bluuebunny/crossref_metadata_2025_split huggingface dataset:
Data-Driven Inference of COVID-19 Clinical Prognosis
Authors: Salas Joaquín , Pulido Dagoberto , Montoya Omar , Ruiz Isaac 
Published: September 2020

AbstractKnowing the most likely clinical prognosis for a patient infected with SARS-Cov-2 could offer guidelines for tracking their medical evolution, improving attention, and assigning resources. Aiming to assess a patient’s status quantitatively, we explore the analysis of existing clinical information using data-driven methods. Our goal is to extract the characteristics distinguishing between those COVID-19 patients that improve and those who die. In our approach, we select the relevant features using the algorithm of Boruta, a wrapper framework that takes input from classifiers generating relevance assessment of the predictors. Using the extracted features, we train machine learning classifiers, including Random Forests, Support Vector Machine, Extreme Gradient Boosting, and Neural Networks. We assess the performance of the classifiers using Precision-Recall and ROC analysis, establishing the ranges at which risk assessment permits effective decision-making. Our research highlights that local regions present unique sets of essential features, that it is possible to construct effective classifiers based on clinical data, and that an ensemble of classifiers results in the best performing discriminant.
Changes in social behavior over time in the COVID-19 pandemic
Authors: Sheehan Megan M. , Pfoh Elizabeth R. , Speaker Sidra , Rothberg Michael B. 
Published: September 2020

AbstractPublic health recommendations aimed at limiting spread of SARS-CoV-2 have encouraged social distancing and masks as economies across the United States re-open. Understanding adherence to these guidelines will inform further efforts to reduce transmission. In this repeated cross-sectional survey study, we describe changes in social behavior in Ohio during periods of declining and rising cases. While essential activities remained consistent over time, more individuals attended gatherings of 10 or more people as cases rose, particularly in the 18-29 age group. A majority of individuals wore masks. It appears necessary to continue limiting gatherings and encourage mask-wearing, particularly among younger groups.
Validation of smartphone-based assessments of depressive symptoms using the Remote Monitoring Application in Psychiatry (ReMAP)
Authors: Goltermann Janik , Emden Daniel , Leehr Elisabeth J. , Dohm Katharina , Redlich Ronny , Dannlowski Udo , Hahn Tim , Opel Nils 
Published: September 2020

AbstractSmartphone-based symptom monitoring has gained increased attention in psychiatric research as a cost-efficient tool for prospective and ecologically valid assessments based on participants’ self-reports. However, a meaningful interpretation of smartphone-based assessments requires knowledge on their psychometric properties; especially their validity. Here, we conducted a systematic investigation of the validity of smartphone-based assessments of affective symptoms by using the smartphone appRemote Monitoring Application in Psychiatry(ReMAP). Beck Depression Inventory (BDI), and single-item mood and sleep information was assessed via the ReMAP app and validated with stationary (nonsmartphone) BDI scores and clinician-rated depression severity using the Hamilton Depression Rating Scale (HDRS).We found overall high comparability between smartphone-based and stationary BDI scores (ICC=.921, p<.001, n=173). Smartphone-based BDI further correlated with stationary HDRS ratings of depression severity (r=.783, p<.001, n=51). Higher agreement between smartphone and stationary assessments was found in affective disorder patients as compared to healthy controls, and anxiety disorder patients. Highly comparable agreement between delivery formats was found across age and gender groups. Similarly, smartphone-based single-item self-ratings of mood correlated with BDI sum scores (r=-.538, p<.001, n=168), while smartphone-based single-item sleep duration correlated with the sleep item of the BDI (r=-.310, p<.001, n=166).The present findings demonstrate that smartphone-based monitoring of depressive symptoms via the ReMAP app provides valid assessments of depressive symptomatology and therefore represents a useful tool for prospective digital phenotyping in affective disorder patients in clinical and research applications.
Systematic Review and Meta-Analysis Identifies Significant Relationships Between Anxiety Disorders and Daytime Lower Urinary Tract Symptoms
Authors: Mahjani Behrang , Koskela Lotta Renström , Batuure Anita , Mahjani Christina Gustavsson , Janecka Magdalena , Hultman Christina M. , Reichenberg Abraham , Buxbaum Joseph D. , Akre Olof , Grice Dorothy E. 
Published: September 2020

