bluuebunny/crossref_metadata_2025 huggingface dataset:
COVID-19 in Portugal: predictability of hospitalization, ICU and respiratory-assistance needs
Authors: Patricio Andre , Costa Rafael S. , Henriques Rui
Published: September 2020

The current SARS-COV-2 epidemic is associated with nearly 1 million estimated deaths and responsible for multiple disturbances around the world, including the overload of health care systems. The timely prediction of the medical needs of infected individuals enables a better and quicker care provision for the necessary cases, supporting the management of available resources.

This work ascertains the predictability of medical needs (as hospitalization, respiratory support, and admission to intensive care units) and the survivability of individuals testing SARS-CoV-2 positive considering a cohort with all infected individuals in Portugal as per June 30, 2020. Predictions are performed at the various stages of a patient’s cycle, namely: pre-hospitalization (testing time), pos-hospitalization, and pos-intensive care. A thorough optimization of state-of-the-art predictors is undertaken to assess the ability to anticipate medical needs and infection outcomes using demographic and comorbidity variables, as well as onset date of symptoms, test and hospitalization.
Causal Analysis of Health Interventions and Environments for Influencing the Spread of COVID-19 in the United States of America
Authors: Li Zhouxuan , Xu Tao , Zhang Kai , Deng Hong-Wen , Boerwinkle Eric , Xiong Momiao
Published: September 2020

As of August 27, 2020, the number of cumulative cases of COVID-19 in the US exceeded 5,863,363 and included 180,595 deaths, thus causing a serious public health crisis. Curbing the spread of Covid-19 is still urgently needed. Given the lack of potential vaccines and effective medications, non-pharmaceutical interventions are the major option to curtail the spread of COVID-19. An accurate estimate of the potential impact of different non-pharmaceutical measures on containing, and identify risk factors influencing the spread of COVID-19 is crucial for planning the most effective interventions to curb the spread of COVID-19 and to reduce the deaths. Additive model-based bivariate causal discovery for scalar factors and multivariate Granger causality tests for time series factors are applied to the surveillance data of lab-confirmed Covid-19 cases in the US, University of Maryland Data (UMD) data, and Google mobility data from March 5, 2020 to August 25, 2020 in order to evaluate the contributions of social-biological factors, economics, the Google mobility indexes, and the rate of the virus test to the number of the new cases and number of deaths from COVID-19. We found that active cases/1000 people, workplaces, tests done/1000 people, imported COVID-19 cases, unemployment rate and unemployment claims/1000 people, mobility trends for places of residence (residential), retail and test capacity were the most significant risk factor for the new cases of COVID-19 in 23, 7, 6, 5, 4, 2, 1 and 1 states, respectively, and that active cases/1000 people, workplaces, residential, unemployment rate, imported COVID cases, unemployment claims/1000 people, transit stations, mobility trends (transit), tests done/1000 people, grocery, testing capacity, retail, percentage of change in consumption, percentage of working from home were the most significant risk factor for the deaths of COVID-19 in 17, 10, 4, 4, 3, 2, 2, 2, 1, 1, 1, 1 states, respectively. We observed that no metrics showed significant evidence in mitigating the COVID-19 epidemic in FL and only a few metrics showed evidence in reducing the number of new cases of COVID-19 in AZ, NY and TX. Our results showed that the majority of non-pharmaceutical interventions had a large effect on slowing the transmission and reducing deaths, and that health interventions were still needed to contain COVID-19.
Probabilistic analysis of COVID-19 patients’ individual length of stay in Swiss intensive care units
Authors: Henzi Alexander , Kleger Gian-Reto , Hilty Matthias P. , Garcia Pedro D. Wendel , Ziegel Johanna F.
Published: September 2020

Rationale

The COVID-19 pandemic induces considerable strain on intensive care unit resources.

Objectives

We aim to provide early predictions of individual patients’ intensive care unit length of stay, which might improve resource allocation and patient care during the on-going pandemic.

Methods

We developed a new semiparametric distributional index model depending on covariates which are available within 24h after intensive care unit admission. The model was trained on a large cohort of acute respiratory distress syndrome patients out of the Minimal Dataset of the Swiss Society of Intensive Care Medicine. Then, we predict individual length of stay of patients in the RISC-19-ICU registry.

Measurements

The RISC-19-ICU Investigators for Switzerland collected data of 557 critically ill patients with COVID-19.

Main Results

The model gives probabilistically and marginally calibrated predictions which are more informative than the empirical length of stay distribution of the training data. However, marginal calibration was worse after approximately 20 days in the whole cohort and in different subgroups. Long staying COVID-19 patients have shorter length of stay than regular acute respiratory distress syndrome patients. We found differences in LoS with respect to age categories and gender but not in regions of Switzerland with different stress of intensive care unit resources.

