bluuebunny/crossref_metadata_2025 huggingface dataset:
Active fatty acid oxidation defines the cellular response towards reactive oxygen species
Authors: Kaiser Lars , Quint Isabel , Csuk René , Jung Manfred , Deigner Hans-Peter
Published: July 2020

Endocrine disrupting compounds (EDC) are ubiquitous in the human environment, displaying a highly relevant research topic. The impact of EDC on the differentiation of primitive cells, e.g. in hematopoiesis, is of particular interest. We found profound inhibitory effects of di-2-ethylhexyl phthalate (DEHP) on erythropoiesis and dendropoiesis, mediated via reactive oxygen species (ROS) generation. Neutrophil differentiation, however, was not affected by DEHP. ROS leads to a shift from glycolysis to the pentose phosphate pathway and diminishes ATP generation from glycolysis, ultimately resulting in apoptosis in both cell types. In neutrophils, ATP generation is held constant by active fatty acid oxidation (FAO), rendering these cells highly resistant against ROS. This relationship also holds true in HUVEC and HepG2 cells, also in combination with other organic peroxides. We, therefore, uncover a key mechanism for ROS quenching which further explains the distinct ROS quenching ability of different tissues.
Regulations of mitochondrial DNA repair by poly(ADP-Ribose) Polymerase 1
Authors: Herrmann Geoffrey K. , Yin Y. Whitney
Published: July 2020

Formation of a repair enzyme complex is beneficial to DNA repair. Despite the fact that mitochondrial base excision repair (mtBER) enzymes DNA polymerase gamma (Pol γ) and poly(ADP-ribose) polymerase 1 (PARP1) were found in the same complex, the functional role of the interaction in mtBER has not been characterized. We report studies that PARP1 regulates Pol γ activity during DNA repair in a metabolic cofactor NAD+(nicotinamide adenosine dinucleotide)-dependent manner. In the absence of NAD+, PARP1 completely inhibits Pol γ, while increasing NAD+level to physiological concentration enables Pol γ to resume maximum repair activity. Pol γ is PARylated when bound to DNA repair intermediates, and PARylation is essential for Pol γ repair activity. The PARP1 inhibitor Olaparib that abolishes PARP1 catalytic activity suppresses Pol γ gap-filling synthesis at physiological concentrations of NAD+, suggesting inhibiting PARP1 activity would increase mtDNA mutations. Because NAD+cellular levels are linked to metabolism and to ATP production via oxidative phosphorylation, our results suggest that mtDNA damage repair is correlated with cellular metabolic state and integrity of the respiratory chain. Our results revealed a molecular basis of drug toxicity from prolonged usage of PARP1 inhibitors in treating cardiac dysfunctions
The dimerisable Cre recombinase allows conditional genome editing in the mosquito stages ofPlasmodium berghei
Authors: Fernandes Priyanka , Briquet Sylvie , Patarot Delphine , Loubens Manon , Hoareau-Coudert Bénédicte , Silvie Olivier
Published: July 2020

Asexual blood stages of the malaria parasite are readily amenable to genetic modification via homologous recombination, allowing functional studies of parasite genes that are not essential in this part of the life cycle. However, conventional reverse genetics cannot be applied for the functional analysis of genes that are essential during asexual blood-stage replication. Various strategies have been developed for conditional mutagenesis ofPlasmodium, including recombinase-based gene deletion, regulatable promoters, and mRNA or protein destabilization systems. Among these, the dimerisable Cre (DiCre) recombinase system has emerged as a powerful approach for conditional gene targeting inP. falciparum. In this system, the bacteriophage Cre is expressed in the form of two separate, enzymatically inactive polypeptides, each fused to a different rapamycin-binding protein. Rapamycin-induced heterodimerization of the two components restores recombinase activity. We have implemented the DiCre system in the rodent malaria parasiteP. berghei, and show that rapamycin-induced excision of floxed DNA sequences can be achieved with very high efficiency in both mammalian and mosquito parasite stages. This tool can be used to investigate the function of essential genes not only in asexual blood stages, but also in other parts of the malaria parasite life cycle.
Beat gestures influence which speech sounds you hear
Authors: Bosker Hans Rutger , Peeters David
Published: July 2020

Beat gestures – spontaneously produced biphasic movements of the hand – are among the most frequently encountered co-speech gestures in human communication. They are closely temporally aligned to the prosodic characteristics of the speech signal, typically occurring on lexically stressed syllables. Despite their prevalence across speakers of the world’s languages, how beat gestures impact spoken word recognition is unclear. Can these simple ‘flicks of the hand’ influence speech perception? Across six experiments, we demonstrate that beat gestures influence the explicit and implicit perception of lexical stress (e.g., distinguishingOBjectfromobJECT), and in turn, can influence what vowels listeners hear. Thus, we provide converging evidence for amanual McGurk effect: even the simplest ‘flicks of the hands’ influence which speech sounds we hear.

