bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Call For Better Methodological Quality Of Reviews On Using Artificial Intelligence For COVID-19 Detection In Medical Imaging – An Umbrella Systematic Review
Authors: Jemioło Paweł , Storman Dawid , Orzechowski Patryk 
Published: May 2021

AbstractObjectiveIn this umbrella systematic review, we screen existing reviews on using artificial intelligence (AI) techniques to diagnose COVID-19 in patients of any age and sex (both hospitalised and ambulatory) using medical images and assess their methodological quality.MethodsWe searched seven databases (MEDLINE, EMBASE, Web of Science, Scopus, dblp, Cochrane Library, IEEE Xplore) and two preprint services (arXiv, OSF Preprints) up to September 1, 2020. Eligible studies were identified as reviews or surveys where any metric of classification of detection of COVID-19 using AI was provided. Two independent reviewers did all steps of identification of records (titles and abstracts screening, full texts assessment, essential data extraction, and quality assessment). Any discrepancies were resolved by discussion. We qualitatively analyse methodological credibility of the reviews using AMSTAR 2 and evaluate reporting using PRISMA-DTA tools, leaving quantitative analysis for further publications.ResultsWe included 22 reviews out of 725 records covering 165 primary studies. This review covers 416,254 participants in total, including 50,022 diagnosed with COVID-19. The methodological quality of all eligible studies was rated as critically low. 91% of papers had significant flaws in reporting quality. More than half of the reviews did not comment on the results of previously published reviews at all. Almost three fourth of the studies included less than 10% of available studies.DiscussionIn this umbrella review, we focus on the descriptive summary of included papers. Much wasting time and resources could be avoided if referring to previous reviews and following methodological guidelines. Due to the low credibility of evidence and flawed reporting, any recommendation about automated COVID-19 clinical diagnosis from medical images using AI at this point cannot be provided.FundingPO was supported by NIH grant AI116794 (the funding body had no role in the design, in any stage of the review, or in writing the manuscript); PJ and DS did not receive any funding.RegistrationThe protocol of this review was registered on the OSF platform [1].
Obstructive sleep apnea is highly prevalent in COVID19 moderate to severe ARDS survivors: Findings of level I Polysomnography in a tertiary care hospital
Authors: Goyal Abhishek , Saxena Khushboo , Kar Avishek , Khurana Alkesh , Bhagtana Parneet Kaur , Rupa Sridevi Chinta Siva Koti , Pakhare Abhijit 
Published: May 2021

AbstractStudy ObjectivesStudies have found Obstructive Sleep Apnea (OSA) as a risk factor for increased risk for COVID19 Acute respiratory Distress Syndrome (ARDS); but most of the studies were done in already known patients of OSA. This study was done to find prevalence of OSA in patients with COVID-19 related acute respiratory distress syndrome.MethodologyA hospital based longitudinal study was conducted among COVID 19 Intensive Care Unit (ICU) survivors. All consecutive COVID19 with moderate to severe ARDS were evaluated for OSA by Level I Polysomnography (PSG) after 4-6 weeks of discharge. Prevalence of OSA and PSG variables {Total sleep time, Sleep efficiency, sleep stage percentage, Apnea Hypopnea Index (AHI), T90, nadir oxygen} was estimated.ResultsOut of 103 patients discharged from ICU during study period (October 2020 to 15 December 2020), 67 underwent Level I PSG. Mean Age was 52.6±10.9 years and mean Body Mass Index was 27.5 ± 6.2 Kg/m2. Total sleep time was 343.2 ± 86 minutes, sleep efficiency was 75.9±14.2%. OSA (AHI ≥5) was seen in 65/67 patients and 49 patients had moderate to severe OSA (i.e. AHI ≥ 15).ConclusionModerate-severe OSA was highly prevalent (73%) in COVID19 moderate to severe ARDS survivors. Role of OSA in pathophysiology of COVID19 ARDS needs further evaluation.HighlightsThis study was done to find prevalence of OSA in patients with COVID-19 related Acute respiratory distress syndromeModerate-severe OSA is highly prevalent (73%) in COVID19 ARDS survivors.To the best of our knowledge, it is first study in which level I PSG was done in COVID19 survivors.
Development and validation protocol for an instrument to measure women’s empowerment in urban sanitation across countries: The Agency, Resources, and Institutional Structures for Sanitation-related Empowerment (ARISE) Scales
Authors: Sinharoy Sheela S. , Conrad Amelia , Patrick Madeleine , McManus Shauna , Caruso Bethany A. 
Published: May 2021