Conclusion

A new probabilistic model permits calibrated and informative probabilistic prediction of LoS of individual patients with COVID-19. Long staying patients could be discovered early. The model may be the basis to simulate stochastic models for bed occupation in intensive care units under different casemix scenarios.
Changes to the sebum lipidome upon COVID-19 infection observed via non-invasive and rapid sampling from the skin
Authors: Spick Matt , Longman Katie , Frampas Cecile , Costa Catia , Walters Deborah Dunn , Stewart Alex , Wilde Mike , Greener Danni , Evetts George , Trivedi Drupad , Barran Perdita , Pitt Andy , Bailey Melanie
Published: September 2020

The COVID-19 pandemic has led to an urgent and unprecedented demand for testing – both for diagnosis and prognosis. Here we explore the potential for using sebum, collected via swabbing of a patient’s skin, as a novel sampling matrix to fulfil these requirements. In this pilot study, sebum samples were collected from 67 hospitalised patients (30 PCR positive and 37 PCR negative). Lipidomics analysis was carried out using liquid chromatography mass spectrometry. Total fatty acid derivative levels were found to be depressed in COVID-19 positive participants, indicative of dyslipidemia. Orthogonal Partial Least Squares-Discriminant Analysis (OPLS-DA) modelling showed promising separation of COVID-19 positive and negative participants when comorbidities and medication were controlled for. Given that sebum sampling is rapid and non-invasive, this work may offer the potential for diagnostic and prognostic testing for COVID-19.
Waist-to-height ratio is a more accurate screening tool for hypertension than waist-to-hip circumference and BMI in type 2 diabetes: A prospective study
Authors: Moosaie Fatemeh , Fatemi Abhari Seyede Marzie , Deravi Niloofar , Behnagh Arman Karimi , Esteghamati Sadaf , Firouzabadi Fatemeh Dehghani , Rabizadeh Soghra , Nakhjavani Manouchehr , Esteghamati Alireza
Published: September 2020

Background

To date, anthropometric measures (i.e. body mass index (BMI), waist to hip ratio (WHR) and waist to height ratio (WHtR) have shown to be associated with prediction of incident hypertension. However, the difference in accuracy of these measures has been of controversy. We aimed to determine whether WHtR is a more accurate tool for HTN than WHR and BMI in patients with type 2 diabetes.

Material and Methods

The study population consisted of 1685 normotensive patients with T2DM. They were followed up for hypertension incidence for a mean of 4.8 years from April 2002 to January 2020. Cox regression was performed to assess the association between anthropometric measures (i.e., BMI, WHR, and WHtR) and incident hypertension during the follow-up period. Area under the ROC curve analysis was performed and optimal cutoff values were calculated using Youden index.

Results

WHtR and BMI were significantly associated with an increased risk of hypertension (HR=3.296(0.936-12.857), P < 0.001 and HR:1.050 (1.030-1.070), P < 0.001, respectively). The discriminative powers of each anthropometric index for HTN were 0.571 (0.540–0.602) for BMI, 0.518 (0.486–0.550) for WHR, and 0.609 (0.578–0.639) for WHtR. The optimal cutoff points for predicting HTN in patients with T2DM were 26.94 (sensitivity=0.739, specificity=0.380) for BMI, 0.90 (sensitivity=0.718, specificity=0.279) for WHR and 0.59 (sensitivity=0.676, specificity=0.517) for WHtR.

Conclusion

In the current study WHtR was a more accurate screening tool for HTN compared to WHR and BMI in patients with type 2 diabetes.
The UK Biobank submaximal cycle ergometer test for assessment of cardiorespiratory fitness: Validity, reliability, and association with disease outcomes
Authors: Gonzales Tomas I. , Westgate Kate , Strain Tessa , Hollidge Stefanie , Jeon Justin , Christensen Dirk L. , Jensen Jorgen , Wareham Nicholas J. , Brage Søren
Published: September 2020

Background

Cardiorespiratory fitness (CRF) was assessed in UK Biobank (UKB) using heart rate response to a submaximal ramped cycle ergometer test that was individualised for participant characteristics including cardiovascular disease risk. Studies have since explored health associations with CRF by estimating maximal oxygen consumption (VO2max) from UKB test data using interpretation methods that have not accounted for this individualisation procedure. Thus, dose-response relationships reported in these studies may be inaccurate. We developed and validated a novel VO2max estimation approach that accounts for the UKB test individualisation procedure and compared dose-response relationships with health outcomes between the novel and previous methods.

Methods

In a cross-over study (n=189), participants completed several UKB tests and VO2max was measured. A multilevel modelling framework was developed that combines heart rate response features from the UKB test to estimate VO2max. Estimates were compared within participants across UKB test protocols, and with directly measured VO2max. Short-term test-retest reliability was assessed in a subsample of participants (n=87). In UKB, we examined associations between estimated CRF and disease endpoints (n=80,259) and compared associations obtained with an unvalidated method. Long-term test-retest reliability was examined (n = 2877).

Results

Estimated and directly measured VO2max were strongly correlated (Pearson’srrange: 0.68 to 0.74) with no mean bias (women bias: −0.8 to 0.4; men bias range: −0.3 to 0.3), outperforming a previous approach for interpreting UKB test data. Agreement between estimated VO2max across different test protocols was strong (Pearson’srrange: 0.94 to 0.99). Short- and long-term reliability was also high (lambda=0.91 and 0.80, respectively). All-cause mortality was 7% (95%CI 4-10%, 2686 deaths) lower and CVD mortality 9% (95%CI 3-14%, 858 deaths) lower for every 1-MET difference in fitness, associations twice as strong as determined by previous methods.

Conclusions

We present a valid and reliable method for estimating CRF in UKB and demonstrate its utility in characterising dose-response relationships with health outcomes. Accounting for the individualisation procedure strengthens observed relationships between CRF and disease and enhances the case for promoting improved fitness in the general population.
Systematic review and meta-analysis of randomized trials of hydroxychloroquine for the prevention of COVID-19
Authors: García-Albéniz Xabier , Amo Julia del , Polo Rosa , Morales-Asencio José Miguel , Hernán Miguel A
Published: September 2020

Background

Recruitment into randomized trials of hydroxychloroquine (HCQ) for prevention of COVID-19 has been adversely affected by a widespread conviction that HCQ is not effective for prevention. In the absence of an updated systematic review, we conducted a meta-analysis of randomized trials that study the effectiveness of HCQ to prevent COVID-19.

