bluuebunny/crossref_metadata_2025_split huggingface dataset:
Laboratory Biomarkers of COVID-19 Disease Severity and Outcome: Findings from a Developing Country
Authors: Leulseged Tigist W. , Hassen Ishmael S. , Ayele Birhanu T. , Tsegay Yakob G. , Abebe Daniel S. , Edo Mesay G. , Maru Endalkachew H. , Zewde Wuletaw C. , Naylor Lydia K. , Semane Dejene F. , Deresse Menayit T. , Tezera Bereket B. 
Published: January 2021

ABSTRACTAimTo identify laboratory biomarkers that predict disease severity and outcome among COVID-19 patients admitted to the Millennium COVID-19 Care Center in Ethiopia.MethodsA retrospective cohort study was conducted among 429 RT-PCR confirmed COVID- 19 patients who were on follow up from July to October 2020 and with complete clinical and laboratory data. Data was described using frequency tables. Robust Poisson regression model was used to identify predictors of COVID-19 disease severity where adjusted relative risk (RR), P-value and 95% CI for RR were used to test significance and interpretation of results. Binary Logistic regression model was used to assess the presence of statistically significant association between the explanatory variables and COVID-19 disease outcome where adjusted odds ratio, P- value and 95% CI for adjusted odds ratio were used for testing significance and interpretation of resultsResultsAmong the 429 patients studied, 182 (42.4%) had Severe disease at admission and the rest 247 (57.6%) had Non-severe disease (15.6% mild and 42.0% moderate). Regarding disease outcome, 45 (10.5%) died and 384 (89.5%) were discharged alive. Age group (ARR= 1.779, 95% CI= 1.405- 2.252, p-value < 0.0001), Neutrophil to Lymphocyte ratio (NLR) (ARR= 4.769, 95% CI= 2.419 - 9.402 p-value <0.0001), Serum glutamic oxaloacetic transaminase (SGOT) (ARR= 1.358, 95% CI= 1.109- 1.662 p-value=0.003), Sodium (ARR= 1.321, 95% CI= 1.091- 1.600 p-value=0.004) and Potassium (ARR= 1.269, 95% CI= 1.059-1.521 p-value=0.010) were found to be significant predictors of COVID-19 disease severity.The following factors were significantly associated with COVID-19 disease outcome; age group (AOR= 2.767, 95% CI= 1.099 - 6.067, p-value=0.031), white blood cell count (AOR= 4.253, 95% CI= 1.918 - 9.429, p-value=0.0001) and sodium level (AOR= 3.435, 95% CI= 1.439, 8.198, p-value=0.005).ConclusionsThe laboratory markers of NLR of above three, raised SGOT and deranged sodium and potassium levels (both hypo- and hyper-states) were found to be significant predictors of developing severe COVID-19 disease. In addition, deranged values of white blood cell count and sodium levels were significantly associated with worse outcome of the disease. Therefore, assessing and monitoring these laboratory markers at the earliest stage of the disease could have a considerable impact in halting disease progression and death.
Insights into the molecular mechanism of anticancer drug ruxolitinib repurposable in COVID-19 therapy
Authors: Mandal Manisha , Mandal Shyamapada 
Published: January 2021

AbstractDue to non-availability of specific therapeutics against COVID-19, repurposing of approved drugs is a reasonable option. Cytokines imbalance in COVID-19 resembles cancer; exploration of anti-inflammatory agents, might reduce COVID-19 mortality. The current study investigates the effect of ruxolitinib treatment in SARS-CoV-2 infected alveolar cells compared to the uninfected one from the GSE5147507 dataset. The protein-protein interaction network, biological process and functional enrichment of differentially expressed genes were studied using STRING App of the Cytoscape software and R programming tools. The present study indicated that ruxolitinib treatment elicited similar response equivalent to that of SARS-CoV-2 uninfected situation by inducing defense response in host against virus infection by RLR and NOD like receptor pathways. Further, the effect of ruxolitinib in SARS-CoV-2 infection was mainly caused by significant suppression of IFIH1, IRF7 and MX1 genes as well as inhibition of DDX58/IFIH1-mediated induction of interferon-I and -II signalling.
An Intrinsic and Extrinsic Evaluation of Learned COVID-19 Concepts using Open-Source Word Embedding Sources
Authors: Parikh Soham , Davoudi Anahita , Yu Shun , Giraldo Carolina , Schriver Emily , Mowery Danielle L. 
Published: January 2021

