bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk perceptions and preventive practices of COVID-19 among healthcare professionals in public hospitals in Ethiopia
Authors: Deressa Wakgari , Worku Alemayehu , Abebe Workeabeba , Gizaw Muluken , Amogne Wondwosson 
Published: November 2020

AbstractHealthcare professionals are at higher risk of contracting the novel coronavirus due to their work exposure in the healthcare settings. Practicing appropriate preventive measures to control COVID-19 infection is one of the most important interventions that healthcare workers are expected to use. The aim of this study was to assess the level of risk perception and practices of preventive measures of COVID-19 among health workers in Addis Ababa, Ethiopia. A hospital-based cross-sectional study was conducted from 9th to 26th June 2020 among healthcare professionals working at six public hospitals in Addis Ababa. Data were collected using a self-administered structured questionnaire. Frequency, percentage, and mean were used to summarize the data. A binary logistic regression analyses were performed to identify factors associated with risk perception about COVID-19. A total of 1,134 participants were surveyed. Wearing facemask (93%), hand washing for at least 20 seconds (93%), covering mouth and nose while coughing or sneezing (91%), and avoiding touching eyes, nose, and mouth (91%) were the commonly self-reported preventive practices. About 88% perceived that they were worried about the risk of becoming infected with coronavirus, and majority (91%) worried about the risk of infection to their family. The mean score of overall fear and worry of COVID-19 was 2.37 on a scale of 1 to 3. Respondents who ever provided clinical care to COVID-19 patients were more likely to report fear and worry (adjusted OR=1.34, 95% CI:1.02-1.91), however those who ever participated in Ebola or SARS outbreaks were less likely to report fear and worry due to COVID-19 crisis (adjusted OR=0.66, 95% CI:0.48-0.90). This study has revealed widespread practices of preventive measures and the highest perceived risk of COVID-19 among healthcare workers. Therefore, an effective risk communication intervention should be implemented to ensure the maintenance of appropriate practices during the current COVID-19 pandemic.
Genetic diversity analysis of the D614G mutation in SARS-CoV-2
Authors: Felix Pierre Teodósio , Venâncio Dallynne Bárbara Ramos , Da Silva Eduarda Doralice Alves Braz , da Silva Ramos Robson 
Published: November 2020

AbstractIn this work, we evaluated the levels of genetic diversity in 18 genomes of SARS-CoV-2 carrying the D614G mutation, coming from Malaysia and Venezuela and publicly available at the National Center of Biotechnology and Information (NCBI). These haplotypes were previously used for phylogenetic analysis, following the LaBECom protocols. All gaps and unconserved sites were extracted for the construction of a phylogenetic tree. As specific methodologies for paired FST estimators, Molecular Variance (AMOVA), Genetic Distance, mismatch, demographic and spatial expansion analyses, molecular diversity and evolutionary divergence time analyses, 20,000 random permutations were always used. The results revealed the presence of only 57 sites of polymorphic and parsimonium-informative among the 29,827bp analyzed and the analyses based on FSTvalues confirmed the presence of two distinct genetic entities with fixation index of 22% and with a higher component of population variation (78.14%). Tau variations revealed a significant time of divergence, supported by mismatch analysis of the observed distribution (τ = 42%). It is safe to say that the small number of existing polymorphisms should not reflect major changes in the protein products of viral populations in both countries and this consideration provides the safety that, although there are differences in the haplotypes studied, these differences are minimal for both regions analyzed geographically and, therefore, it seems safe to extrapolate the levels of polymorphism and molecular diversity found in the samples for other mutant genomes of SARS-CoV-2 in other countries. This reduces speculation about the possibility of large differences between mutant strains of SARS-CoV-2 (D614G) and wild strains, at least at the level of their protein products, although the mutant form has higher transmission speed and infection. The analyses suggest that possible variations in protein products, of the wild virus in relation to its mutant form, should be minimal, bringing peace of mind as to the increased risk of death from the new form of the virus, as well as possible problems of gradual adjustments in some molecular targets for vaccines.
Ontology-Aware Deep Learning Enables Ultrafast, Accurate and Interpretable Source Tracking among Sub-Million Microbial Community Samples from Hundreds of Niches
Authors: Zha Yuguo , Chong Hui , Qiu Hao , Kang Kai , Dun Yuzheng , Chen Zhixue , Cui Xuefeng , Ning Kang 
Published: November 2020