AbstractIntroductionDespite an increasing emphasis on gender and empowerment in water, sanitation, and hygiene (WaSH) programs, no rigorously validated survey instruments exist for measuring empowerment within the WaSH sector. Our objective is to develop and validate quantitative survey instruments to measure women’s empowerment in relation to sanitation in urban areas of low-and middle-income countries.Methods and analysisWe are developing the Agency, Resources, and Institutional Structures for Sanitation-related Empowerment (ARISE) scales through a process that involves three phases: item development; scale development and initial validation; and scale evaluation and further validation. The first phase includes domain specification, item generation, face validity and content validity assessment, and item refinement. The second phase involves a second round of face validity and content validity assessment, followed by survey implementation in two cities (Tiruchirappalli, India and Kampala, Uganda) and data analysis involving factor analysis and item response theory approaches, as well as reliability and validity testing. The third phase involves a final round of face validity and content validity assessment, followed by survey implementation in three additional cities (Narsapur and Warangal, India; and Lusaka, Zambia) and statistical analysis using similar approaches as in Phase 2 for further validation.Ethics and disseminationEthics approvals have been received from ethics boards in all study locations. The study team will share findings with key stakeholders to inform programming activities and will publish results in peer-reviewed journals.Article SummaryStrengths and limitations of this studyWe employ rigorous methods to develop survey instruments, including testing and validating 15 scales, to assess domains of women’s empowerment related to sanitation.Phased data collection is being carried out across five urban locations in South Asia and Africa to ensure that the survey instruments are valid and comparable across contexts.Our survey instruments are specific to women in urban settings; adaptation and further validity testing is needed to develop instruments that can be administered in other settings (e.g. rural, peri-urban) and with men.The survey instruments are focused on empowerment at the individual, household, and community levels; they do not assess empowerment in markets (e.g. across the sanitation value chain) or in relation to policies and formal governance.
Engineering a customizable antibacterial T6SS-based platform inVibrio natriegens
Authors: Jana Biswanath , Keppel Kinga , Salomon Dor 
Published: May 2021

ABSTRACTBacterial pathogens are a major risk to human, animal, and plant health. To counteract the spread of antibiotic resistance, alternative antibacterial strategies are urgently needed. Here, we constructed a proof-of-concept customizable, modular, and inducible antibacterial toxin delivery platform. By engineering a type VI secretion system (T6SS) that is controlled by an externally induced on/off switch, we transformed the safe bacterium,Vibrio natriegens, into an effective antibacterial weapon. Furthermore, we demonstrated that the delivered effector repertoire, and thus the toxicity range of this platform, can be easily manipulated and tested. We believe that this platform can serve as a foundation for novel antibacterial bio-treatments, as well as a unique tool to study antibacterial toxins.
Emerging genetic diversity of SARS-CoV-2 RNA dependent RNA polymerase (RdRp) alters its B-cell epitopes
Authors: Kumar Sushant , Azad Gajendra Kumar 
Published: May 2021

ABSTRACTThe RNA dependent RNA polymerase (RdRp) plays crucial role in virus life cycle by replicating the viral RNA genome. The SARS-CoV-2 is an RNA virus that rapidly spread worldwide and during this process acquired mutations. This study was carried out to identify mutations in RdRp as the SARS-CoV-2 spread in India. We compared the 668 RdRp sequences reported from India with the first reported RdRp sequence from Wuhan, China. Our data revealed that RdRp have acquired sixty mutations among Indian isolates. Our protein modelling study also revealed that several mutants including D833Y, A699S, Y149C and C464F can potentially alter stability and flexibility of RdRp. We also predicted the potential B cell epitopes contributed by RdRp and identified thirty-six linear continuous and twenty-five discontinuous epitopes. Among sixty RdRp mutants identified in this study, 40% of them localises in the B cell epitopes region. Altogether, this study highlights the need to identify and characterize the variations in RdRp to understand the impact of these mutations on SARS-CoV-2.
SARS-CoV-2 cell-to-cell infection is resistant to neutralizing antibodies
Authors: Kruglova Natalia , Siniavin Andrei , Gushchin Vladimir , Mazurov Dmitriy 
Published: May 2021

