bluuebunny/crossref_metadata_2025 huggingface dataset:
Automated cell tracking using StarDist and TrackMate
Authors: Fazeli Elnaz , Roy Nathan H. , Follain Gautier , Laine Romain F. , von Chamier Lucas , Hänninen Pekka E. , Eriksson John E. , Tinevez Jean-Yves , Jacquemet Guillaume
Published: September 2020

The ability of cells to migrate is a fundamental physiological process involved in embryonic development, tissue homeostasis, immune surveillance, and wound healing. Therefore, the mechanisms governing cellular locomotion have been under intense scrutiny over the last 50 years. One of the main tools of this scrutiny is live-cell quantitative imaging, where researchers image cells over time to study their migration and quantitatively analyze their dynamics by tracking them using the recorded images. Despite the availability of computational tools, manual tracking remains widely used among researchers due to the difficulty setting up robust automated cell tracking and large-scale analysis. Here we provide a detailed analysis pipeline illustrating how the deep learning network StarDist can be combined with the popular tracking software TrackMate to perform 2D automated cell tracking and provide fully quantitative readouts. Our proposed protocol is compatible with both fluorescent and widefield images. It only requires freely available and open-source software (ZeroCostDL4Mic and Fiji), and does not require any coding knowledge from the users, making it a versatile and powerful tool for the field. We demonstrate this pipeline’s usability by automatically tracking cancer cells and T cells using fluorescent and brightfield images. Importantly, we provide, as supplementary information, a detailed step-by-step protocol to allow researchers to implement it with their images.
A Highly Conserved 310-Helix Within the Kinesin Motor Domain is Critical for Kinesin Function and Human Health
Authors: Lam Aileen J. , Rao Lu , Anazawa Yuzu , Okada Kyoko , Chiba Kyoko , Niwa Shinsuke , Gennerich Arne , Nowakowski Dan W. , McKenney Richard J.
Published: September 2020

KIF1A, a kinesin-3 family member, plays critical roles as a long-distance cargo-transporter within neurons. Over 100 known KIF1A mutations in humans result inKIF1AAssociated Neurological Disease (KAND), developmental and degenerative neurological conditions for which there is no cure. A de novo missense mutation, P305L, was recently identified in several children diagnosed with KAND, but the underlying molecular basis for the disease phenotype is unknown. Interestingly, this residue is highly conserved in kinesin-family proteins, and together with adjacent conserved residues also implicated in KAND, forms an unusual 310-helical element immediately C-terminal to loop-12 (L12, also known as the K-loop in KIF1A) in the conserved kinesin motor core. In KIF1A, the disordered K-loop contains a highly charged insertion of lysines that is thought to endow the motor with a high microtubule-association rate. Here, we characterize the molecular defects of the P305L mutation in KIF1A using genetic, biochemical, and single-molecule approaches. We find the mutation negatively impacts the velocity, run-length, and force generation of the motor. However, a much more dramatic effect is observed on the microtubule-association rate of the motor, revealing that the presence of an intact K-loop is not sufficient for its function. We hypothesize that an elusive K-loop conformation, mediated by formation of a highly conserved adjacent 310-helix that is modulated via P305, is critically important for the kinesin-microtubule interaction. Importantly, we find that the function of this proline is conserved in the canonical kinesin, KIF5, revealing a fundamental principle of the kinesin motor mechanism.
Aerobic exercise improves hippocampal blood flow for hypertensiveAPOE4carriers
Authors: Kaufman Carolyn S. , Honea Robyn A. , Pleen Joseph , Lepping Rebecca J. , Watts Amber , Morris Jill K , Billinger Sandra A. , Burns Jeffrey M. , Vidoni Eric D.
Published: September 2020

Background

Evidence increasingly suggests cerebrovascular dysfunction plays an early and important role in the pathogenesis of Alzheimer’s disease (AD). Studies have shown the strongest known genetic risk factor for sporadic AD,Apolipoprotein E4(APOE4), may act synergistically with vascular risk factors to promote dementia development. Aerobic exercise may attenuate cognitive decline at least partially through improvements in cerebral blood flow. Therefore, exercise interventions that improve vascular health may be particularly beneficial forAPOE4carriers.

Objectives

To test the hypothesis that exercise would more effectively increase hippocampal blood flow (HBF) in hypertensiveAPOE4carriers than non-carriers, we performed an analysis of arterial spin labeling MRI data (ASL-MRI) from a randomized controlled trial (secondary outcome). Additionally, we tested the hypothesis that changes in systolic blood pressure (ΔSBP) would be more negatively associated with ΔHBF forAPOE4carriers than non-carriers.

Methods

We assigned cognitively normal adults (65–87 years) to a 52-week aerobic exercise intervention or education only. Genotyping was performed by Taqman SNP allelic discrimination assay. ASL-MRI measured HBF before and after the 52-week intervention. We selected participants with hypertension at enrollment (n = 44), defined as SBP ≥ 130mmHg or diastolic blood pressure (DBP) ≥ 80mmHg.

Results

A two-way ANCOVA showed a significant interaction betweenAPOE4carrier status and treatment group on change in HBF (ΔHBF) over the 52 weeks, controlling for age and sex (p= 0.040). ForAPOE4carriers, ΔHBF was significantly (p= 0.006) higher for participants who underwent the exercise intervention (4.09 mL/100g/min) than for the control group (−2.08 mL/100g/min). There was no difference in ΔHBF between the control (−0.32 mL/100g/min) and exercise (−0.54 mL/100g/min) intervention groups forAPOE4non-carriers (p = 0.918). Additionally, a multiple linear regression showed a significant interaction between ΔSBP andAPOE4carrier status on ΔHBF (p= 0.035), with a reduction in SBP associated with an increase in HBF forAPOE4carriers only.