IntroductionScientists are developing new computational methods and prediction models to better clinically understand COVID-19 prevalence, treatment efficacy, and patient outcomes. These efforts could be improved by leveraging documented, COVID-19-related symptoms, findings, and disorders from clinical text sources in the electronic health record. Word embeddings can identify terms related to these clinical concepts from both the biomedical and non-biomedical domains and are being shared with the open-source community at large. However, it’s unclear how useful openly-available word embeddings are for developing lexicons for COVID-19-related concepts.ObjectiveGiven an initial lexicon of COVID-19-related terms, characterize the returned terms by similarity across various, open-source word embeddings and determine common semantic and syntactic patterns between the COVID-19 queried terms and returned terms specific to word embedding source.Materials and MethodsWe compared 7 openly-available word embedding sources. Using a series of COVID-19-related terms for associated symptoms, findings, and disorders, we conducted an inter-annotator agreement study to determine how accurately the most semantically similar returned terms could be classified according to semantic types by three annotators. We conducted a qualitative study of COVID-19 queried terms and their returned terms to identify useful patterns for constructing lexicons. We demonstrated the utility of applying such terms to discharge summaries by reporting the proportion of patients identified by concept for pneumonia, acute respiratory distress syndrome, and COVID-19 cohorts.ResultsWe observed high, pairwise inter-annotator agreement (Cohen’s Kappa) for symptoms (0.86 to 0.99), findings (0.93 to 0.99), and disorders (0.93 to 0.99). Word embedding sources generated based on characters tend to return more lexical variants and synonyms; in contrast, embeddings based on tokens more often return a variety of semantic types. Word embedding sources queried using an adjective phrase compared to a single term (e.g., dry cough vs. cough; muscle pain vs. pain) are more likely to return qualifiers of the same semantic type (e.g., “dry” returns consistency qualifiers like “wet”, “runny”). Terms for fever, cough, shortness of breath, and hypoxia retrieved a higher proportion of patients than other clinical features. Terms for dry cough returned a higher proportion of COVID-19 patients than pneumonia and ARDS populations.DiscussionWord embeddings are a valuable technology for learning terms, including synonyms. When leveraging openly-available word embedding sources, choices made for the construction of the word embeddings can significantly influence the phrases returned.
Argon Laser Photocoagulation for Treatment of Presumed Trematode-induced Granulomatous Anterior Uveitis in Children
Authors: Alsmman AlahmadyHamad , Abdalla Abdelsalam , Ezzeldawla Mohamed , Elmatin Shaimaa Abd , Abozaid Mortada Ahmed 
Published: January 2021

ABSTRACTBackground/AimsTo assess the safety and efficacy of argon laser photocoagulation as a new modality for the treatment of presumed trematode-induced granulomatous anterior uveitis (PTGAU) in children.MethodsForty-eight eyes of 48 children with PTGAU with pearl-like nodule(s) in the anterior chamber were included in this prospective non- randomised controlled clinical trial. Patients were divided into two groups: group A (23 eyes) was treated with one session of argon laser applied to the anterior chamber nodules, and group B (25 eyes) received medical treatment in the form of topical steroid and cycloplegic eye drops with trans-septal triamcinolone injection.All cases were followed up for 3 monthswith measurement of VA, assessment of anterior chamber reaction, and size of the pearl-like nodules.ResultsIn group A, 22 eyes (95.65%) showed regression of the pearl- like nodules with resolution of the anterior chamber reaction (flare and cells) and improvement in visual acuity from 0.52±0.12 to 0.06 ± 0.08logMAR (p value <0.001). Such improvement was maintained within the 3-month follow-up period. In group B, 23 eyes (92%) showed initial regression of the granulomas,whichwas maintained in only 14 eyes (56%),with 9 eyes experiencing recurrence after 3 months of follow-up.ConclusionArgon laser photocoagulation is a safe and effective novel treatment for PTGAU with pearl-like nodules in the anterior chamber in children. Larger studies with longer follow-up periods are needed to confirm these results.PRECISArgon laser photocoagulation is a novel non-invasive line of treatment that can be added to the armamentarium for presumed trematode-induced granulomatous anterior uveitis in children.
Cardiometabolic risks of SARS-CoV-2 hospitalization using Mendelian Randomization
Authors: Lorincz-Comi Noah , Zhu Xiaofeng 
Published: January 2021

