bluuebunny/crossref_metadata_2025 huggingface dataset:
An equivalence of prokaryotic pore forming proteins of Plasmodium triggers cellular dysfunction responsible for malaria pathogenesis
Authors: Shivappagowdar Abhishek , Garg Swati , Srivastava Akriti , Hada Rahul S. , Pati Soumya , Garg Lalit , Singh Shailja
Published: August 2020

Severe malaria caused byPlasmodium falciparumposes a major global health problem with high morbidity and mortality. TheP. falciparumharbours a family of pore forming proteins (PFPs), known as perforin like proteins (PLPs), which are structurally equivalent to prokaryotic PFPs. These PLPs are secreted from the parasites and by interacting to host cells they contribute to disease pathogenesis. The severe malaria pathogenesis is associated with dysfunction of various barrier cells including endothelial cells. A number of factors, including PLPs, secreted by parasite contribute to the host cell dysfunction. Here in, we tested the hypothesis that the PLPs mediate dysfunction of barrier cells and might have a role in disease pathogenesis. We analysed various dysfunction in barrier cells following rPLP2 exposure and demonstrate that it causes an increase in intracellular Ca2+levels. Additionally, rPLP2 exposed barrier cells displayed features of cell death including Annexin/PI positivity, depolarized mitochondrial membrane potential and ROS generation. We further performed the time lapse video microscopy of barrier cells and found the treatment of rPLP2 triggers their membrane blebbing. The cytoplasmic localization of HMGB1, a marker of necrosis, further confirmed the necrotic type of cell death. This study highlights the role of parasite factor PLP in endothelial dysfunction and provides a rational for the design of adjunct therapies against severe malaria.
The mammalian CLU homologFMTcontrols development and behavior inArabidopsis
Authors: Ralevski Alexandra , Apelt Federico , Olas Justyna J. , Mueller-Roeber Bernd , Rugarli Elena I. , Kragler Friedrich , Horvath Tamas L.
Published: August 2020

Mitochondria in animals are associated with development, as well as physiological and pathological behaviors. Several conserved mitochondrial genes exist between plants and higher eukaryotes. Yet, comparative mitochondrial function among plant and animal species is poorly understood. Here, we show thatFMT(FRIENDLYMITOCHONDRIA) fromArabidopsis thaliana, a highly conserved homolog of the mammalianCLU(CLUSTERED MITOCHONDRIA)gene family encoding mitochondrial proteins associated with developmental alterations and adult physiological and pathological behaviors, affects whole plant morphology and development under salt stress and control conditions.FMTwas found to regulate mitochondrial morphology and dynamics as well as germination, root length, and flowering time. Here, we show that it also affects leaf expansion growth, salt stress-responses and hyponasty. Strikingly, FMT impacted the speed of hyponasty with corresponding change in speed of locomotion of CLU heterozygous knockout mice. These observations indicate that homologous genes affect homologous functions in plants and animals offering the possibility to develop plant models for the study of mammalian behaviors.
The ‘C3aR antagonist’ SB290157 is a partial C5aR2 agonist
Authors: Li Xaria X. , Kumar Vinod , Lee John D. , Woodruff Trent M.
Published: August 2020

Innate immune complement activation generates the C3 and C5 protein cleavage products C3a and C5a, defined classically as anaphylatoxins. C3a activates C3a receptors (C3aR), while C5a activates two receptors (C5aR1 and C5aR2) to exert their immunomodulatory activities. The non-peptide compound, SB290157, was originally reported in 2001 as the first C3aR antagonist. In 2005, the first report on non-selective nature of SB290157 was published, where the compound exerted clear agonistic, not antagonistic, activity in variety of cells. Other studies also documented non-selective activities of this drugin vivo. These findings severely hamper data interpretation regarding C3aR when using this compound. Unfortunately, given the dearth of C3aR inhibitors, SB290157 still remains widely used to explore C3aR biology (>70 publications to date). Given these issues, in the present study we aimed to further explore SB290157’s pharmacological selectivity by screening the drug against three human anaphylatoxin receptors, C3aR, C5aR1 and C5aR2, using transfected cells. We first confirmed that SB290157 acts as a potent agonist at human C3aR. We also identified that SB290157 exerts partial agonist activity at C5aR2 by mediating β-arrestin recruitment at higher compound doses. Notably, SB290157’s activity at C5aR2 was more potent and efficacious than the current ‘lead’ C5aR2 agonist P32. Notwithstanding this, SB290157 showed inhibitory effect on C3a-mediated signalling in primary human macrophages. Our results therefore provide even more caution against using SB290157 as a research tool to explore C3aR function. Given the reported immunomodulatory and anti-inflammatory activities of C3aR and C5aR2 agonism, any function observed with SB290157 could be due to these off target activities.
Chromosome painting in cultivated banana and their wild relatives (Musaspp.) reveals differences in chromosome structure
Authors: Šimoníková D , Němečková A , Čížková J , Brown A , Swennen R , Doležel J , Hřibová E
Published: August 2020

Edible banana cultivars are diploid, triploid or tetraploid hybrids which originated by natural cross hybridization between subspecies of diploidMusa acuminata, or betweenM. acuminataand diploidM. balbisiana. Participation of two other wild diploid speciesM. schizocarpaandM. textiliswas also indicated by molecular studies. Fusion of gametes with structurally different chromosome sets may give rise to progenies with structural chromosome heterozygosity and reduced fertility due to aberrant chromosome pairing and unbalanced chromosome segregation. Only a few translocations have been classified on the genomic level so far and a comprehensive molecular cytogenetic characterization of cultivars and species of the familyMusaceaeis still lacking. FISH with chromosome-arm specific oligo painting probes was used for comparative karyotype analysis in a set of wildMusaspecies and edible banana clones. The results revealed large differences in chromosome structure discriminating individual accessions. These results permitted identification of putative progenitors of cultivated clones and clarified genomic constitution and evolution of aneuploid banana clones, which seem to be common among the polyploid banana accessions. New insights into the chromosome organization and structural chromosome changes will be a valuable asset in breeding programs, particularly in selection of appropriate parents for cross hybridization.