Methods

A search of PubMed and medRxiv with expert consultation found ten completed randomized trials: seven pre-exposure prophylaxis trials and three post-exposure prophylaxis trials. We obtained or calculated the risk ratio of COVID-19 diagnosis for assignment to HCQ versus no HCQ (either placebo or usual care) for each trial, and then pooled the risk ratio estimates.

Results

The pooled risk ratio estimate of the pre-exposure prophylaxis trials was 0.72 (95% CI: 0.58-0.91) when using either a fixed effect or a standard random effects approach, and 0.72 (95% CI: 0.52-1.00) when using a conservative modification of the Hartung-Knapp random effects approach. The corresponding estimates for the post-exposure prophylaxis trials were 0.91 (95% CI: 0.71-1.16) and 0.91 (95% CI: 0.54-1.55). All trials found a similar rate of serious adverse effects in the HCQ and no HCQ groups.

Discussion

A benefit of HCQ as prophylaxis for COVID-19 cannot be ruled out based on the available evidence from randomized trials. However, the “not statistically significant” findings from early prophylaxis trials were widely interpreted as definite evidence of lack of effectiveness of HCQ. This interpretation disrupted the timely completion of the remaining trials and thus the generation of precise estimates for pandemic management before the development of vaccines.
Analysis of COVID-19 case numbers: adjustment for diagnostic misclassification on the example of German case reporting data
Authors: Günther Felix , Berger Ursula , Höhle Michael , Bender Andreas , Wildner Manfred , Heid Iris M. , Küchenhoff Helmut
Published: September 2020

Background

Reported COVID-19 case numbers are key to monitoring pandemic spread and decision-making on policy measures but require careful interpretation as they depend substantially on testing strategy. A high and targeted testing activity is essential for a successful Test-Trace-Isolate strategy. However, it also leads to increased numbers of false-positives and can foster a debate on the actual pandemic state, which can slow down action and acceptance of containment measures.

Aim

We evaluate the impact of misclassification in COVID-19 diagnostics on reported case numbers and estimated numbers of disease onsets (epidemic curve).

Methods

We developed a statistical adjustment of reported case numbers for erroneous diagnostic results that facilitates a misclassification-adjusted real-time estimation of the epidemic curve based on nowcasting. Under realistic misclassification scenarios, we provide adjusted case numbers for Germany and illustrate misclassification-adjusted nowcasting for Bavarian data.

Results

We quantify the impact of diagnostic misclassification on time-series of reported case numbers, highlighting the relevance of a specificity smaller than one when test activity changes over time. Adjusting for misclassification, we find that the increase of cases starting in July might have been smaller than indicated by raw case counts, but cannot be fully explained by increasing numbers of false-positives due to increased testing. The effect of misclassification becomes negligible when true incidence is high.

Conclusions

Adjusting case numbers for misclassification can improve this important measure on short-term dynamics of the pandemic and should be considered in data-based surveillance. Further limitations of case reporting data exist and have to be considered.
Self-reported work activities, mucus membrane symptoms, and respiratory health outcomes among an industrial hog operation worker cohort, North Carolina, USA
Authors: Coffman Vanessa R. , Hall Devon J. , Pisanic Nora , Love David C. , Nadimpalli Maya , McCormack Meredith , Diener-West Marie , Davis Meghan F. , Heaney Christopher D.
Published: September 2020

Background

Respiratory disease among industrial hog operation (IHO) workers is well documented; however, it remains unclear whether specific work activities are more harmful and if personal protective equipment (PPE), as used by workers, can reduce adverse health outcomes.

Objectives

To assess the relationship between self-reported IHO work activities and PPE use with mucus membrane and respiratory health symptoms in an occupational cohort.

Methods

IHO workers (n=103) completed baseline and up to eight bi-weekly (i.e., every two weeks) study visits. Workers reported typical (baseline) and transient (bi-weekly) work activities, PPE use, and physical health symptoms. Baseline and longitudinal associations between work activities and health outcomes were assessed using generalized logistic and fixed-effects logistic regression models, respectively.

Results

At baseline, reports of ever versus never drawing pig blood, applying pesticides, and increasing years worked at any IHO were positively associated with reports of eye, nose, and/or throat irritation. Over time, transient exposures, including those associated with dustiness in barns, cleaning of barns, and pig contact were associated with increased odds of symptoms including sneezing, headache, and eye or nose irritation, particularly in the highest categories of exposure. When PPE was used, workers had decreased odds of symptoms interfering with sleep (odds ratio (OR): 0.1; 95% confidence interval (CI): 0.01, 0.8), sneezing (OR: 0.1; 95% CI: 0.01, 1.0), and eye or nose irritation (OR: 0.1; 95% CI: 0.02, 0.9). Similarly, when they washed their hands ≥8 times per shift (the median) versus less frequently, workers had decreased odds of any respiratory symptom (OR: 0.3; 95% CI: 0.1, 0.8).