SIGNIFICANCE STATEMENT

Beat gestures are very common in human face-to-face communication. Yet we know little about their behavioral consequences for spoken language comprehension. We demonstrate that beat gestures influence the explicit and implicit perception of lexical stress, and, in turn, can even shape what vowels we think we hear. This demonstration of amanual McGurk effectprovides some of the first empirical support for a recent multimodal, situated psycholinguistic framework of human communication, while challenging current models of spoken word recognition that do not yet incorporate multimodal prosody. Moreover, it has the potential to enrich human-computer interaction and improve multimodal speech recognition systems.
The heat shock transcription factor HSF-1 protectsCaenorhabditis elegansfrom peroxide stress
Authors: Servello Francesco A. , Apfeld Javier
Published: July 2020

Cells induce conserved defense mechanisms that protect them from oxidative stress. How these defenses are regulated in multicellular organisms is incompletely understood. Using the nematodeCaenorhabditis elegans, we show that the heat shock transcription factor HSF-1 protects the nematode from the oxidative stress induced by environmental peroxide. In response to a heat shock or a mild temperature increase, HSF-1 protects the nematodes from subsequent oxidative stress in a manner that depends on HSF-1’s transactivation domain. At constant temperature, HSF-1 protects the nematodes from oxidative stress independently of its transactivation domain, likely by inducing the expression ofasp-4/cathepsin Danddapk-1/dapk. Thus, two distinct HSF-1-dependent processes protectC. elegansfrom oxidative stress.
Microbiome Dynamics of Bovine Mastitis Progression and Genomic Determinants
Authors: Hoque M. Nazmul , Istiaq Arif , Rahman M. Shaminur , Islam M. Rafiul , Anwar Azraf , Siddiki AMAM Zonaed , Sultana Munawar , Crandall Keith A. , Hossain M. Anwar
Published: July 2020

The milk of lactating cows presents a complex ecosystem of interconnected microbial communities which can impose a significant influence on the pathophysiology of mastitis. Previously, we reported the alteration of microbiome (bacteria, archaea, virus) composition between clinical mastitis (CM) and healthy (H) milk. We hypothesized possible dynamic shifts of microbiome compositions with the progress of different pathological states of mastitis (CM, Recurrent CM; RCM, Subclinical Mastitis; SCM) determined by its favoring genomic potentials. To evaluate this hypothesis, we employed whole metagenome sequencing (WMS) in 20 milk samples (CM = 5, RCM = 6, SCM = 4, H = 5) to unravel the microbiome dynamics, interrelation, and relevant metabolic functions. PathoScope (PS) and MG-RAST (MR) analyses mapped the WMS data to 442 bacterial, 58 archaeal and 48 viral genomes with distinct variation in microbiome composition and abundances across these metagenomes (CM>H>RCM>SCM). PS analysis identified 385, 65, 80 and 144 bacterial strains in CM, RCM, SCM, and H milk, respectively, with an inclusion of 67.19% previously unreported opportunistic strains in mastitis metagenomes. Moreover, MR detected 56, 13, 9 and 46 archaeal, and 40, 24, 11 and 37 viral genera in CM, RCM, SCM and H-milk metagenomes, respectively. The CM-microbiomes had closest association with RCM-microbiomes followed by SCM, and H-microbiomes. Furthermore, we identified 333, 304, 183 and 50 virulence factors-associated genes (VFGs), and 48, 31, 11 and 6 antibiotic resistance genes (AGRs) in CM, RCM, SCM, and H-microbiomes, respectively, showing a significant correlation between the relative abundances of VFGs (p = 0.001), ARGs (p = 0.0001), and associated bacterial taxa. We also detected correlated variations in the presence and abundance of several metabolic functional genes related to bacterial colonization, proliferation, chemotaxis, motility and invasion, oxidative stress, virulence and pathogenicity, phage integration and excision, biofilm-formation, and quorum-sensing to be associated with different episodes of mastitis. Therefore, profiling the dynamics of microbiome in different states of mastitis, concurrent VFGs, ARGs, and genomic functional correlations will contribute to developing microbiome-based diagnostics and therapeutics for bovine mastitis, and carries significant implications on curtailing the economic fallout from this disease.
Comprehensive genotyping of Brazilian Cassava (Manihot esculentaCrantz) Germplasm Bank: insights into diversification and domestication
Authors: Ogbonna Alex C. , de Andrade Luciano Rogerio Braatz , de Oliveira Eder Jorge , Mueller Lukas A. , Bauchet Guillaume J.
Published: July 2020

Cassava (Manihot esculentaCrantz) is a major staple root crop of the tropics, originating from the Amazonas region. In this study, 3,354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 Single Nucleotide Polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1,536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, 1,300 to 4,700 SNP markers were selected for large quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity (Ho), effective population size estimateand polymorphism information content (PIC). Selection footprints and introgressions ofM. glazioviiwere detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggest earliest population split from Amazonas to Atlantic forest and Caatinga eco-regions and active gene flows. This study provides a thorough genetic characterization ofex situgermplasm resources from cassava center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These Findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.