Highlight

Oligo painting FISH revealed chromosomal translocations in subspecies ofMusa acuminata(A genome), their intra-specific hybrids as well as inM. balbisiana(B genome) and in interspecific hybrid clones originating from cross hybridization betweenM. acuminataandM. balbisiana
Integrated Bioinformatics Analysis Deciphering the microRNA Regulation in Protein-Protein Interaction Network in Lung Adenocarcinoma
Authors: Sengupta Pratyay , Saha Sayoni , Maji Moumita , Ghosh Monidipa
Published: August 2020

Background

The architecture of the protein-protein interaction (PPI) network in any organism relies on their gene expression signature. microRNAs (miRNAs) have recently emerged as major post transcriptional regulators that control PPI by targeting mainly untranslated regions of the gene encoding proteins. Here, we aimed to unveil the role of miRNAs in the PPI network for identifying potential molecular targets for lung adenocarcinoma (LUAD).

Materials and methods

The expression profiles of miRNAs and mRNAs were collected from the NCBI Gene Expression Omnibus (GEO) database (GSE74190 and GSE116959). Abnormally expressed mRNAs from the data were appointed to construct a PPI network and hence incorporated with the miRNA-mRNA regulatory network. The miRNAs and mRNAs in this network were subjected to functional enrichment. Through the network analysis, hubs were identified and their mutation rate and probability of cooccurrence were calculated.

Results

We identified 17 miRNAs and 429 mRNAs signature for differentially altered transcriptome in LUAD. The combined miRNA–mRNA regulatory network exhibited scale-free characteristics. Network analysis showed 5 miRNA (including hsa-miR-486-5p, hsa-miR-200b-5p, and hsa-miR-130b-5p) and 10 mRNA (including ASPM, CCNB1, TTN, TPX2, and BIRC5) which expressively contribute in the LUAD. We further investigated the hub genes and noticed that ASPM and TTN had the maximum rate of mutation and possessed a high tendency of cooccurrence in LUAD.

Conclusion

This study provides a unique network approach to the exploration of the underlying molecular mechanism in LUAD. Identified mRNAs and miRNAs may therefore, serve as significant prognostic predictors and therapeutic targets.
Association Between Birth Region and Time to Tuberculosis Diagnosis After US Entry Among Non–US-Born Persons
Authors: Talwar Amish , Li Rongxia , Langer Adam J.
Published: August 2020

Approximately 90% of US tuberculosis (TB) cases among non–US-born persons are attributable to progression of latent TB infection to TB disease. Using survival analysis, we investigated if birthplace is associated with time of progression to TB disease among non–US-born persons. We derived a Cox regression model comparing differences in time to TB diagnosis after US entry among 19 global birth regions, adjusting for sex, birth year, and age at diagnosis. Compared with persons from Western Europe, the adjusted hazard rate of developing TB was significantly higher (p ≤0.05) for persons from all other regions, except North America and Northern Europe, and highest among persons from Middle Africa (adjusted hazard ratio = 7.0; 95% confidence interval: 6.5–7.4). Time to TB diagnosis among non–US-born persons therefore varied by birth region, which represents an important prognostic indicator for progression to TB disease.
Clinical characteristics and antibody response to SARS-CoV-2 spike 1 protein using the VITROS Anti-SARS-CoV-2 antibody tests in COVID-19 patients in Japan
Authors: Nagura-Ikeda Mayu , Imai Kazuo , Kubota Katsumi , Noguchi Sakiko , Kitagawa Yutaro , Matsuoka Masaru , Tabata Sakiko , Miyoshi Kazuyasu , Ito Toshimitsu , Tamura Kaku , Maeda Takuya
Published: August 2020

Background

We evaluated clinical characteristics and the clinical utility of VITROS SARS-CoV-2 antibody tests according to COVID-19 severity in patients in Japan.

Methods

We analyzed 255 serum specimens from 130 COVID-19 patients and examined clinical records and laboratory data. Presence of total (IgA, IgM, and IgG) and specific IgG antibody for the spike 1 antigen of SARS-CoV2 was determined using VITROS Anti-SARS-CoV-2 antibody tests.

Findings

Overall, 98 (75.4%) and 32 (24.6%) patients had mild and severe COVID-19, respectively. On admission, 76 (58.5%) and 45 (34.6%) patients were positive for total and IgG antibody assays. Among 91 patients at discharge, 90 (98.9%) and 81 (89.0%) patients were positive for total and IgG antibody, respectively. Clinical background and laboratory findings on admission, but not the prevalence or concentration of total or IgG antibody, were associated with disease prognosis. Total and IgG antibody intensity were significantly higher in severe cases than in mild cases in serum collected after 11 days from onset, but not within 10 days.