Discussion

In this healthy volunteer IHO worker population, increasingly unfavorable work activities were associated with self-reported mucus membrane and respiratory health outcomes. Strong protective associations were seen between PPE use and handwashing and the odds of symptoms, warranting further investigation in intervention studies.
Discovery and engineering of small SlugCas9 with broad targeting range and high specificity and activity
Authors: Hu Ziying , Zhang Chengdong , Wang Shuai , Wei Jingjing , Li Miaomiao , Hou Linghui , Liu Hongmao , Liu Dong , Lan Feng , Lu Daru , Wang Hongyan , Li Jixi , Wang Yongming
Published: September 2020

The compact CRISPR/Cas9 system, which can be delivered by adeno-associated virus (AAV), is a promising platform for therapeutic applications. However, current compact Cas9 nucleases have limited activity, targeting scope and specificity. Here, we identified three compact SaCas9 orthologs,Staphylococcus lugdunensisCas9 (SlugCas9),Staphylococcus lutraeCas9 (SlutrCas9) andStaphylococcus haemolyticusCas9 (ShaCas9), for mammalian genome editing. Interestingly, SlugCas9 recognizes a simple NNGG PAM and displays comparable activity to SaCas9. We further generated a SlugCas9-SaCas9 chimeric nuclease, which has both high specificity and high activity. We lastly engineered SlugCas9 with mutations to generate a high fidelity variant that maintains high specificity without compromising on-target editing efficiency. Our study offers important minimal Cas9 tools that are ideal for both basic research and clinical applications.
De NovoDiscovery of High Affinity Peptide Binders for the SARS-CoV-2 Spike Protein
Authors: Pomplun Sebastian , Jbara Muhammad , Quartararo Anthony J. , Zhang Genwei , Brown Joseph S. , Lee Yen-Chun , Ye Xiyun , Hanna Stephanie , Pentelute Bradley L.
Published: September 2020

The β-coronavirus SARS-CoV-2 has caused a global pandemic. Affinity reagents targeting the SARS-CoV-2 spike protein, the most exposed surface structure of the virus, are of interest for the development of therapeutics and diagnostics. We used affinity selection-mass spectrometry for the rapid discovery of synthetic high affinity peptide binders for the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. From library screening with 800 million synthetic peptides, we identified three sequences with nanomolar affinities (dissociation constantsKd= 80 to 970 nM) for RBD and selectivity over human serum proteins. Picomolar RBD concentrations in biological matrix could be detected using the biotinylated lead peptide in ELISA format. These peptides might associate with the SARS-CoV-2-spike-RBD at a site unrelated to ACE2 binding, making them potential orthogonal reagents for sandwich immunoassays. We envision our discovery as a robust starting point for the development of SARS-CoV-2 diagnostics or conjugates for virus directed delivery of therapeutics.

Abstract Figure
Ash1 and Tup1 Dependent Repression of theSaccharomyces cerevisiae HOpromoter Requires Activator-Dependent Nucleosome Eviction
Authors: Parnell Emily J. , Parnell Timothy J. , Yan Chao , Bai Lu , Stillman David J.
Published: September 2020

Transcriptional regulation of theSaccharomyces cerevisiae HOgene is highly complex, requiring a balance of multiple activating and repressing factors to ensure that only a few transcripts are produced in mother cells within a narrow window of the cell cycle. Here, we show that the Ash1 repressor associates with two DNA sequences that are usually concealed within nucleosomes in theHOpromoter and recruits the Tup1 corepressor and the Rpd3 histone deacetylase, both of which are required for full repression in daughters. Genome-wide ChIP identified greater than 200 additional sites of co-localization of these factors, primarily within large, intergenic regions from which they could regulate adjacent genes. Most Ash1 binding sites are in nucleosome depleted regions (NDRs), while a small number overlap nucleosomes, similar toHO. We demonstrate that Ash1 binding to theHOpromoter does not occur in the absence of the Swi5 transcription factor, which recruits coactivators that evict nucleosomes, including the nucleosomes obscuring the Ash1 binding sites. In the absence of Swi5, artificial nucleosome depletion allowed Ash1 to bind, demonstrating that nucleosomes are inhibitory to Ash1 binding. The location of binding sites within nucleosomes may therefore be a mechanism for limiting repressive activity to periods of nucleosome eviction that are otherwise associated with activation of the promoter. Our results illustrate that activation and repression can be intricately connected, and events set in motion by an activator may also ensure the appropriate level of repression and reset the promoter for the next activation cycle.
TRIM5α restriction of HIV-1-N74D viruses in lymphocytes is caused by a loss of cyclophilin A protection
Authors: Selyutina Anastasia , Simons Lacy M. , Bulnes-Ramos Angel , Hultquist Judd F. , Diaz-Griffero Felipe
Published: September 2020