Key message

Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups, and spatial genetic differentiation.
Insecticide resistance status of malaria vectorsAnopheles gambiae s.lof southwest Burkina Faso and residual efficacy of indoor residual spraying with microencapsulated pirimiphos-methyl insecticide
Authors: Soma Dieudonné D. , Zogo Barnabas M. , Hien François D. , Hien Aristide S. , Kaboré Didier P.A. , Kientega Mahamadi , Ouédraogo Anicet G. , Pennetier Cédric , Koffi Alphonsine A. , Moiroux Nicolas , Dabiré Roch K.
Published: July 2020

The rapid spread of insecticide resistance in malaria vectors and the rebound in malaria cases observed recently in some endemic areas underscore the urgent need to evaluate and deploy new effective control interventions. A randomized control trial was conducted with the aim to investigate the benefit of deploying complementary strategies, including indoor residual spraying (IRS) with pirimiphos-methyl, in addition to long-lasting insecticidal nets (LLINs) in Diébougou, southwest Burkina Faso. We measured the susceptibility ofAnopheles gambiae s.l.population from Diébougou to conventional insecticides. We further monitored the efficacy and residual activity of pirimiphos-methyl on both cement and mud walls using a laboratory susceptible strain (Kisumu) and the localAn. gambiae s.l.population.An. Gambiae s.l.from Diébougou was resistant to pyrethroids (deltamethrin, permethrin and alphacypermethrin) and bendiocarb but showed susceptibility to organophosphates (pirimiphos-methyl and chlorpyrimiphos-methyl). A mixed-effect generalized linear model predicted that pirimiphos-methyl applied on cement or mud walls was effective for 210 days against the laboratory susceptible strain and 247 days against the local population. The residual efficacy of pirimiphos-methyl against the local population on walls made of mud was similar to that of cement (OR=0.792, [0.55-1.12], Tukey’s test p-value =0.19). This study showed that one round of IRS with pirimiphos-methyl CS has the potential to control the multi-resistantAn. gambiae s.l.population from Southwest Burkina Faso for at least 7 months, regardless of the type of wall.
Contrasting effects of nutrients and consumers on tree colonization and growth during secondary succession
Authors: Heckman Robert W. , Halliday Fletcher W. , Wilfahrt Peter A.
Published: July 2020

For succession to proceed from herbaceous to woody dominance, trees must colonize herbaceous communities and grow. Success across these two phases of succession might result from different interactions with the herbaceous community. First, colonizing trees must compete against larger, established herbs, while subsequent growth occurs among similarly sized or smaller herbs. This shift from colonization to growth may cause three drivers of secondary succession— nutrients, consumers, and herbaceous diversity—to differentially affect tree colonization and growth. Initially, these drivers should favor larger, established herbs, reducing colonization. Later, when established trees can better compete with herbs, these drivers should benefit trees and increase their growth. In a four-year study, we added nutrients to, excluded aboveground consumers from, and manipulated initial richness of, the herbaceous community, then allowed trees to naturally colonize these communities (from intact seedbanks or as seed-rain) and grow. Nutrients and consumers had opposing effects on tree colonization and growth: adding nutrients and excluding consumers reduced tree colonization, but later increased established tree growth (height, basal diameter). Together, this shows stage-specific impacts of nutrients and consumers that may improve predictions of the rate and trajectory of succession: factors that initially limited tree colonization later helped established trees to grow.
Updates on enzymatic and structural properties of human glutamine: fructose-6-phosphate amidotransferase 2 (hGFAT2)
Authors: Oliveira Isadora A. , Allonso Diego , Fernandes Tácio V. A. , Lucena Daniela M. S. , Ventura Gustavo T. , Dias Wagner B. , Mohana-Borges Ronaldo S. , Pascutti Pedro G. , Todeschini Adriane R.
Published: July 2020

Glycoconjugates play a central role in several cellular processes and alteration in their composition is associated to human pathologies. The hexosamine biosynthetic pathway is a route through which cells obtain substrates for cellular glycosylation, and is controlled by the glutamine: fructose-6-phosphate amidotransferase (GFAT). Human isoform 2 GFAT (hGFAT2) has been implicated in diabetes and cancer, however, there is no information about structural and enzymatic properties of this enzyme. Here, we report a successful expression and purification of a catalytically active recombinant hGFAT2 (rhGFAT2) in E. coli cells fused or not to a HisTag at the C-terminal end. Our enzyme kinetics data suggest that hGFAT2 does not follow the ordered bi-bi mechanism, and performs the glucosamine-6-phosphate synthesis much slowly than previously reported for other GFATs. In addition, hGFAT2 is able to isomerase fructose-6-phosphate into glucose-6-phosphate even in presence of equimolar amounts of glutamine, in an unproductive glutamine hydrolysis. Structural analysis of the generated three-dimensional model rhGFAT2, corroborated by circular dichroism data, indicated the presence of a partially structured loop in glutaminase domain, whose sequence is present in eukaryotic enzymes but absent in the E. coli homolog. Molecular dynamics simulations show such loop as the most flexible portion of the protein, which interacts with the protein mainly through the interdomain region, and plays a key role on conformational states of hGFAT2. Altogether, our study provides the first comprehensive set of data on the structure, kinetics and mechanics of hGFAT2, which will certainly contribute for further studies focusing on drug development targeting hGFAT2.
Curation of over 10,000 transcriptomic studies to enable data reuse
Authors: Lim Nathaniel , Tesar Stepan , Belmadani Manuel , Poirier-Morency Guillaume , Mancarci Burak Ogan , Sicherman Jordan , Jacobson Matthew , Leong Justin , Tan Patrick , Pavlidis Paul
Published: July 2020