Conclusion

VITROS Anti-SARS-CoV-2 Total and IgG assays will be useful as supporting diagnostic and surveillance tools and for evaluation of humoral immune response to COVID-19. Clinical background and laboratory findings are preferable predictors of disease prognosis.
Assessment of multiplex digital droplet RT-PCR as an accurate diagnosis tool for SARS-CoV-2 detection in nasopharyngeal swabs and saliva samples
Authors: Cassinari Kévin , Alessandri-Gradt Elodie , Chambon Pascal , Charbonnier Françoise , Gracias Ségolène , Beaussire Ludivine , Alexandre Kevin , Sarafan-Vasseur Nasrin , Houdayer Claude , Etienne Manuel , Caron François , Plantier Jean Christophe , Frebourg Thierry
Published: August 2020

RT-qPCR on nasopharyngeal swabs is currently the reference COVID-19 diagnosis method. We developed a multiplex RT-ddPCR assay, targeting six SARS-CoV-2 genomic regions, and evaluated it on nasopharyngeal swabs and saliva samples collected from 130 COVID-19 positive or negative ambulatory individuals, who presented symptoms suggestive of mild or moderate Sars-CoV2 infection. The 6-plex RT-ddPCR assay was shown to have 100% sensitivity on nasopharyngeal swabs and a higher sensibility than RT-qPCR on saliva (85% versus 62%). Saliva samples from 2 individuals with negative results on nasopharyngeal swabs were found to be positive. These results show that multiplex RT-ddPCR should represent an alternative and complementary tool for the diagnosis of COVID-19, in particular to control RT-qPCR ambiguous results, and its application to saliva an appropriate strategy for repetitive sampling and testing individuals for whom nasopharyngeal swabbing is not possible.
Effectiveness of Convalescent Plasma for Treatment of COVID-19 Patients
Authors: Chen Shanshan , Lu Chunya , Li Ping , Wang Lei , Wang Huaqi , Yang Qiankun , Chen Liyinghui , Li Jianbin , Ma Hongwei , Sang Qian , Li Jing , Xu Luyang , Song Xiangjin , Li Fangfang , Zhang Yi , Kang Yi , Xing Lihua , Zhang Guojun
Published: August 2020

Background and objective

The outbreak of COVID-19 has become a global health concern. In this study, we evaluate the effectiveness and safety of convalescent plasma therapy in patients with severe and critically ill COVID-19.

Methods

Sixteen COVID-19 patients received transfusion of anti-COVID-19 antibody-positive convalescent plasma. The main outcome was time for viral nucleic acid amplification (NAA) test turning negative. Clinical laboratory parameters were measured at the baseline (d0) before plasma transfusion, and day 1 (d1), day 3 (d3) after transfusion as well.

Results

Among the 16 patients, 10 of them had a consistently positive result of viral NAA test before convalescent plasma transfusion. Eight patients (8/10) became negative from day 2 to day 8 after transfusion. Severe patients showed a shorter time for NAA test turning negative after transfusion (mean rank 2.17 vs 5·90, P = 0.036). Two critically ill patients transfused plasma with lower antibody level remained a positive result of NAA test. CRP level demonstrated a decline 1 day after convalescent plasma treatment, compared with the baseline (P = 0.017). No adverse events were observed during convalescent plasma transfusion.

Conclusions

Viral NAA test of most patients with COVID-19 who received convalescent plasma transfusion turned negative on the 2nd to 8th days after transfusion, and the negative time of severe patients was shorter than that of critically ill patients.

Trial Registration

Chinese Clinical Trial Registry; No.: ChiCTR2000030627 URL:http://www.chictr.org
A multi-centre prospective study of COVID-19 transmission following outpatient Gastrointestinal Endoscopy in the United Kingdom
Authors: Hayee Bu’Hussain ,   The SCOTS project group, East James E. , Rees Colin , Penman Ian
Published: August 2020

Message

The COVID-19 pandemic has severely curtailed the practice of endoscopy (as an exemplar for outpatient diagnostic procedures) worldwide. Restart and recovery processes will be influenced by the need to protect patients and staff from disease transmission, but data on the risk of COVID-19 transmission after endoscopy are sparse. This is of particular importance in later pandemic phases when the risk of harm from delayed or missed significant diagnoses is likely to far outweigh the risk of infection. The British Society of Gastroenterology (BSG) guidance for restarting endoscopy included stratification of diagnostic procedures according to aerosol generation or assessment of infectious risk as well as pragmatic guidance on the use of personal protective equipment (PPE). We sought to document the risk of COVID-19 transmission after endoscopy in this “COVID-minimised” environment. Prospective data were collected from 18 UK centres for n=6208 procedures. Pre-endoscopy, 3/2611 (0.11% [95% CI: 0.00-0.33%]) asymptomatic patients tested positive for SARS-CoV-2 on nasopharyngeal swab. Based on follow-up telephone symptom screening of patients at 7 and 14 days, no cases of COVID-19 were detected by any centre after endoscopy in either patients or staff. While these data cannot determine the relative contribution of each component of a COVID-minimised pathway, they provide clear support for such an approach. The rational use of PPE and infection control policies should be continued and will aid planning for outpatient diagnostics in the COVID-19 recovery phase.
The Lebanese Cohort for COVID-19; A Challenge for the ABO Blood Group System
Authors: Khalil Athar , Feghali Rita , Hassoun Mahmoud
Published: August 2020

