acclimate to water stress over time to some extent.
D-Retro Inverso (DRI) Amylin and the Stability of Amylin Fibrils

Motivated by the role that amylin aggregates pay in type-II diabetes, we compare the stability of regular amylin fibrils with the stability of fibrils where L-amino acid chains are replaced by D-Retro Inverso (DRI) amylin, i.e., peptides where the sequence of amino acids is reversed, and at the same time the L-amino acids are replaced by their mirror images. Our molecular dynamics simulations show that despite leading to only marginal difference in fibril structure and stability, aggregating DRI-amylin peptides have different pattern of contacts and hydrogen bonding. Because of these differences does DRI-amylin, when interacting with regular (L) amylin, alter the elongation process and lowers the stability of hybrid amylin fibrils. Our results suggest not only a potential use of DRI-amylin as inhibitor of amylin fibril-formation, but points also to the possibility of using insertion of DRI-proteins in L-assemblies as a way to probe the role of certain kinds of hydrogen bonds in supra-molecular assemblies or aggregates.
The vesicular trafficking system component MIN7 is required for minimizing Fusarium graminearum infection

Plants have developed intricate defense mechanisms, referred to as innate immunity, to defend themselves against a wide range of pathogens. Plants often respond rapidly to pathogen attack by the synthesis and delivery of various antimicrobial compounds, proteins and small RNA in membrane vesicles to the primary infection sites. Much of the evidence regarding the importance of vesicular trafficking in plant-pathogen interactions comes from the studies involving model plants whereas this process is relatively understudied in crop plants. Here we assessed whether the vesicular trafficking system components previously implicated in immunity in Arabidopsis thaliana play a role in the interaction with Fusarium graminearum, a fungal pathogen notoriously famous for its ability to cause Fusarium head blight (FHB) disease in wheat. Among the analyzed vesicular trafficking mutants, two independent T-DNA insertion mutants in the AtMin7 gene displayed a markedly enhanced susceptibility to F. graminearum. Earlier studies identified this gene, encoding an ARF-GEF protein, as a target for the HopM1 effector of the bacterial pathogen Pseudomonas syringae pv. tomato, which destabilizes AtMIN7 leading to its degradation and weakening host defenses. To test whether this key vesicular trafficking component may also contribute to defense in crop plants, we identified the candidate TaMin7 genes in wheat and knocked-down their expression through Virus induced gene silencing. Wheat plants in which TaMIN7 were silenced displayed significantly more FHB disease. This suggests that disruption of MIN7 function in both model and crop plants compromises the trafficking of innate immunity signals or products resulting in hyper-susceptibility to various pathogens. One sentence summary Disruption of an ARF-GEF protein encoding gene AtMin7 in Arabidopsis thaliana and silencing of the orthologous gene in wheat result in hyper susceptibility to the fungal pathogen Fusarium graminearum.
Cortical Depth-Dependent Modeling of Visual Hemodynamic Responses

A physiologically based three-dimensional (3D) hemodynamic model is used to predict the experimentally observed blood oxygen level dependent (BOLD) responses versus the cortical depth induced by visual stimuli. Prior 2D approximations are relaxed in order to analyze 3D blood flow dynamics as a function of cortical depth. Comparison of the predictions with experimental data for typical stimuli demonstrates that the full 3D model matches at least as well as previous approaches while requiring significantly fewer assumptions and model parameters (e.g., there is no more need to define depth-specific parameter values for spatial spreading, peak amplitude, and hemodynamic velocity).
Baseline breath alcohol concentration in Nigerian commercial drivers and motorcyclists

ABSTRACT Objective: We sought to determine breath alcohol concentration (BrAC) in a sample of consenting Nigerian commercial drivers and motorcyclists and relate values obtained to some social parameters and practices. Method: A cross-sectional study of randomly selected, consenting commercial drivers, and motorcyclists in two Nigerian cities was undertaken. We obtained data on subjects’ sociodemographics, driving/riding related experiences and practices with the aid of a pretested structured questionnaire. We determined their BrAC and analyzed data using SPSS version 17.0. Statistical significance was inferred at p ≤ 0.05. Result: One hundred ninety respondents aged 20–65 years mean (SD) 40 (11.28) were studied. They were 112 (58.9%) drivers, 78 (41.1%) motorcyclists, and predominantly males (98.9%). A significant proportion of motorcyclists were aged <40 years and most drivers >40 years (p < 0.001). Respondents’ educational attainment did not differ significantly with age groups and status; however, 6.8% had no formal education. Alcohol use decreased significantly with increasing years of experience (p < 0.001). Note that 68.9% of respondents tested positive with the breathalyzer with blood alcohol concentration (BAC) levels 0.01–1.8 mg/ml with mean (SD) at 0.16 (0.32) mg/ml. In total, 51.1% of respondents had BAC values ≥0.1% while 7.9% had BAC ≥0.5 mg/ml. A total of 92.6% admitted use of various measures to enhance their performances and overcome fatigue. Conclusion: The drink driving/riding law in Nigeria needs to be revised to suit prevailing circumstance and enforced.
A unifying structural and functional model of the coronavirus replication organelle: Tracking down RNA synthesis

Zoonotic coronavirus (CoV) infections, like those responsible for the current SARS-CoV-2 epidemic, cause grave international public health concern. In infected cells, the CoV RNA-synthesizing machinery associates with modified endoplasmic reticulum membranes that are transformed into the viral replication organelle (RO). While double-membrane vesicles (DMVs) appear to be a pan-coronavirus RO element, studies to date describe an assortment of additional coronavirus-induced membrane structures. Despite much speculation, it remains unclear which RO element(s) accommodate viral RNA synthesis. Here we provide detailed 2D and 3D analyses of CoV ROs and show that diverse CoVs essentially induce the same membrane modifications, including the small open double-membrane spherules (DMSs) previously thought to be restricted to gamma- and delta-CoV infections and proposed as sites of replication. Metabolic labelling of newly-synthesized viral RNA followed by quantitative EM autoradiography revealed abundant viral RNA synthesis associated with DMVs in cells infected with the beta-CoVs MERS-CoV and SARS-CoV, and the gamma-CoV infectious bronchitis virus. RNA synthesis could not be linked to DMSs or any other cellular or virus-induced structure. Our results provide a unifying model of the CoV RO and clearly establish DMVs as the central hub for viral RNA synthesis and a potential drug target in coronavirus infection.