Vast amounts of transcriptomic data reside in public repositories, but effective reuse remains challenging. Issues include unstructured dataset metadata, inconsistent data processing and quality control, and inconsistent probe-gene mappings across microarray technologies. Thus, extensive curation and data reprocessing is necessary prior to any reuse. The Gemma bioinformatics system was created to help address these issues. Gemma consists of a database of curated transcriptomic datasets, analytical software, a web interface, and web services. Here we present an update on Gemma’s holdings, data processing and analysis pipelines, our curation guidelines, and software features. As of June 2020, Gemma contains 10,811 manually curated datasets (primarily human, mouse, and rat), over 395,000 samples and hundreds of curated transcriptomic platforms (both microarray and RNA-sequencing). Dataset topics were represented with 10,215 distinct terms from 12 ontologies, for a total of 54,316 topic annotations (mean topics/dataset = 5.2). While Gemma has broad coverage of conditions and tissues, it captures a large majority of available brain-related datasets, accounting for 34% of its holdings. Users can access the curated data and differential expression analyses through the Gemma website, RESTful service, and an R package.

Database URL: https://gemma.msl.ubc.ca/home.html
Stress, Burnout and Depression in Women in Healthcare during COVID-19 Pandemic: Rapid Scoping Review
Authors: Sriharan Abi , Ratnapalan Savithiri , Tricco Andrea C. , Lupea Doina , Ayala Ana Patricia , Pang Hilary , Lee Dongjoo Daniel
Published: July 2020

Objectives

The overall objectives of this rapid scoping review are to (a) synthesize the common triggers of stress, burnout, and depression faced by women in health care during the COVID-19 pandemic, and (b) identify individual-, organizational-, and systems-level interventions that can support the well-being of women HCWs during a pandemic.

Design

This scoping review is registered on Open Science Framework (OSF) and was guided by the JBI guide to scoping reviews and reported using the Preferred Reporting Items for Systematic reviews and Meta-Analysis (PRISMA) extension to scoping reviews. A systematic search of literature databases (Medline, EMBASE, CINAHL, PsycInfo and ERIC) was conducted from 2003 until June 12, 2020. Two reviewers independently assessed full-text articles according to predefined criteria.

Interventions

We included review articles and primary studies that reported on stress, burnout, and depression in HCWs; that primarily focused on women; and that included the percentage or number of women included. All English language studies from any geographical setting where COVID-19 has affected the population were reviewed.

Primary and secondary outcome measures

Studies reporting on mental health outcomes (e.g., stress, burnout, and depression in HCWs), interventions to support mental health well-being were included.

Results

Of the 2,803 papers found, 31 were included. The triggers of stress, burnout and depression are grouped under individual-, organizational-, and systems-level factors. There is a limited amount of evidence on effective interventions that prevents anxiety, stress, burnout and depression during a pandemic.

Conclusions

Our preliminary findings show that women HCWs are at increased risk for stress, burnout, and depression during the COVID-19 pandemic. These negative outcomes are triggered by individual level factors such as lack of social support; family status; organizational factors such as access to personal protective equipment or high workload; and systems-level factors such as prevalence of COVID-19, rapidly changing public health guidelines, and a lack of recognition at work.

Strengths and limitations of this study

A rapid scoping review was conducted to identify stress, burnout and depression faced by women HCWs during COVID-19.

To ensure the relevance of our review, representatives from the women HCWs were engaged in defining the review scope, developing review questions, approving the protocol and literature search strategies, and identifying key messages.

It provides a descriptive synthesis of current evidence on interventions to prevent mental health for women HCWs.

Most studies used cross-sectional surveys, making it difficult to determine the longitudinal impact.

There was significant variability in the tools used to measure mental health.
Predictive performance of international COVID-19 mortality forecasting models
Authors: Friedman Joseph , Liu Patrick , Gakidou Emmanuela ,   the IHME COVID19 Model Comparison Team
Published: July 2020

Background

Forecasts and alternative scenarios of the COVID-19 pandemic have been critical inputs into a range of important decisions by healthcare providers, local and national government agencies and international organizations and actors. Hundreds of COVID-19 models have been released. Decision-makers need information about the predictive performance of these models to help select which ones should be used to guide decision-making.

Methods

We identified 383 published or publicly released COVID-19 forecasting models. Only seven models met the inclusion criteria of: estimating for five or more countries, providing regular updates, forecasting at least 4 weeks from the model release date, estimating mortality, and providing date-versioned sets of previously estimated forecasts. These models included those produced by: a team at MIT (Delphi), Youyang Gu (YYG), the Los Alamos National Laboratory (LANL), Imperial College London (Imperial) the USC Data Science Lab (SIKJalpha), and three models produced by the Institute for Health Metrics and Evaluation (IHME). For each of these models, we examined the median absolute percent error—compared to subsequently observed trends—for weekly and cumulative death forecasts. Errors were stratified by weeks of extrapolation, world region, and month of model estimation. For locations with epidemics showing a clear peak, each model’s accuracy was also evaluated in predicting the timing of peak daily mortality.