AbstractBackgroundClinically, lower urinary tract symptoms (LUTS), such as voiding symptoms, overactive bladder, and interstitial cystitis, are associated with anxiety disorders. However, the existing evidence for the overlap of these conditions has not been systematically evaluated. The aim of this study was to examine this relationship.MethodsWe conducted a systematic review and meta-analysis to examine the relationship between LUTS and anxiety. We searched for articles published from January 1990 to July 2019 in PubMed, CENTRAL, PsycINFO, and Google Scholar. Outcomes were anxiety-related disorders and symptoms “clinical anxiety”) and subtypes of LUTS. We performed random-effect meta-analyses, and inspected funnel plots and applied the Egger’s test to evaluate publication bias. We followed PRISMA guidelines and recorded our protocol on PROSPERO (ID=CRD42019118607).ResultsWe identified 814 articles, of which 94 fulfilled inclusion criteria and 23 had sufficient data for meta-analysis. The odds ratio for clinical anxiety among individuals with LUTS was 2.87 (95% CI: 2.38,3.46, P < 0.001). Very few studies looked at LUTS among individuals ascertained for clinical anxiety, but there appear to be significantly elevated odds ratio here as well. A large I2value suggests high heterogeneity between studies.ConclusionsThe results demonstrate a clinically significant association between clinical anxiety and LUTS. There were limited data on youth, which should motivate further study in this area. Understanding the co-occurrence of these conditions will lead to better prevention and interventions to ameliorate the progression of the symptoms and to improve quality of life.
A Comparison of Covid-19 Patient Characteristics Before versus After Partial Lockdown in Vietnam
Authors: Vo Hoang-Long , Vu Kim-Duy 
Published: September 2020

AbstractBackgroundGiven the Covid-19’ sudden rapid spread in the community since 25 July 2020, an updated analysis of Covid-19 cases was conducted to examine the differences of characteristics of Covid-19 patients before versus after partial lockdown end in Vietnam.MethodsData of 569 Covid-19 patients confirmed SARS-CoV-2 infection from 23 January to 31 July was collected from available official databases. We divided Covid-19 situation timeline into two main periods, before lockdown end (23 January – 22 April) and after lockdown end (23 April – 31 July).ResultsWe found significant variations in the distribution of Covid-19 patients among different provinces between two periods. Covid-19 confirmed patients were older in the time after lockdown end compared to in the period before lockdown end by a median of 5 years. All discharged Covid-19 patients and no Covid-19 death were in the phase before lockdown, while post lockdown period had still remained significant patients being under treatment, especially reported first fatalities. The number of Covid-19 patients who returned from other countries (excluding China) slightly increased through two stages (p >0.05), partially showing that the continuous volume of people returning Vietnam from abroad during the Covid-19 epidemic.ConclusionsOur analysis indicated demographic and epidemiological disparity of Covid-19 patients before versus after loosening the national partial lockdown in Vietnam. It is important to suggest that, proactive efforts in Covid-19 control after partial lockdown end will be effective when the measures to closely control and monitor repatriation and immigration via the borders of Vietnam are strictly enforced.What is already known on this topicMost of Covid-19 confirmed patients in Vietnam were acquired overseas.In Vietnam, Covid-19 epidemic had the low estimated reproduction ratio (R0) and SARS-CoV-2 spread was on the downward trend before July 25.What this study addsCovid-19 confirmed patients were older in the time after lockdown end compared to in the period before lockdown end by a median of 5 years.All discharged Covid-19 patients and no Covid-19 death were in the phase before lockdown, while post lockdown period had still remained significant patients being under treatment, especially reported first fatalities.Continuous volume of people returning Vietnam from abroad through two stages during the Covid-19 epidemic.Our analysis might be considered as a prompt reference source for further in-depth surveys to understand the adaptive models of Covid-19 patients among different provinces.
CIP2A interacts with TopBP1 and is selectively essential for DNA damage-induced basal-like breast cancer tumorigenesis
Authors: Laine Anni , Nagelli Srikar G. , Farrington Caroline , Butt Umar , Cvrljevic Anna N. , Vainonen Julia P. , Feringa Femke M. , Grönroos Tove J. , Gautam Prson , Khan Sofia , Sihto Harri , Qiao Xi , Pavic Karolina , Connolly Denise C. , Kronqvist Pauliina , Elo Laura L. , Maurer Jochen , Wennerberg Krister , Medema Rene H. , Joensuu Heikki , Peuhu Emilia , de Visser Karin , Narla Goutham , Westermarck Jukka 
Published: September 2020