AbstractThe taxonomical structure of microbial community sample is highly habitat-specific, making it possible for source tracking niches where samples are originated. Current methods face challenges when the number of samples and niches are magnitudes more than current in use, under which circumstances they are unable to accurately source track samples in a timely manner, rendering them difficult in knowledge discovery from sub-million heterogeneous samples. Here, we introduce a deep learning method based on Ontology-aware Neural Network approach, ONN4MST (https://github.com/HUST-NingKang-Lab/ONN4MST), which takes into consideration the ontology structure of niches and the relationship of samples from these ontologically-organized niches. ONN4MST’s superiority in accuracy, speed and robustness have been proven, for example with an accuracy of 0.99 and AUC of 0.97 in a microbial source tracking experiment that 125,823 samples and 114 niches were involved. Moreover, ONN4MST has been utilized on several source tracking applications, showing that it could provide highly-interpretable results from samples with previously less-studied niches, detect microbial contaminants, and identify similar samples from ontologically-remote niches, with high fidelity.
AC. elegansneuron both promotes and suppresses motor behavior to fine tune motor output
Authors: Li Zhaoyu , Zhou Jiejun , Wani Khursheed , Yu Teng , Ronan Elizabeth A. , Piggott Beverley J. , Liu Jianfeng , Xu X.Z. Shawn 
Published: November 2020

AbstractHow neural circuits drive behavior is a central question in neuroscience. Proper execution of motor behavior requires the precise coordination of many neurons. Within a motor circuit, individual neurons tend to play discrete roles by promoting or suppressing motor output. How exactly neurons function in specific roles to fine tune motor output is not well understood. InC. elegans, the interneuron RIM plays important yet complex roles in locomotion behavior. Here, we show that RIM both promotes and suppresses distinct features of locomotion behavior to fine tune motor output. This dual function is achieved via the excitation and inhibition of the same motor circuit by electrical and chemical neurotransmission, respectively. Additionally, this bi-directional regulation contributes to motor adaptation in animals placed in novel environments. Our findings reveal that individual neurons within a neural circuit may act in opposing ways to regulate circuit dynamics to fine tune behavioral output.
Control of neurogenic competence in mammalian hypothalamic tanycytes
Authors: Yoo Sooyeon , Kim Juhyun , Lyu Pin , Hoang Thanh V. , Ma Alex , Trinh Vickie , Dai Weina , Jiang Lizhi , Leavey Patrick , Won Jae-Kyung , Park Sung-Hye , Qian Jiang , Brown Solange P. , Blackshaw Seth 
Published: November 2020

AbstractHypothalamic tanycytes, radial glial cells that share many features with neuronal progenitors, generate small numbers of neurons in the postnatal hypothalamus, but the identity of these neurons and the molecular mechanisms that control tanycyte-derived neurogenesis are unknown. In this study, we demonstrate that tanycyte-specific disruption of the NFI family of transcription factors (Nfia/b/x) robustly stimulates tanycyte proliferation and tanycyte-derived neurogenesis. Single-cell RNA- and ATAC-Seq analysis reveals that NFI factors repress Shh and Wnt signaling in tanycytes, and small molecule modulation of these pathways blocks proliferation and tanycyte-derived neurogenesis inNfia/b/x-deficient mice. We show thatNfia/b/x-deficient tanycytes give rise to multiple mediobasal hypothalamic neuronal subtypes that can mature, integrate into hypothalamic synaptic circuitry, and selectively respond to changes in internal states. These findings identify molecular mechanisms that control tanycyte-derived neurogenesis, suggesting a new therapeutic approach to selectively remodel the hypothalamic neural circuitry that controls homeostatic physiological processes.
Topology of synaptic connectivity constrains neuronal stimulus representation, predicting two complementary coding strategies
Authors: Reimann Michael W. , Riihimäki Henri , Smith Jason P. , Lazovskis Jānis , Pokorny Christoph , Levi Ran 
Published: November 2020