The core of HIV-1 viruses bearing the capsid change N74D (HIV-1-N74D) do not bind the human protein cleavage and polyadenylation specificity factor subunit 6 (CPSF6). In addition, HIV-1-N74D viruses have altered patterns of integration site preference in human cell lines. In primary human CD4+ T cells, HIV-1-N74D viruses exhibit infectivity defects when compared to wild type. The reason for this loss of infectivity in primary cells is unknown. We first investigated whether loss of CPSF6 binding accounts for the loss of infectivity. Depletion of CPSF6 in human CD4+T cells did not affect the early stages of wild-type HIV-1 replication, suggesting that defective infectivity in the case of HIV-1-N74D is not due to the loss of CPSF6 binding. Based on our previous result that cyclophilin A (Cyp A) protected HIV-1 from human tripartite motif-containing protein 5α (TRIM5αhu) restriction in CD4+T cells, we tested whether TRIM5αhuwas involved in the decreased infectivity observed for HIV-1-N74D. Depletion of TRIM5αhuin CD4+T cells rescued the infectivity of HIV-1-N74D, suggesting that HIV-1-N74D cores interacted with TRIM5αhu. Accordingly, TRIM5αhubinding to HIV-1-N74D cores was increased compared with that of wild-type cores, and consistently, HIV-1-N74D cores lost their ability to bind Cyp A. In conclusion, we showed that the decreased infectivity of HIV-1-N74D in CD4+T cells is due to a loss of Cyp A protection from TRIM5αhurestriction activity.
Lifestyle-specificS-nitrosylation of protein cysteine thiols regulatesEscherichia colibiofilm formation and resistance to oxidative stress
Authors: Barraud Nicolas , Létoffé Sylvie , Beloin Christophe , Vinh Joelle , Chiappetta Giovanni , Ghigo Jean-Marc
Published: September 2020

Communities of bacteria called biofilms are characterized by reduced diffusion, steep oxygen and redox gradients and specific properties compared to individualized planktonic bacteria. In this study, we investigated whether signaling via nitrosylation of protein cysteine thiols (S-nitrosylation), regulating a wide range of functions in eukaryotes, could also specifically occur in biofilms and contribute to bacterial adaptation to this widespread lifestyle. We used a redox proteomic approach to compare cysteineS-nitrosylation in aerobic and anaerobic biofilm and planktonicEscherichia colicultures and we identified proteins with biofilm-specificS-nitrosylation status. Using bacterial genetics and various phenotypic screens, we showed that impairingS-nitrosylation in proteins involved in redox homeostasis and amino acid synthesis such as OxyR, KatG and GltD altered important biofilm properties, including motility, biofilm maturation or resistance to oxidative stress. Our study therefore revealed thatS-nitrosylation constitutes a physiological basis underlying functions critical forE. coliadaptation to the biofilm environment.
Design, expression, purification and characterization of a YFP-tagged 2019-nCoV spike receptor-binding domain construct
Authors: Bierig Tobias , Collu Gabriella , Blanc Alain , Poghosyan Emiliya , Benoit Roger. M.
Published: September 2020

2019-nCoV is the causative agent of the serious, still ongoing, worldwide COVID-19 pandemic. High quality recombinant virus proteins are required for research related to the development of vaccines and improved assays, and to the general understanding of virus action. The receptor-binding domain (RBD) of the 2019-nCoV spike (S) protein contains disulfide bonds and N-linked glycosylations, therefore, it is typically produced by secretion. Here, we describe a construct and protocol for the expression and purification of yellow fluorescent protein (YFP) labeled 2019-nCoV spike RBD. The fusion protein, in the vector pcDNA 4/TO, comprises an N-terminal interferon alpha 2 (IFNα2) signal peptide, an eYFP, a FLAG-tag, a human rhinovirus 3C protease cleavage site, the RBD of the 2019-nCoV spike protein and a C-terminal 8x His-tag. We stably transfected HEK 293 cells. Following expansion of the cells, the fusion protein was secreted from adherent cells into serum-free medium. Ni-NTA IMAC purification resulted in very high protein purity, based on analysis by SDS-PAGE. The fusion protein was soluble and monodisperse, as confirmed by size-exclusion chromatography (SEC) and negative staining electron microscopy. Deglycosylation experiments confirmed the presence of N-linked glycosylations in the secreted protein. Complex formation with the peptidase domain of human angiotensin-converting enzyme 2 (ACE2), the receptor for the 2019-nCoV spike RBD, was confirmed by SEC, both for the YFP-fused spike RBD and for spike RBD alone, after removal of YFP by proteolytic cleavage. Possible applications for the fusion protein include binding studies on cells orin vitro, fluorescent labeling of potential virus-binding sites on cells, the use as an antigen for immunization studies or as a tool for the development of novel virus- or antibody-detection assays.
The antimicrobial peptide TAT-RasGAP317-326inhibits the formation and the expansion of bacterial biofilmsin vitro
Authors: Heinonen Tytti , Hargraves Simone , Georgieva Maria , Widmann Christian , Jacquier Nicolas
Published: September 2020

Biofilms are structured aggregates of bacteria embedded in a self-produced matrix. Pathogenic bacteria can form biofilms on surfaces and in tissues leading to nosocomial and chronic infections. While antibiotics are largely inefficient in limiting biofilm formation and expansion, antimicrobial peptides (AMPs) are emerging as alternative anti-biofilm treatments. In this study, we explore the effect of the newly described AMP TAT-RasGAP317-326onAcinetobacter baumannii, Pseudomonas aeruginosaandStaphylococcus aureusbiofilms. We observe that TAT-RasGAP317-326inhibits the formation of biofilms at concentrations equivalent or two times superior to the minimal inhibitory concentration (MIC) of the corresponding planktonic bacteria. Moreover, TAT-RasGAP317-326limits the expansion ofA. baumanniiandP. aeruginosaestablished biofilms at concentrations 2-4 times superior to the MIC. These results further confirm the potential of AMPs against biofilms, expand the antimicrobial potential of TAT-RasGAP317-326and support further development of this peptide as an alternative antimicrobial treatment.
Chromosome-level genome assemblies of the malaria vectorsAnopheles coluzziiandAnopheles arabiensis
Authors: Zamyatin Anton , Avdeyev Pavel , Liang Jiangtao , Sharma Atashi , Chen Chujia , Lukyanchikova Varvara , Alexeev Nikita , Tu Zhijian , Alekseyev Max A. , Sharakhov Igor V.
Published: September 2020

Background

Anopheles coluzziiandAn. arabiensisbelong to theAn. gambiaecomplex and are among the major malaria vectors in Sub-Saharan Africa. However, chromosome-level reference genome assemblies are still lacking for these medically important mosquito species.