AbstractDespite saturated genetic profiling of breast cancers, oncogenic drivers for the clinically challenging basal-like breast cancer (BLBC) subtype are still poorly understood. Here, we demonstrate that CIP2A is selectively essential for DNA damage-induced initiation of mouse BLBC tumors, but not of other cancer types. Mechanistically, CIP2A was discovered genome-widely the closest functional homologue for DNA-damage proteins TopBP1, RHNO, POLQ, NBN and PARP1. CIP2A directly interacts with the ATR-activation domain of TopBP1, and dampens both, chromatin binding of TopBP1 and RAD51, and G2/M checkpoint in DNA-damaged cells. CIP2A also drives BLBC-associated proliferative MYC and E2F1 signaling. Consistently with high DNA-damage response activity BLBCs, and CIP2A’s novel role in checkpoint signaling, CIP2A was found essential for DNA-damaged, and BRCA-mutant BLBC cells. Selective role for CIP2A as BLBC driver was supported by association of high CIP2A expression with poor patient prognosis only in BLBC, but not in other breast cancer types. Therapeutically, small molecule reactivators of PP2A (SMAPs) phenocopy CIP2A-dependent DNA damage response, and inhibitin vivogrowth of patient-derived BLBC xenograft. In summary, we discover sub-type selective essential role for CIP2A in BLBC initiation and maintenance that can be explained by its newly discovered association with DNA-damage response, coordinated with regulation of proliferative signaling. The results also identify therapeutic strategy for CIP2A-dependent BLBCs.
Whole-exome imputation within UK Biobank powers rare coding variant association and fine-mapping analyses
Authors: Barton Alison R. , Sherman Maxwell A. , Mukamel Ronen E. , Loh Po-Ru 
Published: September 2020

ABSTRACTExome association studies to date have generally been underpowered to systematically evaluate the phenotypic impact of very rare coding variants. We leveraged extensive haplotype sharing between 49,960 exome-sequenced UK Biobank participants and the remainder of the cohort (total N~500K) to impute exome-wide variants at high accuracy (R2>0.5) down to minor allele frequency (MAF) ~0.00005. Association and fine-mapping analyses of 54 quantitative traits identified 1,189 significant associations (P<5 x 10-8) involving 675 distinct rare protein-altering variants (MAF<0.01) that passed stringent filters for likely causality; 600 of the 675 variants (89%) were not present in the NHGRI-EBI GWAS Catalog. We replicated the effect directions of 28 of 28 height-associated variants genotyped in previous exome array studies, including missense variants in newly-associated collagen genes COL16A1 and COL11A2. Across all traits, 49% of associations (578/1,189) occurred in genes with two or more hits; follow-up analyses of these genes identified long allelic series containing up to 45 distinct likely-causal variants within the same gene (on average exhibiting 93%-concordant effect directions). In particular, 24 rare coding variants in IFRD2 independently associated with reticulocyte indices, suggesting an important role of IFRD2 in red blood cell development, and 11 rare coding variants in NPR2 (a gene previously implicated in Mendelian skeletal disorders) exhibited intermediate-to-strong effects on height (0.18-1.09 s.d.). Our results demonstrate the utility of within-cohort imputation in population-scale GWAS cohorts, provide a catalog of likely-causal, large-effect coding variant associations, and foreshadow the insights that will be revealed as genetic biobank studies continue to grow.
healthcareCOVID: A national cross-sectional observational study identifying risk factors for developing suspected or confirmed COVID-19 in UK healthcare workers
Authors: Kua J , Patel R , Nurmi E , Tian S , Gill H , Wong DJN , Moorley C , Nepogodiev D , Ahmad I , El-Boghdadly K 
Published: September 2020