1AbstractIn motor-related brain regions, movement intention has been successfully decoded from in-vivo spike train by isolating a lower-dimension manifold that the high-dimensional spiking activity is constrained to. The mechanism enforcing this constraint remains unclear, although it has been hypothesized to be implemented by the connectivity of the sampled neurons. We test this idea and explore the interactions between local synaptic connectivity and its ability to encode information in a lower dimensional manifold through simulations of a detailed microcircuit model with realistic sources of noise. We confirm that even in isolation such a model can encode the identity of different stimuli in a lower-dimensional space. We then demonstrate that the reliability of the encoding depends on the connectivity between the sampled neurons by specifically sampling populations whose connectivity maximizes certain topological metrics. Finally, we developed an alternative method for determining stimulus identity from the activity of neurons by combining their spike trains with their recurrent connectivity. We found that this method performs better for sampled groups of neurons that perform worse under the classical approach, predicting the possibility of two separate encoding strategies in a single microcircuit.
Loss of a plant receptor kinase recruits beneficial rhizosphere-associatedPseudomonas
Authors: Song Yi , Wilson Andrew J. , Zhang Xue-Cheng , Thoms David , Sohrabi Reza , Song Siyu , Geissmann Quentin , Liu Yang , Walgren Lauren , He Sheng Yang , Haney Cara H. 
Published: November 2020

AbstractMaintaining microbiome structure is critical for the health of both plants1and animals2. In plants, enrichment of beneficial bacteria is associated with advantageous outcomes including protection from biotic and abiotic stress3,4. However, the genetic and molecular mechanisms by which plants enrich for specific beneficial microbes without general dysbiosis have remained elusive. Here we show that through regulation of NADPH oxidase,FERONIAkinase negatively regulates beneficialPseudomonas fluorescensin theArabidopsisrhizosphere microbiome. By rescreening a collection ofArabidopsismutants that affect root immunity under gnotobiotic conditions, followed by microbiome sequencing in natural soil, we identified aFERONIAmutant (fer-8) with a rhizosphere microbiome enriched inP. fluorescenswithout phylum-level dysbiosis. Using microbiome transplant experiments, we found that thefer-8microbiome was beneficial and promoted plant growth. The effect ofFERon rhizosphere Pseudomonads was independent of its immune coreceptor function, role in development, and jasmonic acid autoimmunity. We found that thefer-8mutant has reduced basal levels of reactive oxygen species (ROS) in roots and that mutants deficient in NADPH oxidase showed elevated rhizosphere Pseudomonad levels. Overexpression of theROP2gene (encoding a client of FER and positive regulator of NADPH oxidase5) infer-8plants suppressed Pseudomonad overgrowth. This work shows thatFER-mediated ROS production regulates levels of beneficial Pseudomonads in the rhizosphere microbiome.
D614G substitution enhances the stability of trimeric SARS-CoV-2 spike protein
Authors: Yazhini Arangasamy , Sidhanta Das Swayam Prakash , Srinivasan Narayanaswamy 
Published: November 2020

AbstractSARS-CoV-2 spike protein with D614G substitution has become the dominant variant in the ongoing COVID-19 pandemic. Several studies to characterize the new virus expressing G614 variant show that it exhibits increased infectivity compared to the ancestral virus having D614 spike protein. Here, usingin-silicomutagenesis and energy calculations, we analyzed inter-residue interaction energies and thermodynamic stability of the dominant (G614) and the ancestral (D614) variants of spike protein trimer in ‘closed’ and ‘partially open’ conformations. We find that the local interactions mediated by aspartate at the 614thposition are energetically frustrated and create unfavourable environment. Whereas, glycine at the same position confers energetically favourable environment and strengthens intra-as well as inter-protomer association. Such changes in the local interaction energies enhance the thermodynamic stability of the spike protein trimer as free energy difference (ΔΔG) upon glycine substitution is −2.6 kcal/mol for closed conformation and −2.0 kcal/mol for open conformation. Our results on the structural and energetic basis of enhanced stability hint that G614 may confer increased availability of functional form of spike protein trimer and consequent in higher infectivity than the D614 variant.
Relating farmers’ perceptions to long term dynamics in maize (Zea maysL.) production: The production of improved maize is coming to a standstill in central Malawi
Authors: Nyirenda Harrington , Mwangomba Wantwa , Nyirenda Ellen M. 
Published: November 2020