Conclusions

Aerobic exercise significantly improved HBF for hypertensiveAPOE4carriers only. Additionally, onlyAPOE4carriers exhibited an inverse relationship between ΔSBP and ΔHBF. This suggests exercise interventions, particularly those that lower SBP, may be beneficial for individuals at highest genetic risk of AD.
Identifying gaps in COVID-19 health equity data reporting in Canada using a scorecard approach
Authors: Blair Alexandra , Warsame Kahiye , Naik Harsh , Byrne Walter , Parnia Abtin , Siddiqi Arjumand
Published: September 2020

Objective

To assess thealth equity-oriented COVID-19 data reporting across Canadian provinces and territories, using a scorecard approach.

Method

A scan was performed of provincial and territorial reporting of five data elements (cumulative totals of tests, cases, hospitalizations, deaths and population size) across three units of aggregation (province or territory-level, health regions, and local areas) (15 “overall” indicators), and for two vulnerable settings (long term care and detention facilities) and six social markers (age, sex, immigration status, race/ethnicity, essential worker status, and income) (120 “equity-related” indicators). Per indicator, one point was awarded if case-delimited data were released, 0.7 points if only summary statistics were reported, and 0 if neither was provided. Results were presented using a scorecard approach.

Results

Overall, information on cases and deaths was more complete than for tests, hospitalizations and population size denominators needed for rate estimation. Information provided on jurisdictions and their regions, overall, tended to be more available (average score of 53%, “B”) than for equity-related indicators (average score of 21%, “D”). Only British Columbia and Alberta provided case-delimited data, and only Alberta provided information for local areas. No jurisdiction reported on outcomes according to patients’ individual-level immigration status, race, or income. Only Ontario and Quebec provided detailed information for long-term care settings and detention facilities.

Conclusion

Socially stratified reporting for COVID-19 outcomes is sparse in Canada. However, several “best practices” in health equity-oriented reporting were observed and set a relevant precedent for all jurisdictions to follow for this pandemic and future ones.
Endometrial epithelial ARID1A is critical for uterine gland function in early pregnancy establishment
Authors: Marquardt Ryan M. , Kim Tae Hoon , Yoo Jung-Yoon , Teasley Hanna E. , Fazleabas Asgerally T. , Young Steven L. , Lessey Bruce A. , Arora Ripla , Jeong Jae-Wook
Published: September 2020

Though endometriosis and infertility are clearly associated, the pathophysiological mechanism remains unclear. Previous work has linked endometrial ARID1A loss to endometriosis-related endometrial non-receptivity. Here, we show in mice that ARID1A binds and regulates transcription of theFoxa2gene required for endometrial gland function. Uterine specific deletion ofArid1acompromises gland development and diminishesFoxa2andLifexpression. Deletion ofArid1awith Ltf-iCre in the adult mouse endometrial epithelium preserves gland development while still compromising gland function. Mice lacking endometrial epithelialArid1aare severely sub-fertile due to defects in implantation, decidualization, and endometrial receptivity from disruption of the LIF-STAT3-EGR1 pathway. FOXA2 is also reduced in the endometrium of women with endometriosis in correlation with diminished ARID1A, and both ARID1A and FOXA2 are reduced in non-human primates induced with endometriosis. Our findings describe a role for ARID1A in the endometrial epithelium supporting early pregnancy establishment through the maintenance of gland function.
Unsupervised tensor decomposition-based method to extract candidate transcription factors as histone modification bookmarks in post-mitotic transcriptional reactivation
Authors: Taguchi Y-h. , Turki Turki
Published: September 2020

The histone group added to a gene sequence must be removed during mitosis to halt transcription during the DNA replication stage of the cell cycle. However, the detailed mechanism of this transcription regulation remains unclear. In particular, it is not realistic to reconstruct all appropriate histone modifications throughout the genome from scratch after mitosis. Thus, it is reasonable to assume that there might be a type of “bookmark” that retains the positions of histone modifications, which can be readily restored after mitosis. We developed a novel computational approach comprising tensor decomposition (TD)-based unsupervised feature extraction (FE) to identify transcription factors (TFs) that bind to genes associated with reactivated histone modifications as candidate histone bookmarks. To the best of our knowledge, this is the first application of TD-based unsupervised FE to the cell division context and phases pertaining to the cell cycle in general. The candidate TFs identified with this approach were functionally related to cell division, suggesting the suitability of this method and the potential of the identified TFs as bookmarks for histone modification during mitosis.
A Joint Deep Learning Model for Simultaneous Batch Effect Correction, Denoising and Clustering in Single-Cell Transcriptomics
Authors: Lakkis Justin , Wang David , Zhang Yuanchao , Hu Gang , Wang Kui , Pan Huize , Ungar Lyle , Reilly Muredach P. , Li Xiangjie , Li Mingyao
Published: September 2020