Findings

In this study, we producedde novochromosome-level genome assemblies forAn. coluzziiandAn. arabiensisusing the long-read Oxford Nanopore sequencing technology and the Hi-C scaffolding approach. We obtained 273.4 Mbp and 256.8 Mbp of the total assemblies forAn. coluzziiandAn. arabiensis, respectively. Each assembly consists of three chromosome-scale scaffolds (X, 2, 3), complete mitochondrion, and unordered contigs identified as autosomal pericentromeric DNA, X pericentromeric DNA, and Y sequences. Comparison of these assemblies with the existing assemblies for these species demonstrated that we obtained improved reference-quality genomes. The new assemblies allowed us to identify genomiccoordinates for the breakpoint regions of fixed and polymorphic chromosomal inversions inAn. coluzziiandAn. arabiensis.

Conclusion

The new chromosome-level assemblies will facilitate functional and population genomic studies inAn. coluzziiandAn. arabiensis. The presented assembly pipeline will accelerate progress toward creating high-quality genome references for other disease vectors.
The roseoloviruses downregulate the protein tyrosine phosphatase PTPRC (CD45)
Authors: Whyte Melissa L. , Smith Kelsey , Buchberger Amanda , Luecke Linda Berg , Tjan Lidya Handayani , Mori Yasuko , Gundry Rebekah L , Hudson Amy W.
Published: September 2020

Like all herpesviruses, the roseoloviruses (HHV6A, -6B, and -7) establish lifelong infection within their host, requiring these viruses to evade host anti-viral responses. One common host-evasion strategy is the downregulation of host-encoded, surface-expressed glycoproteins. Roseoloviruses have been shown to evade host the host immune response by downregulating NK-activating ligands, MHC class I, and the TCR/CD3 complex. To more globally identify glycoproteins that are differentially expressed on the surface of HHV6A-infected cells, we performed cell surface capture of N-linked glycoproteins present on the surface of T cells infected with HHV6A, and compared these to proteins present on the surface of uninfected T cells. We found that the protein tyrosine phosphatase CD45 is downregulated in T cells infected with HHV6A. We also demonstrated that CD45 is similarly downregulated in cells infected with HHV-7. CD45 is essential for signaling through the T cell receptor and as such, is necessary for developing a fully functional immune response. Interestingly, the closely related β-herpesviruses human cytomegalovirus (HCMV) and murine cytomegalovirus (MCMV) have also separately evolved unique mechanisms to target CD45. While HCMV and MCMV target CD45 signaling and trafficking, HHV6A acts to downregulate CD45 transcripts.

Importance

Human herpesviruses-6 and -7 infect essentially 100% of the world’s population before the age of 5 and then remain latent or persistent in their host throughout life. As such, these viruses are among the most pervasive and stealthy of all viruses. Host immune cells rely on the presence of surface-expressed proteins to identify and target virus-infected cells. Here, we investigated the changes that occur to proteins expressed on the cell surface of T cells after infection with human herpesvirus-6A. We discovered that HHV-6A infection results in a reduction of CD45 on the surface of infected cells. Targeting of CD45 may prevent activation of these virus-infected T cells, possibly lengthening the life of the infected T cell so that it can harbor latent virus.
Cell type specific labeling and partial connectomes of dopaminergic circuits reveal non-synaptic communication and large-scale axonal remodeling after exposure to cocaine
Authors: Wildenberg G.A. , Sorokina A.M. , Koranda J.L. , Monical A. , Heer C. , Sheffield M.E. , Zhuang X. , McGehee DS , Kasthuri N.
Published: September 2020

Dopaminergic (DA) neurons exert profound influences on behavior including addiction. However, how DA axons communicate with target neurons and how those communications change, for example, with drug exposure, remains poorly understood. We combine recent advances in cell type specific labeling for electron microscopy with large volume three-dimensional serial electron microscopy – ‘connectomics’- to detail DA connections in the Nucleus Accumbens (NAc) across multiple animals and after exposure to cocaine. We find that DA axonal varicosities are of four general types: 38% are empty, 25% contain few small (∼50 nm diameter) vesicles, 19% contain few large (∼133 nm diameter) vesicles, and 18% have mixed small and large vesicles, suggesting that DA axons may use multiple types of neurotransmitters. Individual DA axons were significantly more likely to contain multiple varicosities of the same type relative to chance, suggesting a new method of DA axon classification. Across all categories, we find only rare examples (<2%, 6/410) of varicosities making specific synapses with any neighboring neuron with the few examples being made exclusively on the shafts and soma of resident NAc neurons. Instead, we find much more frequently (15%) that DA varicosities form spinule-like structures: physical membrane interdigitations with nearby dendrites or excitatory and inhibitory axons. Days after a brief exposure to cocaine, DA axons were extensively branched relative to controls but with similar densities of varicosities and spinules. Additionally, cocaine exposure results in the formation of blind-ended “bulbs” in DA axons, filled with mitochondria, and reminiscent of axonal retraction in the developing and damaged brain. Every bulb was surrounded by elaborated glia further suggestive of active remodeling. Finally, mitochondrial lengths increased by ∼2.2 times relative to control throughout DA axons and NAc spiny dendrites after cocaine exposure but not in DA soma or DA dendrites. We conclude that DA axonal transmission is unlikely to be mediated via classical synapses in the NAc and that the major locus of anatomical plasticity of DA circuits after exposure to cocaine are large scale axonal rearrangements with correlated changes in mitochondria.
Structural and Functional Characterization of Host FHL1 Protein Interaction with Hypervariable Domain of Chikungunya Virus nsP3 Protein
Authors: Lukash Tetyana , Agback Tatiana , Dominguez Francisco , Shiliaev Nikita , Meshram Chetan , Frolova Elena I. , Agback Peter , Frolov Ilya
Published: September 2020