A sudden outbreak of pneumonia caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has rapidly spread all over the world facilitating the declaration of the resultant disease as a pandemic in March,2020. In Lebanon, the fast action of announcing a state of emergency with strict measures was among the factors that helped in achieving a successful containment of the disease in the country. Predisposing factors for acquiring COVID-19 and for developing a severe form of this disease were postulated to be related to epidemiological and clinical characteristics as well as the genomics signature of a given population or its environment. Biological markers such as the ABO blood group system was amongst those factors that were proposed to be linked to the variability in the disease course and/or the prevalence of this infection among different groups. We therefore conducted the first retrospective case-control study in the Middle-East and North Africa that tackles the association between the blood group types and the susceptibility as well as the severity of SARS-CoV2 infection. Opposing to the current acknowledged hypothesis, our results have challenged the association significance of this system with COVID-19. Herein, we highlighted the importance of studying larger cohorts using more rigorous approaches to diminish the potential confounding effect of some underlying comorbidities and genetic variants that are known to be associated with the ABO blood group system.
A Voting Ensemble Approach for Hepatitis Disease Detection
Authors: Dutta Shawni , Bandyopadhyay Samir Kumar
Published: August 2020

The inflammation of the liver is termed as Hepatitis. Several different types of hepatitis are from A to G. For example, Hepatitis A is caused by the hepatitis A virus. Similarly, other type of Hepatitis virus is formed by the name, say Hepatitis G. Some types of virus will not create any serious problems. LongAlasting and cause scarring of the liver, loss of liver function and in some cases, liver cancer are also caused by this disease. Voting ensemble based approach is proposed in this paper as final phase classification that accepts top two classifier models obtained from first and second phase classification respectively. The reason of using the proposed classifier is to enhance the prediction performance so that patients with hepatitis disease are identified correctly.
Introducing causal inference to the medical curriculum using temporal logic to draw directed acyclic graphs
Authors: Ellison George T.H.
Published: August 2020

Directed acyclic graphs (DAGs) might yet transform the statistical modelling of observational data for causal inference. This is because they offer a principled approach to analytical design that draws on existing contextual, empirical and theoretical knowledge, but ultimately relies on temporality alone to objectively specify probabilistic causal relationships amongst measured (and unmeasured) covariates, and the associated exposure and outcome variables. While a working knowledge of phenomenology, critical realism and epistemology seem likely to be useful for mastering the application of DAGs, drawing a DAG appears to require limited technical expertise and might therefore be accessible to even inexperienced and novice analysts. The present study evaluated the inclusion of a novel four-task directed learning exercise for medical undergraduates, which culminated in temporality-driven covariate classification, followed by DAG specification itself. The exercise achieved high levels of student engagement, although the proportion of students completing each of the exercise’s four key tasks declined from close to 100% in tasks 1 and 2 (exposure and outcome specification; and covariate selection) to 83.5% and 77.6% in the third and fourth tasks, respectively. Fewer than 15% of the students successfully classified all of their covariates (as confounders, mediators or competing exposures) using temporality-driven classification, but this improved to more than 35% following DAG specification – an unexpected result given that all of the DAGs displayed at least one substantive technical error. These findings suggest that drawing a DAG, in and of itself, increases the utility of temporality-driven covariate classification for causal inference analysis; although further research is required to better understand: why even poorly specified DAGs might reduce covariate misclassification; how ‘wrong but useful’ DAGs might be identified; and how these marginal benefits might be enhanced with or without improvements in DAG specification.
Optimal seasonal routines across animals and latitudes
Authors: Thygesen Uffe H. , Visser Andy W. , Heilmann Irene , Andersen Ken H.
Published: August 2020

Most animals face seasonal fluctuations in food availability and need to develop an annual routine that maximizes their lifetime reproductive success. Two particularly common strategies are reducing energy expenditure and building storage to sustain the animal in meager periods (winters). Here, we pose a simple and generic model for an animal that can decide, at each time during the season, on its level of foraging effort and on building energy stores. Using dynamic optimization, we identify the optimal annual routines that maximize the trade-off between energy and mortality over a life-long horizon. We investigate how the optimal strategies depend on the body size and longevity of the animal, and upon the seasonal variability in the environment. We find that with large fluctuations, the optimal annual routine for small animals is to develop a surviving egg/spore stage rather than to attempt to survive the winter. Medium sized animals invest heavily in reserves to allow long hibernation, while larger animals only need smaller reserves and a shorter hibernation period. In environments with smaller fluctuations, organisms do not need energy stores or hibernation but reduce foraging activities during spring and summer where their fitness is highest. Our optimization model can be used as a null hypothesis to explain the annual routines of animals of all body sizes across the globe.
The XyloPhone: democratizing access to high-quality macroscopic imaging for wood and other substrates
Authors: Wiedenhoeft Alex C.
Published: August 2020

One rate-limiting factor in the fight against illegal logging is the lack of powerful, affordable, scalable wood identification tools for field screening. Computer vision wood identification using smartphones fitted with customized imaging peripherals offer a potential solution but to date, such peripherals suffer from one or more weaknesses: low image quality, lack of lighting control, uncontrolled magnification, unknown distortion and spherical aberration, and/or no access to or publication of the system design. To address cost, optical concerns, and open access to designs and parameters, I present the XyloPhone, a 3D printed research quality macroscopic imaging attachment adaptable to any smartphone. It provides a fixed focal distance, exclusion of ambient light, selection of visible light or UV illumination, uses the lens from a commercially available loupe, is powered by a rechargeable external battery, is fully open-sourced, and at a price point of less than 110 USD is a highly affordable tool for the laboratory or the field, and can serve as the foundational hardware for a scalable field deployable computer vision wood identification system.
Using Single Protein/Ligand Binding Models to Predict Active Ligands for Unseen Proteins
Authors: Sundar Vikram , Colwell Lucy
Published: August 2020