AbstractThe COVID-19 pandemic caused by SARS-CoV-2 has posed a global threat to human lives and economics. One of the best ways to determine protection against the infection is to quantify the neutralizing activity of serum antibodies. Multiple assays have been developed to validate SARS-CoV-2 neutralization; most of them utilized lentiviral or vesicular stomatitis virus-based particles pseudotyped with the spike (S) protein, making them safe and acceptable to work with in many labs. However, these systems are only capable of measuring infection with purified particles. This study has developed a pseudoviral assay with replication-dependent reporter vectors that can accurately quantify the level of infection directly from the virus producing cell to the permissive target cell. Comparative analysis of cell-free and cell-to-cell infection revealed that the neutralizing activity of convalescent sera was more than tenfold lower in cell cocultures than in the cell-free mode of infection. As the pseudoviral system could not properly model the mechanisms of SARS-CoV-2 transmission, similar experiments were performed with replication-competent coronavirus, which detected nearly complete SARS-CoV-2 cell-to-cell infection resistance to neutralization by convalescent sera. Based on available studies, this is the first attempt to quantitatively measure SARS-CoV-2 cell-to-cell infection, for which the mechanisms are largely unknown. The findings suggest that this route of SARS-CoV-2 transmission could be of great importance for treatment and prevention of COVID-19.ImportanceImmune surveillance of viral or bacterial infections is largely mediated by neutralizing antibodies. Antibodies against the SARS-CoV-2 spike protein are produced after vaccination or infection, but their titers only partly reflect the degree of protection against infection. To identify protective antibodies, a neutralization test with replicating viruses or pseudoviruses (PVs) is required. This study developed lentiviral-based PV neutralization assays that, unlike similar systems reported earlier, enable quantitative measurement of SARS-CoV-2 neutralization in cell cocultures. Using both PVs and replication-competent virus, it was demonstrated that SARS-CoV-2 cell-to-cell infection is considerably more resistant to serum neutralization than infection with purified viral particles. The tests are easy to set up in many labs, and are believed to be more informative for monitoring SARS-CoV-2 collective immunity or entry inhibitor screening.
Preliminary Analysis of Safety and Immunogenicity of a SARS-CoV-2 Variant Vaccine Booster
Authors: Wu Kai , Choi Angela , Koch Matthew , Ma LingZhi , Hill Anna , Nunna Naveen , Huang Wenmei , Oestreicher Judy , Colpitts Tonya , Bennett Hamilton , Legault Holly , Paila Yamuna , Nestorova Biliana , Ding Baoyu , Pajon Rolando , Miller Jacqueline M , Leav Brett , Carfi Andrea , McPhee Roderick , Edwards Darin K 
Published: May 2021