Recent development of single-cell RNA-seq (scRNA-seq) technologies has led to enormous biological discoveries. As the scale of scRNA-seq studies increases, a major challenge in analysis is batch effect, which is inevitable in studies involving human tissues. Most existing methods remove batch effect in a low-dimensional embedding space. Although useful for clustering, batch effect is still present in the gene expression space, leaving downstream gene-level analysis susceptible to batch effect. Recent studies have shown that batch effect correction in the gene expression space is much harder than in the embedding space. Popular methods such as Seurat3.0 rely on the mutual nearest neighbor (MNN) approach to remove batch effect in the gene expression space, but MNN can only analyze two batches at a time and it becomes computationally infeasible when the number of batches is large. Here we present CarDEC, a joint deep learning model that simultaneously clusters and denoises scRNA-seq data, while correcting batch effect both in the embedding and the gene expression space. Comprehensive evaluations spanning different species and tissues showed that CarDEC consistently outperforms scVI, DCA, and MNN. With CarDEC denoising, those non-highly variable genes offer as much signal for clustering as the highly variable genes, suggesting that CarDEC substantially boosted information content in scRNA-seq. We also showed that trajectory analysis using CarDEC’s denoised and batch corrected expression as input revealed marker genes and transcription factors that are otherwise obscured in the presence of batch effect. CarDEC is computationally fast, making it a desirable tool for large-scale scRNA-seq studies.
COVID-19 CG: Tracking SARS-CoV-2 mutations by locations and dates of interest
Authors: Chen Albert Tian , Altschuler Kevin , Zhan Shing Hei , Chan Yujia Alina , Deverman Benjamin E.
Published: September 2020

COVID-19 CG is an open resource for tracking SARS-CoV-2 single-nucleotide variations (SNVs) and lineages while filtering by location, date, gene, and mutation of interest. COVID-19 CG provides significant time, labor, and cost-saving utility to diverse projects on SARS-CoV-2 transmission, evolution, emergence, immune interactions, diagnostics, therapeutics, vaccines, and intervention tracking. Here, we describe case studies in which users can interrogate (1) SNVs in the SARS-CoV-2 Spike receptor binding domain (RBD) across different geographic regions to inform the design and testing of therapeutics, (2) SNVs that may impact the sensitivity of commonly used diagnostic primers, and (3) the recent emergence of a dominant lineage harboring an S477N RBD mutation in Australia. To accelerate COVID-19 research and public health efforts, COVID-19 CG will be continually upgraded with new features for users to quickly and reliably pinpoint mutations as the virus evolves throughout the pandemic and in response to therapeutic and public health interventions.
Short-Term Pediatric Acclimatization to Adaptive Hearing Aid Technology
Authors: Pinkl Joseph , Cash Erin K. , Evans Tommy C. , Neijman Timothy , Hamilton Jean W. , Ferguson Sarah D. , Martinez Jasmin L. , Rumley Johanne , Hunter Lisa L. , Moore David R. , Stewart Hannah J.
Published: September 2020

Purpose

This pilot study assessed the perceptual, cognitive and academic learning effects of an adaptive integrated directionality and noise reduction hearing aid program in pediatric users.

Methods

Fifteen pediatric hearing aid users (6 to 12 years old) participated in a hearing aid pilot with pre- to post-comparisons. Participants received new bilateral, individually fitted Oticon OPN hearing aids programmed with OpenSound Navigator (OSN) processing. Word recognition in noise, sentence repetition in quiet, nonword repetition, vocabulary learning, selective attention, executive function, memory, reading and mathematical abilities were measured within one week of the initial hearing aid fitting and two months post-fit. Caregivers completed questionnaires assessing their child’s listening and communication abilities prior to study enrollment and after two months of using the study hearing aids.

Results

Caregiver reporting indicated significant improvements in speech and sound perception, spatial sound awareness and the ability to participate in conversations. However, there was no positive change in performance in any of the measured skills. Mathematical scores significantly declined after two months.

Conclusions

OSN provided a perceived improvement in functional benefit, compared to their previous hearing aids, as reported by caregivers. However, there was no positive change in listening skills, cognition and academic success after two months of using OSN. Findings may have been impacted by reporter bias, limited sample size and a relatively short trial period. This study took place during the summer when participants were out of school which may have influenced the decline in mathematical scores. The results support further exploration with age and audiogram-matched controls, larger sample sizes, and longer test-retest intervals that correspond to the academic school year.
Serum SARS-CoV-2 nucleocapsid antigen detection is essential for primary diagnostics of SARS-CoV-2-associated pneumonia
Authors: Lebedin Yuri S. , Lyang Olga V. , Galstyan Anaida G. , Panteleeva Anna V. , Belousov Vsevolod V. , Rebrikov Denis V.
Published: September 2020

The article highlights the diagnostic value of SARS-CoV-2 seroconversion in patients with pneumonia based on the results of a retrospective study conducted at the height of the COVID-19 pandemic in Moscow, Russia.
Accessioning and automation compatible anterior nares swab design
Authors: Pettit Mary E. , Boswell Sarah A. , Qian Jason , Novak Richard , Springer Michael
Published: September 2020

The COVID-19 pandemic has resulted in an unparalleled need for viral testing capacity across the world and is a critical requirement for successful re-opening of economies. The logistical barriers to near-universal testing are considerable. We have designed an injection molded polypropylene anterior nares swab, the RHINOstick, with a screw cap integrated into the swab handle that is compatible with fully automated sample accessioning and processing. The ability to collect and release both human and viral material is comparable to that of several commonly used swabs on the market. SARS-CoV-2 is stable on dry RHINOstick swabs for at least 3 days, even at 42°C, and elution can be achieved with small volumes. The swab and barcoded tube set can be produced, sterilized, and packaged at < 2 USD per unit and can easily be adopted by large research institutes to increase throughput and dramatically reduce the cost of a standard SARS-CoV-2 detection pipeline.
Implications of Monsoon Season & UVB Radiation for COVID-19 in India Manuscript
Authors: Kalippurayil Moozhipurath Rahul , Kraft Lennart
Published: September 2020