AbstractMaize production, area and yield dynamics were assessed based on farmer perceptions and production data from 2004/05-2018/19 using 36 000 households in Salima, central Malawi. The results showed that farmers used 16, six and two varieties for hybrid, Open-pollinated varieties (OPV) and local maize respectively. Farmers sourced Hybrid and OPV maize seed from Private Agro dealers while local maize was own-sourced. Farmers preferred local maize for being cheap, good taste, low storage costs, and pest resistance although low yielding. They preferred hybrid and OPV maize for high yielding and early maturity despite demanding high storage costs, pest susceptibility, and low flour. From 2004/05-2018/19, the area under local and OPV maize reduced by 61% and 12% respectively, while that of hybrid maize increased by 49%. However, the consistent decrease in area for hybrid and OPV and significant increase of that of local maize from 2014/15-2018/19 may signal a catastrophic maize production in the region. From 2019/20-2025/26 production of all maize was projected at 44 172 tons by 2025/26, representing a 1.6% increase from the base year 2019/20. This increase will be due to favorable climatic conditions and not increase in area or yield. If maize yield was improved by 30% production would increase to 110 430 tons representing 67% of the food requirement in the study area. The current maize production trend in Salima does not guarantee food security prospects. Therefore, policymakers should consider reviewing the past interventions (input pricing, promotion strategies, sustainable practices, policies) in the maize subsector to enhance maize productivity.
Choice of library preparation and its effects on sequence quality, genome assembly, and precisein silicoprediction of virulence genes in shiga toxin producingEscherichia coli
Authors: Haendiges Julie , Jinneman Karen , Gonzalez-Escalona Narjol 
Published: November 2020

AbstractWhole genome sequencing (WGS) provides essential public health information and is used worldwide for pathogen surveillance, epidemiology, and source tracking. The sequencing of foodborne pathogens is commonly performed with Illumina sequencing chemistry to obtain data with high accuracy. The choice of library preparation method for highly complex organisms is very critical and can affect the final data output. The majority of Illumina sequencing platforms use rapid library preparation such as Nextera XT (transposon-based technology) (Illumina San Diego, CA), but this preparation has the potential to miss randomly distributed segments of genomes that might be important for downstream analyses. The Illumina Nextera DNA Prep library preparation kit, the successor of Nextera XT, shows better overall coverage of the complete genome. This study compared the quality of sequence data generated using Nextera XT and Nextera DNA Prep kits for DNA library preparation on an Illumina MiSeq, using a set of 30 O121:H19 shiga-toxin positiveEscherichia colistrains isolated from flour during a 2016 outbreak. The performance of the two kits were evaluated using several metrics including sequencing quality, assembly quality, uniformity of genome coverage, and virulence gene identification. Overall, the results showed that in all of the analysed metrics, the Nextera DNA Prep kit performed outstanding in comparison to Nextera XT. The Nextera DNA Prep kit allowed for comprehensive detection of all virulence genes, which is of extremely high importance for making an educated assessment of the virulence potential ofEscherichia coli. This comprehensive side-by-side comparison will be of significance for those interested in improving their sequencing workflow for STECs and the determination of health risks using WGS data.
ATF-4 and hydrogen sulfide signalling mediate longevity from inhibition of translation or mTORC1
Authors: Statzer Cyril , Meng Jin , Venz Richard , Bland Monet , Robida-Stubbs Stacey , Patel Krina , Petrovic Dunja , Emsley Raffaella , Liu Pengpeng , Morantte Ianessa , Haynes Cole , Mair William B. , Longchamp Alban , Filipovic Milos , Blackwell T. Keith , Ewald Collin Y. 
Published: November 2020