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of a global pandemic of coronavirus disease 2019 (COVID-19) that has led to more than 3 million deaths worldwide. Safe and effective vaccines are now available, including the mRNA-1273 prototype vaccine, which encodes for the Wuhan SARS-CoV-2 spike (S) protein stabilized in the prefusion conformation by 2 proline substitutions. This vaccine showed 94% efficacy in prevention of symptomatic COVID-19 disease in a phase 3 clinical study. Recently, SARS-CoV-2 variants have emerged, some of which have shown decreased susceptibility to neutralization by vaccine-induced antibody, most notably the B.1.351 variant, although the overall impact on vaccine efficacy remains to be determined. In addition, recent evidence of waning antibody levels after infection or vaccination point to the need for periodic boosting of immunity. Here we present the preliminary evaluation of a clinical study on the use of the prototype mRNA-1273 or modified COVID-19 mRNA vaccines, designed to target emerging SARS-CoV-2 variants as booster vaccines in participants previously vaccinated approximately 6 months earlier with two doses of the prototype vaccine, mRNA-1273. The modified vaccines include a monovalent mRNA-1273.351 encoding for the S protein found in the B.1.351 variant and multivalent mRNA-1273.211 comprising a 1:1 mix of mRNA-1273 and mRNA-1273.351. As single 50 µg booster vaccinations, both mRNA-1273 and mRNA-1273.351 had acceptable safety profiles and were immunogenic. Antibody neutralization titers against B.1.351 and P.1 variants measured by SARS-CoV-2 pseudovirus neutralization (PsVN) assays before the booster vaccinations, approximately 6 to 8 months after the primary series, were low or below the assay limit of quantification, although geometric mean titers versus the wild-type strain remained above levels likely to be protective. Two weeks after the booster vaccinations, titers against the wild-type original strain, B.1.351, and P.1 variants increased to levels similar to or higher than peak titers after the primary series vaccinations. Although both mRNA-1273 and mRNA-1273.351 boosted neutralization of the wild-type original strain, and B.1.351 and P.1 variants, mRNA-1273.351 appeared to be more effective at increasing neutralization of the B.1.351 virus versus a boost with mRNA-1273. The vaccine trial is ongoing and boosting of clinical trial participants with the multivalent mRNA-1273.211 is currently being evaluated.
Rossmann-toolbox: a deep learning-based protocol for the prediction and design of cofactor specificity in Rossmann-fold proteins
Authors: Kaminski Kamil , Ludwiczak Jan , Jasinski Maciej , Bukala Adriana , Madaj Rafal , Szczepaniak Krzysztof , Dunin-Horkawicz Stanislaw 
Published: May 2021

AbstractThe Rossmann fold enzymes are involved in essential biochemical pathways such as nucleotide and amino acid metabolism. Their functioning relies on interaction with cofactors, small nucleoside-based compounds specifically recognized by a conserved βαβ motif shared by all Rossmann fold proteins. While Rossmann methyltransferases recognize only a single cofactor type, the S-Adenosylmethionine (SAM), the oxidoreductases, depending on the family, bind nicotinamide (NAD, NADP) or flavin-based (FAD) cofactors. In this study, we show that despite its short length, the βαβ motif unambiguously defines the specificity towards the cofactor. Following this observation, we trained two complementary deep learning models for the prediction of the cofactor specificity based on the sequence and structural features of the βαβ motif. A benchmark on two independent test sets, one containing βαβ motifs bearing no resemblance to those of the training set, and the other comprising 38 experimentally confirmed cases of rational design of the cofactor specificity, revealed the nearly perfect performance of the two methods. The Rossmann-toolbox protocols can be accessed via the webserver athttps://lbs.cent.uw.edu.pl/rossmann-toolboxand are available as a Python package athttps://github.com/labstructbioinf/rossmann-toolbox.Key pointsThe Rossmann fold encompasses a multitude of diverse enzymes involved in most of the essential cellular pathwaysProteins belonging to the Rossmann fold co-evolved with their nucleoside-based cofactors and require them for the functioningManipulating the cofactor specificity is an important step in the process of enzyme engineeringWe developed an end-to-end pipeline for the prediction and design of the cofactor specificity of the Rossmann fold proteinsOwing to the utilization of deep learning approaches the pipeline achieved nearly perfect accuracy
Neural Representations of Food-Related Attributes in the Human Orbitofrontal Cortex During Choice Deliberation in Anorexia Nervosa
Authors: Xue Alice M. , Foerde Karin , Timothy Walsh B. , Steinglass Joanna E. , Shohamy Daphna , Bakkour Akram 
Published: May 2021