Background

India has recorded 66,333 deaths over 36 administrative regions placing India third in the world after the US and Brazil for COVID-19 deaths as of 2 September 2020. Studies indicate that south-west monsoon season plays a role in the dynamics of contagious diseases, which tend to peak post-monsoon season. Recent studies show that vitamin D and its primary source Ultraviolet-B radiation (UVB) may play a protective role in mitigating COVID-19 deaths. However, the combined roles of the monsoon season and UVB in COVID-19 in India are still unclear. In this observational study, we empirically study the respective roles of monsoon season and UVB, whilst further exploring, whether monsoon season negatively impacts the protective role of UVB in COVID-19 deaths in India.

Methods

We use a log-linear Mundlak model to a panel dataset of 36 administrative regions in India from 14 March 2020 - 8 August 2020 (n=4005). We use the cumulative COVID-19 deaths as the dependent variable. We isolate the association of monsoon season and UVB as measured by Ultraviolet Index (UVI) from other confounding time-constant and time-varying region-specific factors.

Findings

After controlling for various confounding factors, we observe that the monsoon season and a unit increase in UVI are separately associated with 12.8 percentage points and 2.0 percentage points decline in growth rates of COVID-19 deaths in the long run. These associations translate into substantial relative changes. For example, the current monsoon season, that has been going on for two weeks, is associated with a reduction in growth rates of COVID-19 deaths of 59%, whereas a permanent unit increase of UVI is associated with a reduction in growth rates of COVID-19 deaths of 37%. However, the current monsoon season, also reduces the protective role of UVI by 16.3% [0.33 percentage points], plausibly due to lower UVB exposure.

Interpretation

We find independent protective roles of both the monsoon season and UVI in mitigating COVID-19 deaths. Furthermore, we find evidence that monsoon season is associated with a significant reduction in the protective role of UVI. The protective role of monsoon season is plausibly due to limited outdoor activities of people. Our study outlines the role of the monsoon season and UVB in COVID-19 in India and supports health-related policy decision making in India.
Clinical manifestations along with biochemical and psychological outcomes of COVID-19 cases in diabetic individuals in Bangladesh
Authors: Akter Farhana , Mannan Adnan , Mehedi H. M. Hamidullah , Rob Abdur , Ahmed Shakeel , Salauddin Asma , Hossain Md. Shakhawat , Hasan Md Mahbub
Published: September 2020

Background and aims

This study investigated the clinical manifestations, outcomes and long-term complications of COVID-19 inpatients in Bangladesh while emphasizing on individuals having diabetes.

Methods

A cross-sectional study was conducted for a sample of COVID-19 inpatients across four different hospitals of Bangladesh between April 1st and June 30, 2020. Variation in clinical characteristics, contact history, comorbidities, treatment pattern, and long-term complications were investigated.

Results

There were 734 COVID-19 presentations in this study of which 19.8% of patients had diabetes. 76% were male and 85% of the patients had been administered with all vaccine doses during childhood. The most frequently occurring blood groups among patients with diabetes were B (+) ve (35%) and O (+) ve (31%). Among biochemical parameters, glucose, D-dimer, C-reactive protein (CRP) and Troponin levels were significantly elevated amidst the cohort with diabetes. The frequency of insulin dependent individuals increased three-fold during COVID-19. A number of COVID-19 patients with diabetes have been suffering from long term complications post recovery including pain, discomfort, memory loss and sleep disturbance.

Conclusion

Individuals with diabetes have experienced severe manifestation of COVID-19 and post disease complications. Further in-depth studies focused on larger sample sizes are entailed to assess the relationships elaborately.
NeuroPM toolbox: integrating Molecular, Neuroimaging and Clinical data for Characterizing Neuropathological Progression and Individual Therapeutic Needs
Authors: Iturria-Medina Yasser , Carbonell Félix , Assadi Atousa , Adewale Quadri , Khan Ahmed F. , Baumeister Robert , Sanchez-Rodriguez Lazaro ,   for the Alzheimer’s Neuroimaging Initiative
Published: September 2020