AbstractIntroMany cardiometabolic conditions have demonstrated associative evidence with COVID-19 hospitalization risk. However, the observational designs of the studies in which these associations are observed preclude causal inferences of hospitalization risk. Mendelian Randomization (MR) is an alternative risk estimation method more robust to these limitations that allows for causal inferences.Methods & materialsWe applied four MR methods (MRMix, IMRP, IVW, MREgger) to publicly available GWAS summary statistics from European (COVID-19 GWAS n=2,956) and multi-ethnic populations (COVID-19 GWAS n=10,808) to better understand extant causal associations between Type II Diabetes (GWAS n=659,316), BMI (n=681,275), diastolic and systolic blood pressure, and pulse pressure (n=757,601 for each) and COVID-19 hospitalization risk across populations.ResultsAlthough no significant causal effect evidence was observed, our data suggested a trend of increasing hospitalization risk for Type II diabetes (IMRP OR, 95% CI: 1.67, 0.96-2.92) and pulse pressure (OR, 95% CI: 1.27, 0.97-1.66) in the multi-ethnic sample.ConclusionsType II diabetes and Pulse pressure demonstrates a potential causal association with COVID-19 hospitalization risk, the proper treatment of which may work to reduce the risk of a severe COVID-19 illness requiring hospitalization. However, GWAS of COVID-19 with large sample size is warranted to confirm the causality.
Estimation of Daily Reproduction rates in COVID-19 Outbreak
Authors: Demongeot Jacques , Oshinubi Kayode , Seligmann Hervé , Thuderoz Florence 
Published: January 2021

Abstract(1) BackgroundThe estimation of daily reproduction rates throughout the infectivity period is rarely considered and only their sumRois calculated to quantify the level of virulence of an infectious agent;(2) MethodsWe give the equation of the discrete dynamics of epidemic growth and we obtain an estimation of the daily reproduction rates, by using a technique of deconvolution of the series of observed new cases of Covid-19;(3) ResultsWe give both simulation results as well as estimations for several countries for the Covid-19 outbreak;(4) ConclusionsWe discuss the role of the noise on the precision of the estimation and we open on perspectives of forecasting methods to predict the distribution of daily reproduction rates along the infectivity period.
Primary care during the COVID-19 pandemic – observations and challenges identified through a survey and interviews with community paediatricians: the calm before the storm
Authors: Vasconcelos Malte Kohns , Weil Katharina , Vesterling-Hörner Daniela , Klemm Mehrsad , Scheich Tarik el , Renk Hanna , Remke Katharina , Bosse Hans Martin 
Published: January 2021

AbstractBackgroundGlobally, the COVID-19 pandemic has a major impact on healthcare provision. The effects in primary care are understudied.AimTo document changes in consultation numbers and patient management during the COVID-19 pandemic, and to identify challenges for patient care.MethodsSurvey of 44 paediatric primary care practices on consultation numbers and patient management changes (response rate 50%), and semi-structured interviews to identify challenges for patient care.ResultsNumbers of consultations for scheduled developmental examinations remained unchanged compared to the previous year while emergency visits were strongly reduced (mean 87.3 less/week in March–May 2020 compared to 2019, median reduction 55.0%). Children dependent on developmental therapy and with chronic health conditions were identified as patient groups receiving deteriorated care. High patient numbers, including of mildly symptomatic children presenting for health certificates, in combination with increased organisational demands and expected staff outages are priority concerns for the winter.ConclusionPrimary care paediatricians offered stable service through the early pandemic but expect strained resources for the upcoming winter. Unambiguous guidance on which children should present to primary care and who should be tested would help to allocate resources appropriately, and this guidance needs to consider age group specific issues including high prevalence of respiratory symptoms, dependency on carers and high contact rates.
Is sickle cell disease a risk factor for severe COVID-19 : a multicenter national retrospective cohort
Authors: Abdulrahman Abdulkarim , Wael Mohammed , AlAmmadi Fajer , AlMosawi Zahra , Alsherooqi Reem , AlSayed Manal , Kumar Nitya , AlQahtani Manaf 
Published: January 2021