Results

Across models, the median absolute percent error (MAPE) on cumulative deaths for models released in June rose with increased weeks of extrapolation, from 2.3% at one week to 32.6% at ten weeks. Globally, ten-week MAPE values were lowest for IHME-MS-SEIR (20.3%) and YYG (22.1). Across models, MAPE at six weeks were the highest in Sub-Saharan Africa (55.6%), and the lowest in high-income countries (7.7%). Median absolute errors (MAE) for peak timing also rose with increased forecasting weeks, from 14 days at one week to 30 days at eight weeks. Peak timing MAE at eight weeks ranged from 24 days for the IHME Curve Fit model, to 48 days for LANL.

Interpretation

Five of the models, from IHME, YYG, Delphi, SIKJalpha and LANL, had less than 20% MAPE at six weeks. Despite the complexities of modelling human behavioural responses and government interventions related to COVID-19, predictions among these better-performing models were surprisingly accurate. Forecasts and alternative scenarios can be a useful input to decision-makers, although users should be aware of increasing errors with a greater amount of extrapolation time, and corresponding steadily widening uncertainty intervals further in the future. The framework and publicly available codebase presented can be routinely used to evaluate the performance of all publicly released models meeting inclusion criteria in the future, and compare current model predictions.
Discrete simulation analysis of COVID-19 and prediction of isolation bed numbers
Authors: Li Xinyu , Cai Yufeng , Ding Yinghe , Li Jia-da , Huang Guoqing , Liang Ye , Xu Linyong
Published: July 2020

The outbreak of COVID-19 has caused tremendous pressure on medical systems. Adequate isolation facilities are essential to control outbreaks, so this study aims to quickly estimate the demand and number of isolation beds. We established a discrete simulation model for epidemiology. By adjusting or fitting necessary epidemic parameters, the effects of the following indicators on the development of the epidemic and the occupation of medical resources were explained: (1) incubation period, (2) response speed and detection capacity of the hospital, (3) disease cure time, and (4) population mobility. Finally, a method for predicting the reasonable number of isolation beds was summarized through multiple linear regression. The prediction equation can be easily and quickly applied to estimate the demanded number of isolation beds in a COVID-19-affected city. A detailed explanation is given for the specific measurement of each parameter in the article.
O Group is a protective factor for COVID19 in Basque population
Authors: Muñoz-Culla M , Roncancio-Clavijo A , Martínez B , Gorostidi M , Piñeiro L , Azkune A , Alberro A , Monge-Ruiz J , Castillo-Trivino T , Prada A , Otaegui D
Published: July 2020

ABO blood groups have been related to COVID19 infection. ABO blood groups are slightly differently distributed in the populations and therefore these results should be replicated in the specific areas with a proper control population. In this work, we present data from 412 COVID19 patients and 17796 blood donors from Gipuzkoa, a region in Northern Spain. Our data shows the importance of group O as a protective factor.
Prevalence of Nonsuppressed Viral Load and Associated Factors Among Adults Receiving Antiretroviral Therapy in Eswatini, Lesotho, Malawi, Zambia, and Zimbabwe (2015-2017): Results from Population-Based Nationally-Representative Surveys
Authors: Haas Andreas D. , Radin Elizabeth , Hakim Avi J. , Jahn Andreas , Philip Neena , Jonnalagadda Sasi , Saito Suzue , Low Andrea , Patel Hetal , Schwitters Amee , Rogers John , Frederix Koen , Kim Evelyn , Bello George , Williams Daniel B , Parekh Bharat , Sachathep Karampreet , Barradas Danielle T. , Kalua Thokozani , Birhanu Sehin , Musuka Godfrey , Mugurungi Owen , Tippett Barr Beth A. , Sleeman Katrina , Mulenga Lloyd B , Thin Kyaw , Ao Trong , Brown Kristin , Voetsch Andrew C. , Justman Jessica J.
Published: July 2020

Introduction

The Joint United Nations Programme on HIV/AIDS (UNAIDS) has set a target of ≥90% of people living with HIV (PLHIV) receiving antiretroviral therapy (ART) to have viral load suppression (VLS). We examined factors associated with nonsuppressed viral Load (NVL).

Methods

We included PLHIV receiving ART aged 15–59 years from Eswatini, Lesotho, Malawi, Zambia, and Zimbabwe. Blood samples from PLHIV were analyzed for HIV RNA and recent exposure to antiretroviral drugs (ARVs). Outcomes were NVL (viral load ≥1000 copies/mL), virologic failure (VF; ARVs present and viral load ≥1000 copies/mL), interrupted ART (ARVs absent and viral load ≥1000 copies/mL), and receiving second-line ART. We calculated odds ratios and incidence rate ratios for factors associated with NVL, VF, interrupted ART, and switching to second-line ART.