ABSTRACTObjectiveTo establish the prevalence and risk factors for the development of suspected or confirmed coronavirus disease 2019 (COVID-19) infection among healthcare workers (HCWs) in the United Kingdom (UK).DesignCross-sectional observational study.SettingUK-based primary and secondary care.ParticipantsHCWs aged ≥18 years working between 1 February and 25 May 2020.Main outcome measuresA composite endpoint of laboratory-confirmed diagnosis of SARS-CoV-2, or self-isolation or hospitalisation due to suspected or confirmed COVID-19.ResultsOf 6152 eligible responses, the composite endpoint was present in 1806 (29.4%) HCWs, of whom 49 (0.8%) were hospitalised, 459 (7.5%) tested positive for SARS-CoV-2, and 1776 (28.9%) reported self-isolation. The strongest risk factor associated with the presence of the primary composite endpoint was increasing frequency of contact with suspected or confirmed COVID-19 cases without adequate personal protective equipment (PPE): “Never” (reference), “Rarely” (adjusted odds ratio 1.06, (95% confidence interval: 0.87 to 1.29)), “Sometimes” (1.7 (1.37 to 2.10)), “Often” (1.84 (1.28 to 2.63)), “Always” (2.93, (1.75 to 5.06)). Additionally, several comorbidities (cancer, respiratory disease, and obesity); working in a ‘doctors’ role; using public transportation for work; regular contact with suspected or confirmed COVID-19 patients; and lack of PPE were also associated with the presence of the primary endpoint. 1382 (22.5%) HCWs reported lacking access to PPE items while having clinical contact with suspected or confirmed COVID-19 cases. Overall, between 11,870 and 21,158 days of self-isolation were required by the cohort, equalling approximately 71 to 127 working days lost per 1000 working days.ConclusionsSuspected or confirmed COVID-19 was more common in HCWs than in the general population. Risk factors included inadequate PPE, which was reported by nearly a quarter of HCWs. Governments and policymakers must ensure adequate PPE is available as well as developing strategies to mitigate risk for high-risk HCWs during future COVID-19 waves.
Do Lockdowns Bring about Additional Mortality Benefits or Costs? Evidence based on Death Records from 300 Million Chinese People
Authors: Qi Jinlei , Zhang Dandan , Zhang Xiang , Yin Peng , Liu Jiangmei , Pan Yuhang , Takana Tanakao , Xie Peiyu , Wang Zhaoguang , Liu Shuocen , Gao George F. , He Guojun , Zhou Maigeng 
Published: September 2020

AbstractAfter the COVID-19 outbreak, China immediately adopted stringent lockdown policies to contain the virus. Using comprehensive death records covering around 300 million Chinese people, we estimate the impacts of city and community lockdowns on non-COVID-19 mortality outside of Wuhan. Employing a difference-in-differences method, we find that lockdowns reduced the number of non-COVID-19 deaths by 4.9% (cardiovascular deaths by 6.2%, injuries by 9.2%, and non-COVID-19 pneumonia deaths by 14.3%). The health benefits are likely driven by significant reductions in air pollution, traffic, and human interactions. A back-of-the-envelope calculation shows that more than 32,000 lives could have been saved from non-COVID-19 diseases/causes during the 40 days of the lockdown on which we focus. The results suggest that the rapid and strict virus countermeasures not only effectively controlled the spread of COVID-19 but also brought about massive unintended public health benefits. These findings can help better inform policymakers around the world about the benefits and costs of city and community lockdowns policies in dealing with the COVID-19 pandemic.
Backward and Hopf bifurcation analysis of an SEIRS COVID-19 epidemic model with saturated incidence and saturated treatment response
Authors: Oluyori David A. , Pérez Ángel G. C. , Okhuese Victor A. , Akram Muhammad 
Published: September 2020

AbstractIn this work, we further the investigation of an SEIRS model to study the dynamics of the Coronavirus Disease 2019 pandemic. We derive the basic reproduction number R0 and study the local stability of the disease-free and endemic states. Since the condition R0 < 1 for our model does not determine if the disease will die out, we consider the backward bifurcation and Hopf bifurcation to understand the dynamics of the disease at the occurrence of a second wave and the kind of treatment measures needed to curtail it. Our results show that the limited availability of medical resources favours the emergence of complex dynamics that complicates the control of the outbreak.
Participatory syndromic surveillance as a tool for tracking COVID-19 in Bangladesh
Authors: Mahmud Ayesha S. , Chowdhury Shayan , Sojib Kawsar Hossain , Chowdhury Anir , Quader Md. Tanvir , Paul Sangita , Saidy Md. Sheikh , Uddin Ramiz , Engø-Monsen Kenth , Buckee Caroline 
Published: September 2020

AbstractLimitations in laboratory diagnostic capacity and reporting delays have hampered efforts to mitigate and control the ongoing coronavirus disease 2019 (COVID-19) pandemic globally. To augment traditional lab and hospital-based surveillance, Bangladesh established a participatory surveillance system for the public to self-report symptoms consistent with COVID-19 through multiple channels. Here, we report on the use of this system, which received over 3 million responses within two months, for tracking the COVID-19 outbreak in Bangladesh. Although we observe considerable noise in the data and initial volatility in the use of the different reporting mechanisms, the self-reported syndromic data exhibits a strong association with lab-confirmed cases at a local scale. Moreover, the syndromic data also suggests an earlier spread of the outbreak across Bangladesh than is evident from the confirmed case counts, consistent with predicted spread of the outbreak based on population mobility data. Our results highlight the usefulness of participatory syndromic surveillance for mapping disease burden generally, and particularly during the initial phases of an emerging outbreak.
GSTP1 positive prostatic adenocarcinomas are more common in Black than White men in the United States
Authors: Vidal Igor , Zheng Qizhi , Hicks Jessica L. , Chen Jiayu , Platz Elizabeth A. , Trock Bruce J. , Kulac Ibrahim , Baena-Del Valle Javier , Sfanos Karen S. , Ernst Sarah , Jones Tracy , Glavaris Stephanie , Nelson William G. , Yegnasubramanian Srinivasan , De Marzo Angelo M. 
Published: September 2020