AbstractIntroductionCoronavirus disease (COVID-19) caused by the novel coronavirus SARS-CoV-2 is an infectious disease which has evolved into a worldwide pandemic. Growing evidence suggests that individuals with pre-existing comorbidities are at higher risk of a more serious COVID-19 illness. Sickle cell disease (SCD) is an inherited hemoglobinopathy which increases the susceptibility to infections and as a consequent has higher risks of morbidity and mortality.The impact of COVID-19 on SCD patients could lead to further increase in disease severity and mortality. Studies that examine the effect of SCD on COVID-19 outcomes are lacking. This study aims to determine whether SCD is a risk factor for severe COVID-19 infection in regards to the requirement of non-invasive ventilation/high flow nasal cannula (NIV/HFNC), mechanical intubation (MV) or death.MethodsRetrospective cohort study which included COVID-19 patients admitted to four Ministry of Health COVID-19 treatment facilities in Bahrain during the period of 24, February 2020, to 31, July 2020. All SCD patients with COVID-19 were included and compared to randomly selected non-SCD patients with COVID-19. Data for the selected patients were collected from the medical records. Multivariate logistic regression models were used to control for confounders and estimate the effect of SCD on the outcomes.ResultsA total of 1,792 patients with COVID-19 were included; 38 of whom were diagnosed with SCD as well. In the SCD group, one (2.6%) patient required NIV/HFNC, one (2.6%) required MV and one (2.6%) death occurred. In comparison, 56 (3.2%) of the non-SCD patients required NIV/HFNC, 47 (2.7%) required MV and death occurred in 58 (3.3%) patients. Upon adjusting for confounders, SCD had an odds ratio of 1.847 (95% CI: 0.39 – 8.83; p=0.442).ConclusionOur results indicate that SCD is not a risk factor for worse disease outcomes in COVID-19 patients.
Evaluation of three rapid lateral flow antigen detection tests for the diagnosis of SARS-CoV-2 infection
Authors: Jääskeläinen AE , Ahava MJ , Jokela P , Szirovicza L , Pohjala S , Vapalahti O , Lappalainen M , Hepojoki J , Kurkela S 
Published: January 2021

AbstractIntroductionThe COVID-19 pandemic has led to high demand of diagnostic tools. Rapid antigen detection tests have been developed and many have received regulatory acceptance such as CE IVD or FDA markings. Their performance needs to be carefully assessed.Materials and Methods158 positive and 40 negative retrospective samples collected in saline and analyzed by a laboratory-developed RT-PCR test were used to evaluate Sofia (Quidel), Standard Q (SD Biosensor), and Panbio™ (Abbott) rapid antigen detection tests (RADTs). A subset of the specimens was subjected to virus culture.ResultsThe specificity of all RADTs was 100% and the sensitivity and percent agreement was 80% and 85% for Sofia, 81% and 85% for Standard Q, and 83% and 86% for Panbio™, respectively. All three RADTs evaluated in this study reached a more than 90% sensitivity for samples with a high viral load as estimated from the low Ct values in the reference RT-PCR. Virus culture was successful in 80% of specimens with a Ct value <25.ConclusionsAs expected, the RADTs were less sensitive than RT-PCR. However, they benefit from the speed and ease of testing, and lower price as compared to RT-PCR. Repeated testing in appropriate settings may improve the overall performance.
WITHDRAWN:Staphylococcus aureus-serineprotease-like protein B (SplB) activates PAR2 and induces endothelial barrier dysfunction
Authors: Chandrabalan Arundhasa , Thibeault Pierre E , Smiljanov Bojan , Mittmann Laura A , Deinhardt-Emmer Stefanie , Nordengrün Maria , Iqbal Jawad , Mrochen Daniel M , Chamling Bishwas , Rauch Bernhard H , Reichel Christoph A , Ramachandran Rithwik , Bröker Barbara M , Darisipudi Murty N 
Published: January 2021

Withdrawal StatementThe authors have withdrawn their manuscript owing to the following reason: Unfortunately, the preparation of the recombinant serine protease-like protein B (SplB) used in this study was found to contain impurities, so that the effects presented cannot be unambiguously attributed to the protease SplB. We therefore retract the manuscript from bioRxiv. We apologize for any inconvenience this may have caused. Therefore, the authors do not wish this work to be cited as reference for the project. We want to clarify that the issue was identified in the preparation of the SplB protein and does not reflect on the contributions of individual authors. If you have any questions, please contact the corresponding author.
Tele-Rehabilitation for People with Visual Disabilities During COVID-19 Pandemic: Lesson Learned
Authors: Senjam Suraj Singh , Manna Souvik , Vashist Praveen , Gupta Vivek 
Published: January 2021