Machine learning models that predict which small molecule ligands bind a single protein target report high levels of accuracy for held-out test data. An important challenge is to extrapolate and make accurate predictions for new protein targets. Improvements in drug-target interaction (DTI) models that address this challenge would have significant impact on drug discovery by eliminating the need for high-throughput screening experiments against new protein targets. Here we propose a data augmentation strategy that addresses this challenge to enable accurate prediction in cases where no experimental data is available. To proceed, we first build single protein-ligand binding models and use these models to predict whether additional ligands bind to each protein. We then use these predictions to augment the experimental data, train standard DTI models, and predict interactions between unseen test proteins and ligands. This approach achieves Area Under the Receiver Operator Characteristic (AUC) > 0.9 consistently on test sets consisting exclusively of proteins and ligands for which the model is given no experimental data. We verify that performance improvements extend to held-out test proteins distant from the training set. Our data augmentation framework can be applied to any DTI model, and enhances performance on a range of simple models.
REGN-COV2 antibody cocktail prevents and treats SARS-CoV-2 infection in rhesus macaques and hamsters
Authors: Baum Alina , Copin Richard , Ajithdoss Dharani , Zhou Anbo , Lanza Kathryn , Negron Nicole , Ni Min , Wei Yi , Atwal Gurinder S. , Oyejide Adelekan , Goez-Gazi Yenny , Dutton John , Clemmons Elizabeth , Staples Hilary M. , Bartley Carmen , Klaffke Benjamin , Alfson Kendra , Gazi Michal , Gonzales Olga , Dick Edward , Carrion Ricardo , Pessaint Laurent , Porto Maciel , Cook Anthony , Brown Renita , Ali Vaneesha , Greenhouse Jack , Taylor Tammy , Andersen Hanne , Lewis Mark G. , Stahl Neil , Murphy Andrew J. , Yancopoulos George D. , Kyratsous Christos A.
Published: August 2020

An urgent global quest for effective therapies to prevent and treat COVID-19 disease is ongoing. We previously described REGN-COV2, a cocktail of two potent neutralizing antibodies (REGN10987+REGN10933) targeting non-overlapping epitopes on the SARS-CoV-2 spike protein. In this report, we evaluate the in vivo efficacy of this antibody cocktail in both rhesus macaques and golden hamsters and demonstrate that REGN-COV-2 can greatly reduce virus load in lower and upper airway and decrease virus induced pathological sequalae when administered prophylactically or therapeutically. Our results provide evidence of the therapeutic potential of this antibody cocktail.
“A novel Organ-Chip system emulates three-dimensional architecture of the human epithelia and allows fine control of mechanical forces acting on it.”
Authors: Varone Antonio , Nguyen Justin Ke , Leng Lian , Barrile Riccardo , Sliz Josiah , Lucchesi Carolina , Wen Norman , Gravanis Achille , Hamilton Geraldine A. , Karalis Katia C. , Hinojosa Christopher D.
Published: August 2020

Successful translation ofin vivoexperimental data to human patients is an unmet need and a bottleneck in the development of effective therapeutics. micro technology aims to address this need with significant advancements reported recently that enable modeling of organ level function. These microengineered chips enable researcher to recreate critical elements such asin vivorelevant tissue-tissue interface, air-liquid interface, and mechanical forces, such as mechanical stretch and fluidic shear stress, are crucial in emulating tissue level functions. Here, we present the development of a new, comprehensive 3D cell-culture system, where we combined our proprietary Organ-Chip technology with recent advantages in three-dimensional organotypic culture. Leveraging microfabrication techniques, we engineered a flexible chip that consists of a channel containing an organotypic epithelium surrounded by two vacuum channels that can be actuated to stretch the hydrogel throughout its thickness. Furthermore, the ceiling of this channel is a removable lid with a built-in microchannel that can be perfused with liquid or air and removed as needed for direct access to the tissue. The floor of this channel is a porous flexible membrane in contact with a microfluidic channel that provides diffusive mass transport to and from the channel. This additional microfluidic channel can be coated with endothelial cells to emulate a blood vessel and capture endothelial interactions. Our results show that the Open-Top Chip design successfully addresses common challenges associated with the Organs-on-Chips technology, including the capability to incorporate a tissue-specific extracellular matrix gel seeded with primary stromal cells, to reproduce the architectural complexity of tissues by micropatterning the gel, that can be extracted for H&E staining. We provide proof-of-concept data on the feasibility of the system using skin and alveolar epithelial primary cells and by simulating alveolar inflammation.
Mechanism of duplex unwinding by coronavirus nsp13 helicases
Authors: Hu Xiao , Hao Wei , Qin Bo , Tian Zhiqi , Li Ziheng , Hou Pengjiao , Zhao Rong , Cui Sheng , Diao Jiajie
Published: August 2020

The current COVID-19 pandemic urges in-depth investigation into proteins encoded with coronavirus (CoV), especially conserved CoV replicases. The nsp13 of highly pathogenic MERS-CoV, SARS-CoV-2, and SARS-CoV exhibit the most conserved CoV replicases. Using single-molecule FRET, we observed that MERS-CoV nsp13 unwound DNA in discrete steps of approximately 9 bp when ATP was used. If another NTP was used, then the steps were only 4 to 5 bp. In dwell time analysis, we detected 3 or 4 hidden steps in each unwinding process, which indicated the hydrolysis of 3 or 4 dTTP. Based on crystallographic and biochemical studies of CoV nsp13 helicases, we modeled an unwinding mechanism similar to the spring-loaded mechanism of HCV NS3 helicase, although our model proposes that flexible 1B and stalk domains, by allowing a lag greater than 4 bp during unwinding, cause the accumulated tension on the nsp13-DNA complex. The hinge region between two RecA-like domains in SARS-CoV-2 nsp13 is intrinsically more flexible than in MERS-CoV nsp13 due to the difference of a single amino acid, which causes the former to induce significantly greater NTP hydrolysis. Our findings thus establish a blueprint for determining the unwinding mechanism of a unique helicase family.