AbstractGSTP1 is a member of the Glutathione-S-transferase (GSTS) family silenced by CpG island DNA hypermethylation in 90-95% of prostate cancers. However, prostate cancers expressing GSTP1 have not been well characterized. We used immunohistochemistry against GSTP1 to examine 1673 primary prostatic adenocarcinomas on TMAs with redundant sampling from the index tumor from prostatectomies. GSTP1 protein was positive in at least one TMA core in 7.7% of cases and in all TMA cores in 4.4% of cases. The percentage of adenocarcinomas from Black patients who had any GSTP1 positive TMA cores was 14.9%, which was 2.5 times higher than the percentage from White patients (5.9%; P < 0.001). Further, the percentages of tumors from Black patients who had all TMA spots positive for GSTP1 (9.5%) was 3-fold higher than the percentage from White patients (3.2%; P<0.001). The increased percentage of GSTP1 positive cases in Black men was present only in ERG positive cases. By in situ hybridization, GSTP1 mRNA expression was concordant with protein staining, supporting the lack of silencing of at least some GSTP1 alleles in GSTPI-positive tumor cells. This is the first report revealing that the GSTPI-positive prostate cancer subset is substantially over-represented among prostate cancers from Black compared to White men. This observation should prompt additional studies to determine whether GSTP1 positive cases represent a distinct molecular subtype of prostate cancer and whether GSTP1 expression could provide a biological underpinning for the observed disparate outcomes for Black men.
Microfluidic nano-scale qPCR enables ultra-sensitive detection of SARS-CoV-2
Authors: Xie Xin , Gjorgjieva Tamara , Attieh Zaynoun , Dieng Mame Massar , Arnoux Marc , Khair Mostafa , Moussa Yasmine , Al Jallaf Fatima , Rahiman Nabil , Jackson Christopher A. , Victoria Zyrone , Zafar Mohammed , Ali Raghib , Piano Fabio , Gunsalus Kristin C. , Idaghdour Youssef 
Published: September 2020

AbstractBackgroundA major challenge in controlling the COVID-19 pandemic is the high false-negative rate of the commonly used standard RT-PCR methods for SARS-CoV-2 detection in clinical samples. Accurate detection is particularly challenging in samples with low viral loads that are below the limit of detection (LoD) of standard one- or two-step RT-PCR methods.MethodsWe implement a three-step approach for SARS-CoV-2 detection and quantification that employs reverse transcription, targeted cDNA preamplification and nano-scale qPCR based on the Fluidigm 192.24 microfluidic chip. We validate the method using both positive controls and nasopharyngeal swab samples.ResultsUsing SARS-CoV-2 synthetic RNA and plasmid controls, we demonstrate that the addition of a preamplification step enhances the LoD of the Fluidigm method by 1,000-fold, enabling detection below 1 copy/μl. We applied this method to analyze 182 clinical NP swab samples previously diagnosed using a standard RT-qPCR protocol (91 positive, 91 negative) and demonstrate reproducible detection of SARS-CoV-2 over five orders of magnitude (< 1 to 106viral copies/μl). Crucially, we detect SARS-CoV-2 with relatively low viral load estimates (<1 to 40 viral copies/μl) in 17 samples with negative clinical diagnosis, indicating a potential false negative rate of 18.7% by clinical diagnostic procedures.ConclusionThe three-step nano-scale RT-qPCR method can robustly detect SARS-CoV-2 in samples with relatively low viral loads (< 1 viral copy/μl) and has the potential to reduce the false negative rate of standard RT-PCR-based diagnostic tests for SARS-CoV-2 and other viral infections.SummaryWe test, implement and report the results of a microfluidic RT-qPCR assay system involving sequential RT, preamplification and nano-scale qPCR that can robustly detect SARS-CoV-2 in clinical samples with viral loads less than 1 copy/ul.