There is a critical need for a better multiscale and multifactorial understanding of neurological disorders, covering from genes to neuroimaging to clinical factors and treatments effects. Here we present NeuroPM-box, a cross-platform, user-friendly and open-access software for characterizing multiscale and multifactorial brain pathological mechanisms and identifying individual therapeutic needs. The implemented methods have been extensively tested and validated in the neurodegenerative context, but there is not restriction in the kind of disorders that can be analyzed. By using advanced analytic modeling of molecular, neuroimaging and/or cognitive/behavioral data, this framework allows multiple applications, including characterization of: (i) the series of sequential states (e.g. transcriptomic, imaging or clinical alterations) covering decades of disease progression, (ii) intra-brain spreading of pathological factors (e.g. amyloid and tau misfolded proteins), (iii) synergistic interactions between multiple brain biological factors (e.g. direct tau effects on vascular and structural properties), and (iv) biologically-defined patients stratification based on therapeutic needs (i.e. optimum treatments for each patient). All models’ outputs are biologically interpretable. A 4D-viewer allows visualization of spatiotemporal brain (dis)organization. Originally implemented in MATLAB, NeuroPM-box is compiled as standalone application for Windows, Linux and Mac environments: neuropm-lab.com/software. In a “regular” workstation, it can analyze over 150 subjects per day, reducing the need for using clusters or High-Performance Computing (HPC) for large-scale datasets. This open-access tool for academic researchers may significantly contribute to a better understanding of complex brain processes and to accelerating the implementation of Precision Medicine (PM) in neurology.
Outcomes associated with SARS-CoV-2 viral clades in COVID-19
Authors: Nakamichi Kenji , Shen Jolie Z. , Lee Cecilia S. , Lee Aaron , Roberts Emma A. , Simonson Paul D. , Roychoudhury Pavitra , Andriesen Jessica , Randhawa April K. , Mathias Patrick C. , Greninger Alex L. , Jerome Keith R. , Van Gelder Russell N.
Published: September 2020

Background

The COVID-19 epidemic of 2019-20 is due to the novel coronavirus SARS-CoV-2. Following first case description in December, 2019 this virus has infected over 10 million individuals and resulted in at least 500,000 deaths world-wide. The virus is undergoing rapid mutation, with two major clades of sequence variants emerging. This study sought to determine whether SARS-CoV-2 sequence variants are associated with differing outcomes among COVID-19 patients in a single medical system.

Methods

Whole genome SARS-CoV-2 RNA sequence was obtained from isolates collected from patients registered in the University of Washington Medicine health system between March 1 and April 15, 2020. Demographic and baseline medical data along with outcomes of hospitalization and death were collected. Statistical and machine learning models were applied to determine if viral genetic variants were associated with specific outcomes of hospitalization or death.

Findings

Full length SARS-CoV-2 sequence was obtained 190 subjects with clinical outcome data. 35 (18.4%) were hospitalized and 14 (7.4%) died from complications of infection. A total of 289 single nucleotide variants were identified. Clustering methods demonstrated two major viral clades, which could be readily distinguished by 12 polymorphisms in 5 genes. A trend toward higher rates of hospitalization of patients with Clade 2 was observed (p=0.06). Machine learning models utilizing patient demographics and co-morbidities achieved area-under-the-curve (AUC) values of 0.93 for predicting hospitalization. Addition of viral clade or sequence information did not significantly improve models for outcome prediction.

Conclusion

SARS-CoV-2 shows substantial sequence diversity in a community-based sample. Two dominant clades of virus are in circulation. Among patients sufficiently ill to warrant testing for virus, no significant difference in outcomes of hospitalization or death could be discerned between clades in this sample. Major risk factors for hospitalization and death for either major clade of virus include patient age and comorbid conditions.

Funding

Supported by NIH P30EY001730, the Mark J. Daily, MD Research Fund (RVG), the Alida and Christopher Latham Research Fund (RVG, AYL, CSL), NIH K23EY029246 (AYL), US Food and Drug Administration (QYL)
Psychological preparedness for pandemic (COVID-19) management: Perceptions of nurses and nursing students in India
Authors: Gandhi Sailaxmi , Sahu Maya , Radhakrishnan G , Nattala Prasanthi , Sudhir Paulomi M. , Balachandran Rathi
Published: September 2020

Introduction

The growing COVID-19 pandemic has posed a great threat to millions of people worldwide. Nurses and nursing students are an important group of health professionals who are most likely to face many challenges in this unprecedented scenario. The present study aimed at exploring the perception of nurses and nursing students regarding psychological preparedness for the pandemic (COVID-19) management.

Materials & Methods

The study employed a quantitative cross-sectional online survey research design. Purposive sampling was used with an attempt to represent the entire nurses (i.e. nursing officers, nurse administrators and nursing teachers) and nursing students group of India. The survey link was shared to their email ID and they were invited to participate in the study. Data were collected using Psychological Preparedness for Disaster Threat Scale (PPDTS)-Modified, General Self Efficacy (GSE) Scale, Optimism Scale and Brief Resilient Coping Scale (BRS). Totally 685 responses were received and 676 forms were completed which were analyzed using SPSS software (version 24).

Results

The mean age of the subjects was 31.72 (SD=9.58) years. Around 20% of the subjects previously had some kind of psychological training and 4% of the subjects had taken care of persons with COVID-19. Findings revealed that mean score for PPDTS, GSE, BRCS and Optimism was 73.44 (SD=10.82, 33.19 (SD=5.23), 16.79 (SD=2.73) and 9.61 (SD=2.26) respectively indicating that the subjects had moderate level of psychological preparedness, self-efficacy and resilience but higher level of optimism. Psychological preparedness, self-efficacy, optimism and resilience were positively correlated to each other. Self-efficacy, optimism, and resilience emerged as predictors of psychological preparedness.