When dTTP was used as the energy source, 4 hidden steps in each individual unwinding step after 3 - 4 NTP hydrolysis were observed.

An unwinding model of MERS-CoV-nsp13 which is similar to the spring-loaded mechanism of HCV NS3 helicase, except the accumulation of tension on nsp13/DNA complex is caused by the flexible 1B and stalk domains that allow a lag of 4-bp in unwinding.

Comparing to MERS-CoV nsp13, the hinge region between two RecA-like domains in SARS-CoV-2 nsp13 is intrinsically more flexible due to a single amino acid difference, which contributes to the significantly higher NTP hydrolysis by SARS-CoV-2 nsp13.
Ancestry Influences on the Molecular Presentation of Tumours
Authors: Li Constance H. , Haider Syed , Boutros Paul C.
Published: August 2020

Epidemiological studies have identified innumerable ways in which cancer presentation and behaviour is associated with patient ancestry. The molecular bases for these relationships remain largely unknown. We analyzed ancestry associations in the somatic mutational landscape of 12,774 tumours across 33 tumour-types, including 2,562 with whole-genome sequencing. Ancestry influences both the number of mutations in a tumour and the evolutionary timing of when they occur. Specific mutational signatures are associated with ancestry, reflecting potential differences in exogenous and endogenous oncogenic processes. A subset of known cancer driver genes was mutated in ancestry-associated patterns, with transcriptomic consequences. Cancer genome sequencing data is not well-balanced in epidemiologic factors; these data suggest ancestry strongly shapes the somatic mutational landscape of cancer, with potential functional implications.
Integrating geostatistical maps and transmission models using adaptive multiple importance sampling
Authors: Retkute Renata , Touloupou Panayiota , Basanez Maria-Gloria , Hollingsworth Deirdre T , Spencer Simon
Published: August 2020

The Adaptive Multiple Importance Sampling algorithm (AMIS) is an iterative technique which recycles samples from all previous iterations in order to improve the efficiency of the proposal distribution. We have formulated a new statistical framework based on AMIS to sample parameters of transmission models based on high-resolution geospatial maps of disease prevalence, incidence, or relative risk. We tested the performance of our algorithm on four case studies: ascariasis in Ethiopia, onchocerciasis in Togo, HIV in Botswana, and malaria in the Democratic Republic of the Congo.
Assessment of a Laboratory-Based SARS-CoV-2 Antibody Test Among Hemodialysis Patients: A Quality Improvement Initiative
Authors: Cohen Dena E. , Marlowe Gilbert , Contreras Gabriel , Sosa Marie Ann , Mendoza Jair Munoz , Lenz Oliver , Mithani Zain , Teixeiro Pura Margarita , Queija Nery , Moneda Araceli , Jeanty Jean S. , Swanzy Katie , Palecek Misha , Krishnan Mahesh , Giullian Jeffrey , Brunelli Steven M.
Published: August 2020

Introduction

The coronavirus disease 2019 (COVID-19) pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Although tests to detect anti-SARS-CoV-2 antibodies have been developed, their sensitivity and specificity in hemodialysis patients have not been previously assessed.

Methods

As part of a quality improvement (QI) initiative, nasopharyngeal swabs and predialysis blood samples were collected on the same day from adult patients receiving routine hemodialysis care at clinics managed by a large dialysis organization in the greater Miami, Florida region (23 – 30 Apr 2020). Polymerase chain reaction (PCR) tests for SARS-CoV-2 and chemiluminescence immunoassays for anti-SARS-CoV2 antibodies were performed according to manufacturer-specified protocols.

Results

Of 715 participants in the QI initiative, 38 had symptomatology consistent with COVID-19 prior to or during the initiative. Among these, COVID-19 was PCR-confirmed in 14 and ruled out in 20, with the remaining 4 being inconclusive. Among the 34 patients with known COVID-19 status, the sensitivity and specificity of the antibody test were 57.1% and 85.0% when either antibody was considered. The remaining 677 patients had no record of symptoms consistent with COVID-19, nor any known exposure. Of these, 38 patients (5.6%) tested positive for anti-SARS-CoV-2 antibodies.

Conclusions

The operational characteristics of the laboratory-based antibody test make it sufficient to rule in, but not rule out, SARS-CoV-2 infection in the appropriate clinical circumstance. A substantial proportion of dialysis patients may have had asymptomatic SARS-CoV-2 infection.
Simply saliva: stability of SARS-CoV-2 detection negates the need for expensive collection devices
Authors: Ott Isabel M. , Strine Madison S. , Watkins Anne E. , Boot Maikel , Kalinich Chaney C. , Harden Christina A. , Vogels Chantal B.F. , Casanovas-Massana Arnau , Moore Adam J. , Muenker M. Catherine , Nakahata Maura , Tokuyama Maria , Nelson Allison , Fournier John , Bermejo Santos , Campbell Melissa , Datta Rupak ,   the Yale IMPACT Research team, Cruz Charles S. Dela , Farhadian Shelli F. , Ko Albert I. , Iwasaki Akiko , Grubaugh Nathan D. , Wilen Craig B. , Wyllie Anne L.
Published: August 2020