Results

The prevalence of NVL was 11.2%: 8.2% experienced VF, and 3.0% interrupted ART. Younger age, male gender, less education, suboptimal adherence, receiving nevirapine, HIV non-disclosure, never having married, and residing in Zimbabwe, Lesotho, or Zambia were associated with higher odds of NVL. Among people with NVL, marriage, female gender, shorter ART duration, higher CD4 count, and alcohol use were associated with higher odds for interrupted ART and lower odds for VF. Many people with VF (44.8%) had CD4 counts <200 cells/µL, but few (0.31% per year) switched to second-line ART.

Conclusions

Countries are approaching UNAIDS VLS targets for adults. Treatment support for people initiating ART with asymptomatic HIV infection, scale-up of viral load monitoring, and optimized ART regimens may further reduce NVL prevalence.
Linear epitope landscape of SARS-CoV-2 Spike protein constructed from 1,051 COVID-19 patients
Authors: Li Yang , Ma Ming-liang , Lei Qing , Wang Feng , Lai Dan-yun , Hou Hongyan , Xu Zhao-wei , Zhang Bo , Chen Hong , Yu Caizheng , Xue Jun-biao , Zheng Yun-xiao , Wang Xue-ning , Jiang He-wei , Zhang Hai-nan , Qi Huan , Guo Shu-juan , Zhang Yandi , Lin Xiaosong , Yao Zongjie , Wu Jiaoxiang , Sheng Huiming , Sun Ziyong , Fan Xionglin , Tao Sheng-ce
Published: July 2020

Neutralization antibodies and vaccines for treating COVID-19 are desperately needed. For precise development of antibodies and vaccines, the key is to understand which part of SARS-CoV-2 Spike protein is highly immunogenic on a systematic way. We generate a linear epitope landscape of Spike protein by analyzing serum IgG response of 1,051 COVID-19 patients with a peptide microarray. We reveal two regions that rich of linear epitopes,i.e., CTD and a region close to the S2’ cleavage site and fusion peptide. Unexpectedly, we find RBD is lack of linear epitope. Besides 3 moderate immunogenic peptides from RBD, 16 highly immunogenic peptides from other regions of Spike protein are determined. These peptides could serve as the base for precise development of antibodies and vaccines for COVID-19 on a systematic level.

One sentence summary

A linear epitope landscape of SARS-CoV-2 Spike protein is generated by analyzing serum IgG response of 1,051 COVID-19 patients.
Excess mortality in mental health service users during the COVID-19 pandemic described by ethnic group: South London and Maudsley data.
Authors: Stewart Robert , Broadbent Matthew , Das-Munshi Jayati
Published: July 2020

The COVID-19 pandemic in the UK was accompanied by excess all-cause mortality at a national level, only part of which was accounted for by known infections. Excess mortality has previously been described in people who had received care from the South London and Maudsley NHS Foundation Trust (SLaM), a large mental health service provider for 1.2m residents in south London. SLaM’s Clinical Record Interactive Search (CRIS) data resource receives 24-hourly updates from its full electronic health record, including regularly sourced national mortality on all past and present SLaM service users. SLaM’s urban catchment has high levels of deprivation and is ethnically diverse, so the objective of the descriptive analyses reported in this manuscript was to compare mortality in SLaM service users from 16th March to 15th May 2020 to that for the same period in 2019 within specific ethnic groups: i) White British, ii) Other White, iii) Black African/Caribbean, iv) South Asian, v) Other, and vi) missing/not stated. For Black African/Caribbean patients (the largest minority ethnic group) this ratio was 3.33, compared to 2.47 for White British patients. Considering premature mortality (restricting to deaths below age 70), these ratios were 2.74 and 1.96 respectively. Ratios were also high for those from Other ethnic groups (2.63 for all mortality, 3.07 for premature mortality).
Improved virus isoelectric point estimation by exclusion of known and predicted genome-binding regions
Authors: Heffron Joe , Mayer Brooke K.
Published: July 2020

Accurate prediction of the isoelectric point (pI) of viruses is beneficial for modeling virus behavior in environmental transport and physical/chemical treatment applications. However, the empirically measured pIs of many viruses have thus far defied simple explanation, let alone prediction, based on the ionizable amino acid composition of the virus capsid. Here, we suggest an approach for predicting virus pI by excluding capsid regions that stabilize the virus polynucleotide via electrostatic interactions. This method was applied first to viruses with known polynucleotide-binding regions (PBRs) and/or 3D structures. Then, PBRs were predicted in a group of 32 unique viral capsid proteome sequences via conserved structures and sequence motifs. Removing predicted PBRs resulted in a significantly better fit to empirical pI values. After modification, mean differences between theoretical and empirical pI values were reduced from 2.1 ± 2.4 to 0.1 ± 1.7 pH units.

Importance

This model is the first to fit predicted pIs to empirical values for a diverse set of viruses. The results suggest that many previously-reported discrepancies between theoretical and empirical virus pIs can be explained by coulombic neutralization of PBRs of the inner capsid. Given the diversity of virus capsid structures, this nonarbitrary, heuristic approach to predicting virus pI offers an effective alternative to a simplistic, one-size-fits-all charge model of the virion. The accurate, structure-based prediction of PBRs of the virus capsid employed here may also be of general interest to structural virologists.
Intelligent planning of product assembly sequences based on spatio-temporal semantic knowledge
Authors: Yang Hongjuan , Chen Jiwen , Wang Chen , Cui Jiajia , Wei Wensheng
Published: July 2020

Purpose

The implied assembly constraints of a computer-aided design (CAD) model (e.g. hierarchical constraints, geometric constraints and topological constraints) represent an important basis for product assembly sequence intelligent planning. Assembly prior knowledge contains factual assembly knowledge and experience assembly knowledge, which are important factors for assembly sequence intelligent planning. This paper aims to improve monotonous assembly sequence planning for a rigid product, intelligent planning of product assembly sequences based on spatio-temporal semantic knowledge is proposed.