Decades of insufficient control resulted in unprecedented spread of chikungunya virus (CHIKV) around the globe and millions already suffered from the highly debilitating disease. Nevertheless, the current understanding of CHIKV-host interactions and adaptability of the virus to replication in mosquitoes and mammalian hosts is still elusive. Our new study shows that four-and-a-half LIM domain protein (FHL1) is one of the host factors that interact with hypervariable domain (HVD) of CHIKV nsP3. Unlike G3BPs, FHL1 is not a pre-requisite of CHIKV replication, and many commonly used cell lines do not express FHL1. However, its expression has detectable stimulatory effect(s) on CHIKV replication, and theFhl1KO cell lines demonstrate slower infection spread. The NMR-based studies revealed that the binding site of FHL1 in CHIKV nsP3 HVD overlaps with that of another pro-viral host factor, CD2AP. The structural data also demonstrated that FHL1-HVD interaction is mostly determined by LIM1 domain of FHL1. However, it does not mirror binding of the entire protein, suggesting that other LIM domains are involved. In agreement with previously published data, our biological experiments showed that interactions of CHIKV HVD with CD2AP and FHL1 have additive positive effects on the efficiency of CHIKV replication. This study shows that CHIKV mutants with extensive modifications of FHL1- or both FHL1- and CD2AP- binding sites remain viable and develop spreading infection in multiple cell types. Thus, such modifications of HVD may improve live CHIKV vaccine candidates in terms of their safety and stability of the attenuated phenotype.

IMPORTANCE

Replication of chikungunya virus (CHIKV) is determined by a wide range of host factors. Previously, we have demonstrated that the hypervariable domain (HVD) of CHIKV nsP3 protein contains linear motifs that recruit defined families of host proteins into formation of functional viral replication complexes. Now, using NMR-based structural and biological approaches, we have characterized the binding site of cellular FHL1 protein in CHIKV HVD and defined the biological significance of this interaction. In contrast to previously described binding of G3BP to CHIKV HVD, the FHL1-HVD interaction was found to not be a prerequisite of viral replication. However, the presence of FHL1 has a stimulatory effect on CHIKV infectivity and subsequently, the infection spread. FHL1 and CD2AP proteins were found to have overlapping binding sites in CHIKV HVD and additive pro-viral functions. Elimination of FHL1-binding site in nsP3 HVD can be used for the development of stable, live attenuated vaccine candidates.
A real-time, transient kinetic study ofDrosophila melanogasterDicer-2 elucidates mechanism of termini-dependent cleavage of dsRNA
Authors: Singh Raushan K. , Jonely McKenzie , Leslie Evan , Rejali Nick A. , Noriega Rodrigo , Bass Brenda L.
Published: September 2020

Drosophila melanogasterDicer-2 (dmDcr-2) differentially processes dsRNA with blunt or 2 nucleotide 3’-overhanging termini. We investigated the transient kinetic mechanism of these reactions using a rapid reaction stopped-flow technique and time-resolved fluorescence spectroscopy. We found that ATP binding to dmDcr-2’s helicase domain impacts the kinetics of dsRNA binding and dissociation in a termini-dependent manner, emphasizing the termini-dependent discrimination of dsRNA on a biologically-relevant time-scale. ATP-hydrolysis mediates local unwinding of dsRNA, and directional translocation on unwound single-stranded RNA, which is concurrent with a slow rewinding prior to dsRNA cleavage. Time-resolved fluorescence anisotropy reveals a nucleotide-dependent change in conformational dynamics of the helicase and Platform•PAZ domains in the nanosecond timescale that is correlated with termini-dependent dsRNA cleavage. Our study delineates kinetic events and transient intermediates for a Dicer-catalyzed reaction, thus establishing a framework for understanding other Dicers and how accessory factors modulate the reaction.
A small-molecule oral agonist of the human glucagon-like peptide-1 receptor
Authors: Griffith David A. , Edmonds David J. , Fortin Jean-Phillipe , Kalgutkar Amit S. , Kuzmiski J. Brent , Loria Paula M. , Saxena Aditi R. , Bagley Scott W. , Buckeridge Clare , Curto John M. , Derksen David R. , Dias João M. , Griffor Matthew C. , Han Seungil , Jackson V. Margaret , Landis Margaret S. , Lettiere Daniel J. , Limberakis Chris , Liu Yuhang , Mathiowetz Alan M. , Piotrowski David W. , Price David A. , Ruggeri Roger B. , Tess David A.
Published: September 2020

Peptide agonists of the glucagon-like peptide-1 receptor (GLP-1R) have revolutionized diabetes therapy, but their use has been limited by the requirement for injection. Here we describe the first effective, orally bioavailable small molecule GLP-1R agonists. A sensitized high-throughput screen identified a series of small molecule GLP-1R agonists that were optimized to promote endogenous GLP-1R signaling with nM potency. These small molecule agonists increased insulin levels in primates but not rodents, which is explained by a cryo-EM structure that revealed a binding pocket requiring primate-specific tryptophan 33. Importantly, oral administration of agonist PF-06882961 to healthy humans produced dose-dependent declines in serum glucose (NCT03309241). This opens the door to a new era of oral small molecule therapies that target the well-validated GLP-1R pathway for metabolic health.