Conclusion

The findings suggested that self-efficacy, optimism and resilience can be considered as predictors for psychological preparedness in pandemic management. Appropriate training could influence self-efficacy while programs addressing resilience and coping may strengthen psychological preparedness which can help in further management of ongoing pandemic.
Reproductive Maternal and Newborn Health providers assessment of facility preparedness and its Determinants during the COVID-19 pandemic in Lagos, Nigeria
Authors: Charles Ameh , Aduragbemi Banke-Thomas , Mobolanle Balogun , Chigozie Makwe Christian , Bukola Afolabi Bosede
Published: September 2020

The global COVID-19 pandemic is predicted to compromise the achievement of global reproductive, maternal and newborn health (RMNH) targets. The objective of this study was to determine the health facility (HF) preparedness for RMNH service delivery during the outbreak from the perspective of RMNH providers and to determine what factors significantly predict this. An anonymous cross-sectional online survey of RMNH providers was conducted from 1st to 21st July 2020 in Lagos state Nigeria. We conducted a descriptive and ordinal regression analysis, with RMNH worker perception of HF preparedness for RMNH service delivery during the outbreak as the dependent variable.

Two hundred and fifty-six RMNH workers participated, 35.2% reported that RMNH services were unavailable at some time since March 2020, 39% felt moderate or extreme work-related burnout, 84% were moderately or extremely concerned about the availability of PPE and related guidelines, and only 11.7% were extremely satisfied with the preparedness of their HFs. Our final model was a statistically significant predictor of RMNH worker perception of HF preparedness explaining 54.7% of the variation in the outcome variable. A one-unit increase in the level of satisfaction with the communication from HF management and level of concern about the availability of PPE and COVID-19 guidelines would increase the odds of observing a higher category of satisfaction with HF COVID-19 preparedness (OR 0.79-2.92, p<0.001 and 0.02-0.15 p<0.001 respectively).

Adequate support of RMNH providers particularly provision of PPE and guidelines, appropriate communications about COVID- 19 should be prioritised as part of health system preparedness.
NMJ-Analyser: high-throughput morphological screening of neuromuscular junctions identifies subtle changes in mouse neuromuscular disease models
Authors: Maza Alan Mejia , Jarvis Seth , Lee Weaverly Colleen , Cunningham Thomas J. , Schiavo Giampietro , Secrier Maria , Fratta Pietro , Sleigh James N. , Sudre Carole H. , Fisher Elizabeth M.C.
Published: September 2020

The neuromuscular junction (NMJ) is the peripheral synapse formed between a motor neuron axon terminal and a muscle fibre. NMJs are thought to be the primary site of peripheral pathology in many neuromuscular diseases, but innervation/denervation status is often assessed qualitatively with poor systematic criteria across studies, and separately from 3D morphological structure. Here, we describe the development of ‘NMJ-Analyser’, to comprehensively screen the morphology of NMJs and their corresponding innervation status automatically. NMJ-Analyser generates 29 biologically relevant features to quantitatively define healthy and aberrant neuromuscular synapses and applies machine learning to diagnose NMJ degeneration. We validated this framework in longitudinal analyses of wildtype mice, as well as in four different neuromuscular disease models: three for amyotrophic lateral sclerosis (ALS) and one for peripheral neuropathy. We showed that structural changes at the NMJ initially occur in the nerve terminal of mutant TDP43 and FUS ALS models. Using a machine learning algorithm, healthy and aberrant neuromuscular synapses are identified with 95% accuracy, with 88% sensitivity and 97% specificity. Our results validate NMJ-Analyser as a robust platform for systematic and structural screening of NMJs, and pave the way for transferrable, and cross-comparison and high-throughput studies in neuromuscular diseases.
Pentapeptide repeat proteins QnrB1 and AlbG require ATP hydrolysis to rejuvenate poisoned gyrase complexes
Authors: Mazurek Łukasz , Ghilarov Dmitry , Michalczyk Elizabeth , Pakosz Zuzanna , Czyszczoń Wojciech , Wawro Karolina , Behroz Iraj , Süssmuth Roderich D. , Heddle Jonathan G.
Published: September 2020

DNA gyrase, a type II topoisomerase found predominantly in bacteria, is the target for a variety of “poisons”, namely natural product toxins (e.g. albicidin. microcin B17) and clinically important synthetic molecules (e.g. fluoroquinolones). Resistance to both groups can be mediated by pentapeptide repeat proteins (PRPs). Despite long-term studies, the mechanism of action of these protective PRPs is not known. We compared activities of two such proteins, QnrB1 and AlbGin vitro. Each of them provided specific protection against its cognate toxin (fluoroquinolone or albicidin), which strictly required ATP hydrolysis by gyrase. Through a combination of fluorescence anisotropy, pull-downs and photocrosslinking we show that QnrB1 binds to the GyrB protein. We further probed the QnrB1 binding site using site-specific incorporation of a photoreactive amino acid and mapped strong and specific crosslinks to the N-terminal ATPase/transducer domain. We propose a model in which protective PRPs bind to the enzyme as T-segment DNA mimics to promote dissociation of the bound poison molecule.
Systematic analysis of key parameters for genomics-based real-time detection and tracking of multidrug-resistant bacteria
Authors: Gorrie Claire L , Da Silva Anders Goncalves , Ingle Danielle J , Higgs Charlie , Seemann Torsten , Stinear Timothy P , Williamson Deborah A , Kwong Jason C , Grayson M Lindsay , Sherry Norelle L , Howden Benjamin P
Published: September 2020

Background

Pairwise single nucleotide polymorphisms (SNPs) are a cornerstone for genomic approaches to multidrug-resistant organisms (MDROs) transmission inference in hospitals. However, the impact of key analysis parameters on these inferences has not been systematically analysed.