Design/methodology/approach

A spatio-temporal semantic assembly information model is established. The internal data of the CAD model are accessed to extract spatio-temporal semantic assembly information. The knowledge system for assembly sequence intelligent planning is built using an ontology model. The assembly sequence for the sub-assembly and assembly is generated via attribute retrieval and rule reasoning of spatio-temporal semantic knowledge. The optimal assembly sequence is achieved via a fuzzy comprehensive evaluation.

Findings

The proposed spatio-temporal semantic information model and knowledge system can simultaneously express CAD model knowledge and prior knowledge for intelligent planning of product assembly sequences. Attribute retrieval and rule reasoning of spatio-temporal semantic knowledge can be used to generate product assembly sequences.

Practical implications

The assembly sequence intelligent planning example of linear motor highlights the validity of intelligent planning of product assembly sequences based on spatio-temporal semantic knowledge.

Originality/value

The spatio-temporal semantic information model and knowledge system are built to simultaneously express CAD model knowledge and assembly prior knowledge. The generation algorithm via attribute retrieval and rule reasoning of spatio-temporal semantic knowledge is given for intelligent planning of product assembly sequences in this paper. The proposed method is efficient because of the small search space.
Knowledge-based society and emerging disciplines: a correlation of academic performance
Authors: Rafi Muhammad , Ahmad Khurshid , Naeem Salman Bin , Khan Asad Ullah , JianMing Zheng
Published: July 2020

Purpose

Digital libraries promote and accelerate scientific research in academic institutions. The subscribed database resources of digital libraries have become an increasingly valuable asset for researchers. Database resources help generate new ideas, determine research directions and promote productive academic interaction between teachers and students in the information age. The purpose of this study is to examine the use of electronic resources by students in various databases, the research productivity of the faculty in the science network and the number of students who graduate each year.

Design/methodology/approach

This study uses a quantitative method to collect secondary data from the central database of the Higher Education Commission (HEC) for the population of 26 universities for 2 years (2015–2016). In addition to the HEC digital library, data was also collected from the Web of Science to determine the quality academic performance of faculty and researchers. Moreover, in the study, the total strength of teaching staff and doctoral faculty was extracted from the HEC website for investigation. The authors applied the Spearman’s correlation test to the secondary data using Statistical Package for Social Sciences version 25.

Findings

The correlation results of the enrolled students and the downloaded papers from various databases were statistically insignificant (p > 0.05). However, the result showed a positive correlation (p < 0.05) between the use of selected/known databases from a number of databases accessed by the HEC. More importantly, it turns out that the faculty’s productivity in the scientific network and the number of students who graduated from public and private universities are found to be insignificant (p > 0.05). However, the authors found a positive correlation (p < 0.05) between doctoral and non-doctoral faculties, which show that a significant number of non-doctoral faculties are still actively involved in teaching and research.

Originality/value

Research based on academic activities by faculties and students, performed for the first time on the basis of secondary data, will help the HEC and university management to determine the right direction and develop plans to improve academic performance and research quality.
A conceptual model for university-society research collaboration facilitating societal impact for local innovation
Authors: Olsson Anna Karin , Bernhard Iréne , Arvemo Tobias , Lundh Snis Ulrika
Published: July 2020

Purpose

The purpose is to develop a work-integrated learning (WIL) model for university-society research collaboration facilitating societal impact toward short lag yet sustainable societal impact for local innovation.

Design/methodology/approach

The methodology applied was engaged scholarship based on a WIL approach involving a network of collaborating partners from different sectors of society and cross-disciplinary university researchers. Mixed data collection methods were applied.

Findings

Conceptualization of university-society research collaboration for local innovation is presented as a WIL model including the elements of continuity and commitment, coordination, communication and relationships, trust, courage and creativity and co-creation opportunities. Short lag societal impact as local innovation was identified as product and process innovations.

Research limitations/implications

Further validation of the model is encouraged for the model to be viable in various contexts and to generate different kinds of societal impact.

Practical implications

The model may act as a governing tool for project management to facilitate co-creative and short lag societal impact for local innovation to ensure that engaged and learning activities are embedded in the collaborative process.

Social implications

The model has implications for inclusiveness and co-creation fostering transparency, respect and mutuality in university-society research collaboration and to equate both academic and practice knowledge.