AbstractBackgroundThe COVID-19 outbreak poses a global crisis in health care delivery system, including habilitation and rehabilitation services. In the present study, we shared our experiences on telerehabilitation services established primarily for students with visual disabilities (SwVD) amidst COVID-19 pandemic and its outputs.MethodsFollowing the lockdown declared on March 23, 2020, the rehabilitative team of a tertiary eye center in north India received information that many VCS were stranded in schools for the blind in Delhi, and feeling with anxiety and panic in absence of teachers. Shortly, the room for vision rehabilitation clinic was set-up for tele-facilities. The intended services was explained while disseminating the mobile numbers. A semi-structured questionnaire consisting of closed and open-ended was developed to record COVID-19 knowledge and concerns. Inductive content analysis was used to report the qualitative information.ResultsAs of June 30, 2020, a total of 492 clients contacted the team, with maximum from Delhi (41.5%), and predominantly males (78.8%). Around 80.3% of callers were VCS with age range of 11 to 30 years. The two most frequently encountered health needs were itching in eyes (36.1%) and headache (29%). Television news was the most used medium among callers to get COVID-19 information. Cough is a less frequently known mode of transmission (28%), similarly handwashing as a less known for prevention (17.2%). Eight concerns were recorded based on qualitative data analysis.ConclusionTele-rehabilitation provides valuable insights and has the potential to address various concerns, uncertainty, anxiety, and fear among SVD during the pandemic.
Time- and cell-dependent atypia and cell death are caused by progressive deficiency in DNA replication
Authors: Lin Alex Y. , Thomas Georgia K. , Ang Khai Chung , van Rossum Damian B. , Canfield Victor A. , Cheng Keith C. 
Published: January 2021

AbstractPleiotropy caused by single-gene mutations is common and poorly understood. A zebrafish null mutant of DNA polymerase α subunit B,huli hutu(hht), evolves a complex pleiotropy associated with DNA damage and S phase arrest across multiple organ systems over 5-7 days, including nuclear atypia, a common cellular feature in human cancers and pre-cancers, in gastrointestinal organs, and nuclear fragmentation in the eye and brain. The pleiotropic pattern ofhhtphenotypes is explained by progressive loss of wild-type maternalpola2function in homozygous mutant embryos whosepola2mRNA becomes undetectable by 24 hours post-fertilization (hpf). Inhibition of DNA synthesis by aphidicolin or hydroxyurea in wild-type embryos from 24 hpf phenocopied the pleiotropic pattern ofhht. These results are consistent with a model in which time-sensitive, reduced capacity for DNA synthesis results in cell death in fast-replicating cells, and nuclear atypia in tissues with fewer and larger cells.
On the lag between deaths and infections in the first phase of the Covid-19 pandemic
Authors: Chruściel Piotr T. , Szybka Sebastian J. 
Published: January 2021

AbstractOne of the key issues in fighting the current pandemic, or the ones to come, is to obtain objective quantitative indicators of the effectiveness of the measures taken to contain the epidemic. The aim of this work is to point out that the lag between the daily number of infections and casualties provides one such indicator. For this we determined the lag during the first phase of the Covid-19 pandemic for a series of countries using the data available at the server of the John Hopkins University using three different methods. Somewhat surprisingly, we find a lag varying substantially between countries, taking negative values (thus the maximum daily number of casulties preceding the maximum daily namber of new infections) in countries where no steps to contain the epidemic have been taken at the outset, with an average lag of 7 ± 0.3 days. Our results can be useful to health authorities in a search for the best strategy to fight the epidemic.Key MessagesThe lags between the maximum daily infections and casualties during the first phase of the Covid-19 pandemic differ widely between countries.These lags are clear for some countries, but impossible to determine confidently for most.In some countries the day at which the maximal number of daily deaths is attained precedes the day of the maximal number of casualties, indicating a failure to protect the most vulnerable part of the population.The lags can serve as an objective quantitative measure of the effectiveness of the measures taken to contain the epidemic.