One Sentence Summary

PF-06882961 is an orally administered small molecule that activates the GLP-1 receptor to lower blood glucose in humans.
Humanistic leadership in the UAE context
Authors: Anadol Yaprak , Behery Mohamed
Published: September 2020

Purpose

The main intention of this paper is to understand humanistic leadership through an eminent leader representing the United Arab Emirates (UAE) culture. The authors identified a prominent humanistic leader of a well-known private university in Dubai as an example, analyzing his leadership approach from a humanistic lens and demonstrating humanistic leadership characteristics linked to the cultural roots.

Design/methodology/approach

This paper is designed as a single case to examine how humanistic leadership behaviors and practices are applied in an organization and how they are connected to the UAE culture. The leader and his seven followers are interviewed by using semi-structured forms, and inductive conventional content analysis was utilized to identify common themes and concepts related to humanistic leadership traits in the UAE.

Findings

The paper highlights ten themes named humility, respect, care, fairness, transparency, well-being orientation, generosity, family focus and will with humanistic determination. These themes coincide with the various well-accepted humanistic literature theories and are also aligned with salient Islamic values and the existing humanistic leadership theories. A humanistic leadership description is provided to show the implications to the UAE context.

Research limitations/implications

This study only focuses on a single higher education institution, and further studies need to be conducted to reach a generalization.

Practical implications

The paper offers an alternative humanistic leadership for government departments, semi private and private companies to create an organizational culture where those values are flourished and creating an awareness in youth leadership programs to include humanistic leadership principles that will eventually increase social welfare.

Originality/value

This study provides an insight into humanistic leadership phenomenon by giving a contextual example from the UAE. As there has been no attempt to link humanistic leadership to the UAE culture, the findings of this paper will contribute to cross-cultural leadership research.
Manninen’s mixture model for conjugate conduction and mixed convection heat transfer of a nanofluid in a rotational/stationary circular enclosure
Authors: Hoseininejad Faraz , Dinarvand Saeed , Yazdi Mohammad Eftekhari
Published: September 2020

Purpose

This study aims to investigate numerically the problem of conjugate conduction and mixed convection heat transfer of a nanofluid in a rotational/stationary circular enclosure using a two-phase mixture model.

Design/methodology/approach

Hot and cold surfaces on the wall or inside the enclosure (heater and cooler) are maintained at constant temperature of Th and Tc, respectively, whereas other parts are thermally insulated. To examine the effects of various parameters such as Richardson number (0.01 = Ri =100), thermal conductivity ratio of solid to base fluid (1 = Kr = 100), volume fraction of nanoparticle (0 = φ = 0.05), insertion of conductive covers (C.Cs) around the heater in a different shape (triangular, circular or square), segmentation and arrangement of the conductive blocks (C.Bs) and rotation direction of the enclosure on the flow structure and heat transfer rate, two-dimensional equations of mass, momentum and energy conservation, as well as volume fraction, are solved using finite volume method and Semi-Implicit Method for Pressure Linked Equations (SIMPLE) algorithm.

Findings

The results show that inserting C.C around heater can increase or decrease heat transfer rate, and it depends on thermal conductivity ratio of solid to pure fluid. Also, it is found that by the division of C.B and location of its portions in a horizontal configuration, heat transfer rate reduces. Moreover, it is observed that external heating and cooling of the enclosure causes enhancement of heat transfer relative to that of internal heating and cooling. Finally, results illustrate that under the condition that cylinders rotate in the same direction, the heat transfer rate increases as compared to those that rotate in the opposite direction. Hence rotation direction of cylinders can be used as a desired parameter for controlling heat transfer rate.

Originality/value

A comprehensive report of results for the problem of conjugate conduction and mixed convection heat transfer in a circular cylinder containing different shapes of C.C, conducting obstacle and heater and cooler has been presented. An efficient numerical technique has been developed to solve this problem. The achievements of this paper are purely original, and the numerical results were never published by any researcher.
B2B social media content: engagement on LinkedIn
Authors: Sundström Malin , Alm Klas Håkan , Larsson Niklas , Dahlin Oskar
Published: September 2020

Purpose

This paper aims to identify content strategies on social media that influence engagement and to analyze those operations to describe important features for co-creation and trust.

Design/methodology/approach

This paper addresses the question of how social media content can influence engagement by using a medium-sized Swedish company for an empirical case study. This empirical study is based on a participatory action research methodology. By using the company account on LinkedIn, the authors experimented with relational content to understand the effects on customer-perceived value and trust.

Findings

Results reveal that action-oriented messages had a more significant impact on engagement than product-oriented messages and value-based messages.

Originality/value

This paper builds on the existing literature in two ways: drawing upon business-to-business relationships and perceived value and using recent advances in the use of social networking sites to understand the value of co-creation through a participatory culture.