Methods

We conducted a multi-hospital 15-month prospective study, sequencing 1537 MDRO genomes for comparison; methicillin-resistantStaphylococcus aureus, vancomycin-resistantEnterococcus faecium, and extended-spectrum beta-lactamase-producingEscherichia coliandKlebsiella pneumoniae. We systematically assessed the impact of sample and reference genome diversity, masking of prophage and regions of recombination, cumulative genome analysis compared to a three-month sliding-window, and the comparative effects each of these had when applying a SNP threshold for inferring likely transmission (≤15 SNPs forS. aureus, ≤25 for other species).

Findings

Across the species, using a reference genome of the same sequence type provided a greater degree of pairwise SNP resolution, compared to species and outgroup-reference alignments that typically resulted in inflated SNP distances and the possibility of missed transmission events. Omitting prophage regions had minimal impacts, however, omitting recombination regions a highly variable effect, often inflating the number of closely related pairs. Estimating pairwise SNP distances was more consistent using a sliding-window than a cumulative approach.

Interpretation

The use of a closely-related reference genome, without masking of prophage or recombination regions, and a sliding-window for isolate inclusion is best for accurate and consistent MDRO transmission inference. The increased stability and resolution provided by these approaches means SNP thresholds for putative transmission inference can be more reliably applied among diverse MDROs.

Funding

This work was supported by the Melbourne Genomics Health Alliance (funded by the State Government of Victoria, Department of Health and Human Services, and the ten member organizations); an National Health and Medical Research Council (Australia) Partnership grant (GNT1149991) and individual grants from National Health and Medical Research Council (Australia) to NLS (GNT1093468), JCK (GNT1008549) and BPH (GNT1105905).
ZETA: a parameter-free statistical test for neuronal responsiveness
Authors: Montijn Jorrit S. , Seignette Koen , Howlett Marcus H. , Cazemier J. Leonie , Kamermans Maarten , Levelt Christiaan N. , Heimel J. Alexander
Published: September 2020

Neurophysiological studies depend on a reliable quantification of whether and when a neuron responds to stimulation. Simple methods to determine responsiveness require arbitrary parameter choices, such as binning size, while more advanced model-based methods require fitting and hyperparameter tuning. These parameter choices can change the results, which invites bad statistical practice and reduces the replicability. New recording techniques that yield increasingly large numbers of cells would benefit from a test for cell-inclusion that requires no manual curation. Here, we present the parameter-free ZETA-test, which outperforms t-tests, ANOVAs, and renewal-process-based methods by including more cells at a similar false-positive rate. We show that our procedure works across brain regions and recording techniques, including calcium imaging and Neuropixels data. Furthermore, in illustration of the method, we show in mouse visual cortex that 1) visuomotor-mismatch and spatial location are encoded by different neuronal subpopulations; and 2) optogenetic stimulation of VIP cells leads to early inhibition and subsequent disinhibition.
Horizontal gene transfer-mediated bacterial strain variation affects host fitness
Authors: Wang Yun , Baumdicker Franz , Kuenzel Sven , Staubach Fabian
Published: September 2020

How microbes affect host fitness and environmental adaptation has become a fundamental research question in evolutionary biology. We tested for associations of bacterial genomic variation andDrosophila melanogasteroffspring number in a microbial Genome Wide Association Study (GWAS). Leveraging strain variation in the genusGluconobacter, a genus of bacteria that are commonly associated withDrosophilaunder natural conditions, we pinpoint the thiamine biosynthesis pathway (TBP) as contributing to differences in fitness conferred to the fly host. By tracing the evolutionary history of TBP genes inGluconobacter, we find that TBP genes were most likely lost and reacquired by horizontal gene transfer (HGT). We suggest that HGT might contribute to microbiome flexibility and speculate that it can also more generally contribute to host adaptation.
The intrinsically disordered N-terminus of the voltage-dependent anion channel
Authors: Preto Jordane , Krimm Isabelle
Published: September 2020

The voltage-dependent anion channel (VDAC) is a critical β-barrel membrane protein of the mitochondrial outer membrane, which regulates the transport of ions and ATP between mitochondria and the cytoplasm. In addition, VDAC plays a central role in the control of apoptosis and is therefore of great interest in both cancer and neurodegenerative diseases. Although not fully understood, it is presumed that the gating mechanism of VDAC is governed by its N-terminal region which, in the open state of the channel, exhibits an α-helical structure positioned midway inside the pore and strongly interacting with the β-barrel wall.

In the present work, we performed molecular simulations with a recently developed force field for disordered systems to shed new light on known experimental results, showing that the N-terminus of VDAC is an intrinsically disordered region (IDR). First, simulation of the N-terminal segment as a free peptide highlighted its disordered nature and the importance of using an IDR-specific force field to properly sample its conformational landscape. Secondly, accelerated dynamics simulation of a double cysteine VDAC mutant under applied voltage revealed metastable low conducting states of the channel representative of closed states observed experimentally. Related structures were characterized by partial unfolding and rearrangement of the N-terminal tail, that led to steric hindrance of the pore. Our results indicate that the disordered properties of the N-terminus are crucial to properly account for the gating mechanism of VDAC.