Most currently approved strategies for the collection of saliva for COVID-19 diagnostics require specialized tubes containing buffers promoted for the stabilization of SARS-CoV-2 RNA and virus inactivation. Yet many of these are expensive, in limited supply, and not necessarily validated specifically for viral RNA. While saliva is a promising sample type as it can be reliably self-collected for the sensitive detection of SARS-CoV-2, the expense and availability of these collection tubes are prohibitive to mass testing efforts. Therefore, we investigated the stability of SARS-CoV-2 RNA and infectious virus detection from saliva without supplementation. We tested RNA stability over extended periods of time (2-25 days) and at temperatures representing at-home storage and elevated temperatures which might be experienced when cold chain transport may be unavailable. We found SARS-CoV-2 RNA in saliva from infected individuals is stable at 4°C, room temperature (∼19°C), and 30°C for prolonged periods and found limited evidence for viral replication in stored saliva samples. This work demonstrates that expensive saliva collection options involving RNA stabilization and virus inactivation buffers are not always needed, permitting the use of cheaper collection options. Affordable testing methods are urgently needed to meet current testing demands and for continued surveillance in reopening strategies.
Cost-effectiveness modelling to optimise active screening strategy for gambiense human African trypanosomiasis in the Democratic Republic of Congo
Authors: Davis Christopher N. , Rock Kat S. , Antillón Marina , Miaka Erick Mwamba , Keeling Matt J.
Published: August 2020

Gambiense human African trypanosomiasis (gHAT) has been brought under control recently with village-based active screening playing a major role in case reduction. In the eve of elimination, we investigate how to optimise active screening in villages in the Democratic Republic of Congo, such that the expenses of screening programmes can be efficiently allocated while continuing to avert morbidity and mortality. We implement a cost-effectiveness analysis using a stochastic gHAT infection model for a range of active screening strategies and we calculate the net monetary benefit (NMB) of each strategy. High-coverage active screening strategies, occurring approximately annually, attain the highest NMB. We find that, for strategies stopping after one to three years of zero case reporting, the expected cost-benefits are very similar and we highlight the current recommended strategy (three years before stopping) is likely cost-effective, in addition to providing valuable information on whether transmission has been interrupted.
The mental health and experiences of discrimination of LGBTQ+ people during the COVID-19 pandemic: Initial findings from the Queerantine Study
Authors: Kneale Dylan , Bécares Laia
Published: August 2020

Objective

To assess mental health status and experiences of discrimination amongst a sample of Lesbian, Gay, Bisexual, Transgender, Queer people (LGBTQ+, the “plus” including those who don’t identify with any such label) during the COVID-19 pandemic.

Design

Cross-sectional web-based survey.

Setting

Responses were collected during the COVID-19 pandemic between April 27thand July 13th.

Participants

398 LGBTQ+ respondents forming an analytical sample of 310 in the main models.

Methods

We used a combined measure of gender identity or expression and sexual orientation as the main explanatory variable. We assessed mental health with the 4-item Perceived Stress Scale (PSS-4), and with the 10-item Center for Epidemiological Studies Depression scale (CES-D-10). We measured experiences of discrimination with a battery of questions that asked respondents whether they had experienced a set of discriminatory experiences because of their LGBTQ+ identity during the coronavirus pandemic. Experiences of discrimination was considered a mediating factor and examined both as an outcome as well as an explanatory variable. Models were adjusted for a range of demographic and socioeconomic variables.

Results

The prevalence of depression and stress were both high, with the majority of the sample exhibiting significant depressive symptomology (69%). Around one-in-six respondents reported some form of discrimination since the start of the pandemic because they were LGBTQ+ (16.7%). In regression models, the average score for perceived stress increased by 1.44 (95% Confidence Interval (CI): 0.517-2.354) for those who had experienced an instance of homophobic or transphobic harassment, compared to respondents who had not. Similarly, the odds of exhibiting significant depressive symptomology (CES-D-10 scores of 10 or more) increased three-fold among those who had experienced harassment based on their gender or sexuality compared to those who had not (OR: 3.251; 95% CI: 1.168-9.052). These marked associations remained after adjustment for a number of socioeconomic and demographic covariates. Cis-female respondents who identify as gay or lesbian had the lowest scores for perceived social or depressive symptoms; conversely transgender and gender diverse individuals had the highest scores.

Conclusions

We found high levels of stress and depressive symptoms, particularly among younger and transgender and gender diverse respondents. These associations were partially explained by experiences of discrimination which had a large, consistent and pernicious impact on stress and mental health.
Improved prediction of schizophrenia by leveraging genetic overlap with brain morphology
Authors: van der Meer Dennis , Shadrin Alexey A. , O’Connell Kevin , Bettella Francesco , Djurovic Srdjan , Wolfers Thomas , Alnæs Dag , Agartz Ingrid , Smeland Olav B. , Melle Ingrid , Sánchez Jennifer Monereo , Linden David E.J. , Dale Anders M. , Westlye Lars T. , Andreassen Ole A. , Frei Oleksandr , Kaufmann Tobias
Published: August 2020

Schizophrenia is a complex, polygenic disorder associated with subtle, distributed abnormalities in brain morphology. Here, we report large genetic overlap between schizophrenia and brain morphology, which enabled derivation of polygenic risk scores more predictive of schizophrenia diagnosis than the current state-of-the-art. Our results illustrate the potential of exploiting genetic overlap in imaging genetics studies, and how pleiotropy-enriched risk scores may improve prediction of polygenic brain disorders.
Automated brain morphometric biomarkers from MRI at term predict motor development in very preterm infants
Authors: Kline Julia E. , Illapani Venkata Sita Priyanka , He Lili , Parikh Nehal A.
Published: August 2020