AbstractInhibition of the master growth regulator mTORC1 (mechanistic target of rapamycin complex 1) slows ageing across phyla, in part by reducing protein synthesis. Various stresses globally suppress protein synthesis through the integrated stress response (ISR), resulting in preferential translation of the transcription factor ATF-4. Here we show inC. elegansthat inhibition of translation or mTORC1 increases ATF-4 expression, and that ATF-4 mediates longevity under these conditions independently of ISR signalling. ATF-4 promotes longevity by activating canonical anti-ageing mechanisms, but also by elevating expression of the transsulfuration enzyme CTH-2 to increase hydrogen sulfide (H2S) production. This H2S boost increases protein persulfidation, a protective modification of redox-reactive cysteines. The ATF-4/CTH-2/H2S pathway also mediates longevity and increased stress resistance from mTORC1 suppression. Increasing H2S levels, or enhancing mechanisms that H2S influences through persulfidation, may represent promising strategies for mobilising therapeutic benefits of the ISR, translation suppression, or mTORC1 inhibition.
CENP-C regulates centromere assembly, asymmetry and epigenetic age in Drosophila germline stem cells
Authors: Carty Ben L , Dattoli Anna A , Dunleavy Elaine M 
Published: November 2020

AbstractGermline stem cells divide asymmetrically to produce one new daughter stem cell and one daughter cell that will subsequently undergo meiosis and differentiate to generate the mature gamete. The silent sister hypothesis proposes that in asymmetric divisions, the selective inheritance of sister chromatids carrying specific epigenetic marks between stem and daughter cells impacts cell fate. To facilitate this selective inheritance, the hypothesis specifically proposes that the centromeric region of each sister chromatid is distinct. In Drosophila germ line stem cells (GSCs), it has recently been shown that the centromeric histone CENP-A (called CID in flies) - the epigenetic determinant of centromere identity - is asymmetrically distributed between sister chromatids. In these cells, CID deposition occurs in G2phase such that sister chromatids destined to end up in the stem cell harbour more CENP-A, assemble more kinetochore proteins and capture more spindle microtubules. These results suggest a potential mechanism of ‘mitotic drive’ that might bias chromosome segregation. Here we report that the inner kinetochore protein CENP-C, is required for the assembly of CID in G2phase in GSCs. Moreover, CENP-C is required to maintain a normal asymmetric distribution of CID between stem and daughter cells. In addition, we find that CID is lost from centromeres in aged GSCs and that a reduction in CENP-C accelerates this loss. Finally, we show that CENP-C depletion in GSCs disrupts the balance of stem and daughter cells in the ovary, shifting GSCs toward a self-renewal tendency. Ultimately, we provide evidence that centromere assembly and maintenance via CENP-C is required to sustain asymmetric divisions in female Drosophila GSCs.
Synaptotagmin-7 places dense-core vesicles at the cell membrane to promote Munc13-2- and Ca2+-dependent priming
Authors: Tawfik Bassam , Martins Joana S. , Houy Sébastien , Imig Cordelia , Pinheiro Paulo S. , Wojcik Sonja M. , Brose Nils , Cooper Benjamin H. , Sørensen Jakob B. 
Published: November 2020

AbstractThe functional consequences of the co-expression of synaptotagmin-1 and synaptotagmin-7 are unclear. We show that when present separately, synaptotagmin-1 and synaptotagmin-7 act as standalone fast and slow Ca2+-sensors for vesicle fusion in mouse chromaffin cells. When present together, synaptotagmin-7 stimulates Ca2+-dependent vesicle priming and inhibits depriming. The priming effect of Synaptotagmin-7 extends to the Readily Releasable Pool, whose fusion is executed by synaptotagmin-1, indicating synergistic action of the two Ca2+-sensors, although they are only partially colocalized. Synaptotagmin-7 promotes ubMunc13-2-dependent priming and the absence of synaptotagmin-7 renders phorbolesters less effective in stimulating priming, although synaptotagmin-7 independent priming is also observed. Morphologically, synaptotagmin-7 places vesicles in close membrane apposition (< 6 nm); in its absence vesicles accumulate out of reach of the fusion complex (20-40 nm). We suggest that a synaptotagmin-7-dependent movement toward the membrane is involved in Munc13-2/phorbolester/Ca2+-dependent priming and sets the stage for fast and slow exocytosis triggering.