Author summary

The voltage-dependent anion channel (VDAC) is a membrane protein playing a pivotal role in the transport of ions or ATP across the mitochondrial outer membrane as well as in the induction of apoptosis. At high enough membrane potential, VDAC is known to transition from an open state to multiple closed states, reducing the flow of ions through the channel and blocking the passage of large metabolites. While the structure of the open state was resolved more than a decade ago, a molecular description of the gating mechanism of the channel is still missing. Here we show that the N-terminus of VDAC is an intrinsically disordered region and that such a property has a profound impact on its dynamics either as a free peptide or as part of the channel. By taking disordered properties of the N-terminus into account, we managed to generate long-lived closed conformations of the channel at experimental values of the membrane potential. Our results provide new insights into the molecular mechanism driving the gating of VDAC.
A novel method for sensor-based quantification of single/multi-cellular traction dynamics and remodeling in 3D matrices
Authors: Emon Bashar , Li Zhengwei , Joy Md Saddam Hossain , Doha Umnia , Kosari Farhad , Saif M Taher A
Published: September 2020

Cellsin vivogenerate mechanical forces (traction) on surrounding 3D extra cellular matrix (ECM) and cells. Such traction and biochemical cues may remodel the matrix, e.g. increase stiffness, which in turn influences cell functions and forces. This dynamic reciprocity mediates development and tumorigenesis. Currently, there is no method available to directly quantify single cell traction and matrix remodeling in 3D. Here, we introduce a method to fulfil this long-standing need. We developed a high-resolution microfabricated sensor which hosts a 3D cell-ECM tissue formed by self-assembly. It measures cell forces and tissue-stiffness and can apply mechanical stimulation to the tissue. We measured single and multicellular force dynamics of fibroblasts (3T3), human colon (FET) and lung (A549) cancer cells and cancer associated fibroblasts (CAF05) with 1 nN resolution. Single cells show significant force fluctuations in 3D. FET/CAF co-culture system, mimicking cancer tumor microenvironment, increased tissue stiffness by 3 times within 24 hours.
A vaccine built from potential immunogenic pieces derived from the SARS-CoV-2 spike glycoprotein
Authors: Marchan Jose
Published: September 2020

Coronavirus Disease 2019 (COVID-19) represents a new global threat demanding a multidisciplinary effort to fight its etiological agent—severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this regard, immunoinformatics may aid to predict prominent immunogenic regions from critical SARS-CoV-2 structural proteins, such as the spike (S) glycoprotein, for their use in prophylactic or therapeutic interventions against this rapidly emerging coronavirus. Accordingly, in this study, an integrated immunoinformatics approach was applied to identify cytotoxic T cell (CTC), T helper cell (THC), and Linear B cell (BC) epitopes from the S glycoprotein in an attempt to design a high-quality multi-epitope vaccine. The best CTC, THC, and BC epitopes showed high viral antigenicity, lack of allergenic or toxic residues, and suitable HLA-viral peptide interactions. Remarkably, SARS-CoV-2 receptor-binding domain (RBD) and its receptor-binding motif (RBM) harbour several potential epitopes. The structure prediction, refinement, and validation data indicate that the multi-epitope vaccine has an appropriate conformation and stability. Three conformational epitopes and an efficient binding between Toll-like receptor 4 (TLR4) and the vaccine model were observed. Importantly, the population coverage analysis showed that the multi-epitope vaccine could be used globally. Notably, computer-based simulations suggest that the vaccine model has a robust potential to evoke and maximize both immune effector responses and immunological memory to SARS-CoV-2. Further research is needed to accomplish with the mandatory international guidelines for human vaccine formulations.

Graphical Abstract
The susceptibility analysis ofEchinococcus multilocularisprotoscoleces tubulin to mebendazole and RNA interference
Authors: Shi Qiqi , Huo Lele , Jiang Bin , Gao Haijun , Zheng Jinxin , Tao Yi , Zhang Haobing
Published: September 2020

Alveolar echinococcosis, caused by the larval (metacestode) stage of the tapewormEchinococcus multilocularis, is a lethal parasitosis of the liver prevalent in the Northern Hemisphere. For chemotherapy the benzimidazole derivatives mebendazole and albendazole were introduced, which were found to disrupt the microtubules by inhibition of the polymerization of tubulin into microtubules, and β-tubulin was determined to be the drug target molecule. In the present study, we evaluated the chemosensitivity ofE. multilocularisprotoscoleces tubulin to mebendazole and RNA interference in vitro, and to explore whether the molecular level and ultrastructure ofE. multilocularisprotoscoleces microtubules change post-mebendazole and RNA interference. We identified that mebendazole is parasitostatic toE. multilocularisprotoscoleces through suppression the tubulin expression and change the flame cell morphology in molecular level, besides RNA interference indicated thatβ 2tubulin is probably one of the vital tubulin gene to form the flame cell and the protonephridial system tubules (collective tubes) ofE. multilocularisprotoscoleces. Molecular level and ultrastructure detection were performed by reverse transcription-PCR, western blotting and transmission electron microscope. The RNA interference would be probably as a parasitocidal method to disrupt the survival of PSCs, extend that the relevant tubulin maybe as potential target for drug development against AE.
An easy, reliable and rapid SARS-CoV2 RT-LAMP based test for Point-of-Care and diagnostic lab
Authors: Gouilh Meriadeg AR , Cassier Renaud , Maille Elodie , Schanen Cécile , Rocque Louis-Marie , Vabret Astrid
Published: September 2020

This study presents and evaluates a rapid and all-in-one SARS-CoV-2 RT-LAMP based molecular detection system, including RNA extraction or not, for point-of-care or massive testing of naso-pharyngeal swabs. The point-of-care format uses LoopX©, a small portative device ensuring optimal LAMP reaction and automated reading with 95.2% and 95.5% sensitivity and specificity respectively. This system might also be useful for testing other sample types such as saliva.