Very preterm infants are at high risk for motor impairments. Early intervention can improve outcomes in this cohort, but it would be most effective if clinicians could accurately identify the highest risk infants early. A number of biomarkers for motor development exist, but currently none are sufficiently accurate for early risk-stratification. We prospectively enrolled very preterm (gestational age ≤31 weeks) infants from four level-III NICUs. Structural brain MRI was performed at term-equivalent age. We used a well-established pipeline to automatically derive brain volumetrics and cortical morphometrics, cortical surface area, sulcal depth, gyrification index, and inner cortical curvature, from structural MRI. We related these objective measures to Bayley-III motor scores (overall, gross, and fine) at two-years corrected age. Lasso regression identified the three best predictive biomarkers for each motor scale from our initial feature set. In multivariable regression, we assessed the independent value of these brain biomarkers, over-and-above known predictors of motor development, to predict motor scores. 75 very preterm infants had high-quality T2-weighted MRI and completed Bayley-III motor testing. All three motor scores were positively associated with regional cortical surface area and subcortical volumes and negatively associated with cortical curvature throughout the majority of brain regions. In multivariable regression modeling, thalamic volume, curvature of the temporal lobe, and curvature of the insula were significant predictors of overall motor development on the Bayley-III, independent of known predictors. Objective brain morphometric biomarkers at term show promise in predicting motor development in very preterm infants.
The Bacterial and Viral Complexity of Postinfectious Hydrocephalus in Uganda
Authors: Paulson Joseph N. , Williams Brent L. , Hehnly Christine , Mishra Nischay , Sinnar Shamim A. , Zhang Lijun , Ssentongo Paddy , Mbabazi-Kabachelor Edith , Wijetunge Dona S. S. , von Bredow Benjamin , Mulondo Ronnie , Kiwanuka Julius , Bajunirwe Francis , Bazira Joel , Bebell Lisa M. , Burgoine Kathy , Couto-Rodriguez Mara , Ericson Jessica E. , Erickson Tim , Ferrari Matthew , Gladstone Melissa , Guo Cheng , Haran Murali , Hornig Mady , Isaacs Albert M. , Kaaya Brian Nsubuga , Kangere Sheila M. , Kulkarni Abhaya V. , Kumbakumba Elias , Li Xiaoxiao , Limbrick David D. , Magombe Joshua , Morton Sarah U. , Mugamba John , Ng James , Olupot-Olupot Peter , Onen Justin , Peterson Mallory R. , Roy Farrah , Sheldon Kathryn , Townsend Reid , Weeks Andrew D. , Whalen Andrew J. , Quackenbush John , Ssenyonga Peter , Galperin Michael Y. , Almeida Mathieu , Atkins Hannah , Warf Benjamin C. , Lipkin W. Ian , Broach James R. , Schiff Steven J.
Published: August 2020

Postinfectious hydrocephalus (PIH), often following neonatal sepsis, is the most common cause of pediatric hydrocephalus world-wide, yet the microbial pathogens remain uncharacterized. Characterization of the microbial agents causing PIH would lead to an emphasis shift from surgical palliation of cerebrospinal fluid (CSF) accumulation to prevention. We examined blood and CSF from 100 consecutive cases of PIH and control cases of non-postinfectious hydrocephalus (NPIH) in infants in Uganda. Genomic testing was undertaken for bacterial, fungal, and parasitic DNA, DNA and RNA sequencing for viral identification, and extensive bacterial culture recovery. We uncovered a major contribution to PIH fromPaenibacillus, upon a background of frequent cytomegalovirus (CMV) infection. CMV was only found in CSF in PIH cases. A facultatively anaerobic isolate was recovered. Assembly of the genome revealed a strain ofP. thiaminolyticus. In mice, this isolate designated strainMbale, was lethal in contrast with the benign reference strain. These findings point to the value of an unbiased pan-microbial approach to characterize PIH in settings where the organisms remain unknown, and enables a pathway towards more optimal treatment and prevention of the proximate neonatal infections.

One Sentence Summary

We have discovered a novel strain of bacteria upon a frequent viral background underlying postinfectious hydrocephalus in Uganda.
Diagnostic Prediction with Sequence-of-sets Representation Learning for Clinical Events
Authors: Zhang Tianran , Chen Muhao , Bui Alex A. T.
Published: August 2020

Electronic health records (EHRs) contain both ordered and unordered chronologies of clinical events that occur during a patient encounter. However, during data preprocessing steps, many predictive models impose a predefined order on unordered clinical events sets (e.g., alphabetical, natural order from the chart, etc.), which is potentially incompatible with the temporal nature of the sequence and predictive task. To address this issue, we propose DPSS, which seeks to capture each patient’s clinical event records as sequences of event sets. For each clinical event set, we assume that the predictive model should be invariant to the order of concurrent events and thus employ a novel permutation sampling mechanism. This paper evaluates the use of this permuted sampling method given different data-driven models for predicting a heart failure (HF) diagnosis in subsequent patient visits. Experimental results using the MIMIC-III dataset show that the permutation sampling mechanism offers improved discriminative power based on the area under the receiver operating curve (AUROC) and precision-recall curve (pr-AUC) metrics as HF diagnosis prediction becomes more robust to different data ordering schemes.