AbstractDecisions about what to eat recruit the orbitofrontal cortex (OFC) and involve the evaluation of food-related attributes, such as taste and health. These attributes are utilized differently by healthy individuals and patients with disordered eating behavior, but it is unclear whether these attributes are decodable from activity in the OFC in both groups and whether neural representations of these attributes are differentially related to decisions about food. We used fMRI combined with behavioral tasks to investigate the representation of taste and health attributes in the human OFC and the role of these representations in food choices in healthy individuals and patients with anorexia nervosa (AN). We found that subjective ratings of tastiness and healthiness could be decoded from patterns of activity in the OFC in both groups. However, health-related patterns of activity in the OFC were more related to the magnitude of choice preferences among patients with AN than healthy individuals. These findings suggest that maladaptive decision-making in AN is associated with more consideration of health information represented by the OFC during deliberation about what to eat.Significance StatementAn open question about the orbitofrontal cortex (OFC) is whether it supports the evaluation of food-related attributes during deliberation about what to eat. We found that healthiness and tastiness information were decodable from patterns of neural activity in the OFC in both patients with anorexia nervosa (AN) and healthy controls. Critically, neural representations of health were more strongly related to choices in patients with AN, suggesting that maladaptive overconsideration of healthiness during deliberation about what to eat is related to activity in the OFC. More broadly, these results show that activity in the human OFC is associated with the evaluation of relevant attributes during value-based decision-making. These findings may also guide future research into the development of treatments for AN.
Cell Types of Origin in the Cell Free Transcriptome in Human Health and Disease
Authors: Vorperian Sevahn K. , Moufarrej Mira N. ,   Tabula Sapiens Consortium, Quake Stephen R. 
Published: May 2021

AbstractCell-free RNA (cfRNA) can be used to noninvasively measure dynamic and longitudinal physiological changes throughout the body. While there is considerable effort in the liquid biopsy field to determine disease tissue-of-origin, pathophysiology occurs at the cellular level. Here, we describe two approaches to identify cell type contributions to cfRNA. First we usedTabula Sapiens, a transcriptomic cell atlas of the human body to computationally deconvolve the cell-free transcriptome into a sum of cell type specific transcriptomes, thus revealing the spectrum of cell types readily detectable in the blood. Second, we used individual tissue transcriptomic cell atlases in combination with the Human Protein Atlas RNA consensus dataset to create cell type signature scores which can be used to infer the implicated cell types from cfRNA for a variety of diseases. Taken together, these results demonstrate that cfRNA reflects cellular contributions in health and disease from diverse cell types, potentially enabling determination of pathophysiological changes of many cell types from a single blood test.
Unbiased integration of single cell transcriptome replicates
Authors: Lopez Martin Loza , Teraguchi Shunsuke , Standley Daron M. , Diez Diego 
Published: May 2021

AbstractSingle cell transcriptomic approaches are becoming mainstream, with replicate experiments commonly performed with the same single cell technology. Methods that enable integration of these datasets by removing batch effects while preserving biological information are required for unbiased data interpretation. Here we introduce Canek for this purpose. Canek leverages information from mutual nearest neighbor to combine local linear corrections with cell-specific non-linear corrections within a fuzzy logic framework. Using a combination of real and synthetic datasets, we show that Canek corrects batch effects while introducing the least amount of bias compared with competing methods. Canek is computationally efficient and can easily integrate thousands of single-cell transcriptomes from replicated experiments.
Ferries and environmental DNA: underway sampling from commercial vessels provides new opportunities for systematic genetic surveys of marine biodiversity
Authors: Valsecchi Elena , Arcangeli Antonella , Lombardi Roberto , Boyse Elizabeth , Carr Ian M. , Galli Paolo , Goodman Simon J. 
Published: May 2021

ABSTRACTMarine environmental DNA (eDNA) is an important tool for biodiversity research and monitoring but challenges remain in scaling surveys over large spatial areas, and increasing the frequency of sampling in remote locations at reasonable cost. Here we demonstrate the feasibility of sampling from commercial vessels (Mediterranean ferries) while underway, as a strategy to facilitate replicable, systematic marine eDNA surveys in locations that would normally be challenging and expensive for researchers to access. Sixteen eDNA samples were collected from 4 fixed sampling stations, and in response to 4 cetacean sightings, across three cruises undertaken along the 300 km ferry route between Livorno (Tuscany) and Golfo Aranci (Sardinia) in the Ligurian/Tyrrhenian Seas, June-July 2018. Using 12SrDNA and 16SrDNA metabarcoding markers, we recovered diverse marine vertebrate Molecular Operational Taxonomic Units (MOTUs) from teleost fish, elasmobranchs, and cetaceans. We detected sample heterogeneity consistent with previously known variation in species occurrences, including putative species spawning peaks associated with specific sea surface temperature ranges, and increased night time abundance of bathypelagic species known to undertake diel migrations through the water column. We suggest commercial vessel based marine eDNA sampling using the global shipping network has potential to facilitate broad-scale biodiversity monitoring in the world’s oceans.