Originality/value

The conclusions drawn support the understanding of a WIL approach practicing engaged scholarship in research collaborations. The main theoretical and practical contributions of the article are the conceptual model for university-society research collaboration generating short lag societal implications and local innovation.
Diagnosing and routing electronic service quality improvement of academic libraries with the FMEA approach in an intuitionistic fuzzy environment
Authors: Mirghafoori Seyyed Habibollah , Sayyadi Tooranloo Hossein , Saghafi Sepideh
Published: July 2020

Purpose

In this way, the aim of this study is to expand and evelop the application of this technique in FMEA to rank failure modes of ESQ of academic libraries in an intuitionistic fuzzy environment. Assessment of electronic service quality (ESQ) of libraries is significantly important according to their major roles. It should be noted that the ESQ has a significant impact on customer satisfaction, which improves organizational performance. Accordingly, low ESQ means waste of organizational resources and poor user satisfaction. So, there is a dire need to reflect reasons inducing failure modes in academic library ESQ. Thus, investigation of failure modes affecting academic library ESQ is highly important. One solution in this area is utilization of the intuitionistic fuzzy (IF) failure mode and effects analysis (FMEA) as one of the widely used methods for prediction and identification of failure modes.

Design/methodology/approach

The present study in terms of objective is applied and in terms of the type of method is descriptive-analytical. The research sample included four experts of Yazd academic Libraries (Iran). To collect data, three types of questionnaires were distributed among experts. The purpose of the first questionnaire was to identify and reach an agreement on e-library failure modes. Type II questionnaire was used to determine the importance of identified risk factors and Type III questionnaire was used to prioritize the factors.

Findings

Results indicate that the difficulty of using websites, lack of provided information feedback to users and lack of links on the website to users' are the main priorities for improving ESQ in the studied academic libraries.

Originality/value

In this approach, the Intuitionistic fuzzy Elimination Et Choix Traduisant la REalité and technique for order of preference by similarity to ideal solution method were used to rank failure modes in academic library ESQ within the FMEA framework.]
Coronavirus disease (COVID-19) and sport entrepreneurship
Authors: Ratten Vanessa
Published: July 2020

Purpose

Coronavirus disease (COVID-19) has affected all sectors of the global economy but some have been affected more than others. The sport sector has been especially influenced by the COVID-19 crisis in a way that has never been seen before. This has meant an urgent need for most sport enterprises to think about new business models in order to cope with the change. The purpose of this article is to discuss in more detail how the sport sector can utilise entrepreneurship as a way of combatting uncertainty whilst promoting the recognition of new opportunities.

Design/methodology/approach

A review of the existing literature on COVID-19 in terms of crisis management, entrepreneurship and sport is undertaken. This helps to understand the linkage between sport and entrepreneurship and how this can be used in times of the COVID-19 crisis.

Findings

All sport businesses, athletes, managers, fans and consumers need to utilise entrepreneurial thinking in order to act creatively. This will help combat the unease and uncertainty, associated with the COVID-19 crisis and create more entrepreneurial ecosystems to develop.

Originality/value

This article is the first to explicitly state the need for sport businesses to harness the entrepreneurial potential of the COVID-19 crisis thereby contributing to new practices that will help the sport sector survive this uncertain time period and flourish in the future.
They support, so we talk: the effects of other users on self-disclosure on social networking sites
Authors: Lin Cheng-Yu , Chou En-Yi , Huang Heng-Chiang
Published: July 2020

Purpose

Social networking sites (SNSs) have significantly influenced people's lives and changed their behavior. Although previous research has explored self-disclosure in virtual communities, little is known about the impact of other users, particularly their online social support, on self-disclosure. The aim of this study is to explore how online social support dimensions (i.e., emotional, informational, esteem, instrumental and network support) influence people's self-disclosure, which in turn affects their commitment to SNSs.

Design/methodology/approach

Based on social exchange theory, this study proposes a research model that explores the role of other users on self-disclosure. This study collects data from a sample of 558 respondents and applies the structural equation modeling technique to test the research model.

Findings

The findings show that users are motivated to disclose information and commit to a specific SNS because of the supportive climate. Results also show that self-disclosure mediates the effect of online social support on users' commitment to SNSs.

Originality/value

This study focuses on the influence of other users' roles on self-disclosure on SNSs, extending the application of social exchange theory.
Testing the impact of athlete brand image attributes on fan loyalty
Authors: Mahmoudian Abed , Sadeghi Boroujerdi Saeed , Mohammadi Sardar , Delshab Vahid , Pyun Do Young
Published: July 2020

Purpose

Athlete brand image management has become a popular topic among sport marketing scholars. This study aims to test the impacts of the attributes of an athlete brand image on fan loyalty.

Design/methodology/approach

In total, 500 questionnaires were delivered to university students and 472 completed questionnaires were returned. Confirmatory factor analysis was conducted to test the psychometric properties of the measures and structural equation modeling was carried out to test the hypotheses.

Findings

The findings of this study show that three attributes of athlete brand image (e.g. marketable lifestyle, athletic performance and attractive appearance) positively influenced fan loyalty.

Research limitations/implications

To increase the loyalty of fans, effective marketing strategies could be designed to create positive images of athletes with both athletes’ on-field (e.g. athletic skills, competition style and excellence in sport) and off-field performance (e.g. engagement with fans, community involvement, public relation and charity activities).

Originality/value

This paper provides valuable insights into the measurement of athlete brand image and fan loyalty and offers a foundation for future research on athlete brand management.