bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrating epidemiological and clinical predictors of SARS-CoV-2 infection in students and school staff in the state of São Paulo
Authors: Quijano Fredi A. Diaz , da Silva José Mário Nunes , D’Agostini Tatiana Lang , de Camargo Jéssica Pires , de Moraes Nathalia Cristina Soares Franceschi , Haddad Ricardo , Pereira Maria Cecília Gomes , Covas Dimas Tadeu , de Paula Regiane A. Cardoso 
Published: June 2021

AbstractBackgroundThere is a great deal of uncertainty concerning which contexts would be safe for returning to school and about individual criteria that would reduce contact between the infected and susceptible people in the school setting. Therefore, the purpose of this study was to estimate the prevalence of infection by SARS-CoV-2 in students and school staff; and to identify predictors of infection, including both municipal epidemiological indicators and individual variables reported by the participants.MethodsThis was a virological survey carried out among students (over 14 years old) and school staff in São Paulo state, between epidemiological weeks 43 to 49 of the year 2020. A self-administrated questionnaire including sociodemographic and clinical information was applied. Moreover, a nasopharynx swab was performed for virological testing (RT-PCR). We evaluate the relationship of COVID-19 epidemiological indicators of the residence municipality with the odds of SARS-CoV-2 infection. For this, a composite index relating recent mortality and previous incidence (RM/PI) was proposed based on the ratio of deaths recorded in the second and third week counted back to the sum of cases during the previous seven weeks (weeks 4 to 10 counted back). We obtained a multiple model using random-effects logit regression integrating epidemiological indicators and individual variables.ResultsIn total, 3436 participants were included, residents of 72 municipalities. The overall prevalence of infection was 1.7% (95%CI: 1.3%-2.2%). SARS-CoV-2 infection was independently associated with loss of smell, a history of pulmonary disease, and a recent trip outside the municipality. Moreover, the RM/PI index consistently predicted the SARS-CoV-2 infection (adjusted OR: 1.45; 95%CI 1.02-2.04). Based on these associations, we proposed a classification in four groups with different SARS-Cov-2 infection prevalence (0.54%, 1.27%, 3.8%, and 4.13%).ConclusionEpidemiological and individual variables allowed classifying groups according to the infection probability in a school population of the state of São Paulo. This classification could help guide the return to classes in situations in which epidemiological control is evident, maintaining basic protection measures and increasing vaccination coverage.
Evaluation of the Panbio™ rapid antigen test for COVID-19 diagnosis in symptomatic health care workers
Authors: Bruins Marjan J. , dos Santos Claudy Oliveira , Spoelman-Lunsche Marjan , van den Bos-Kromhout Marieke I. , Debast Sylvia B. 
Published: June 2021

AbstractIf a health care workers (HCW) experiences COVID-19 associated symptoms, SARS-CoV-2 testing must be performed as soon as possible, to prevent transmission of the virus and to guarantee continuity of care. The gold standard for the detection of SARS-CoV-2, RT-PCR, has a high sensitivity but usually takes 6-8 hours. Lateral flow antigen assays take only 15-30 minutes and do not need any high tech equipment.In a prospective study of our hospital’s HCWs, we evaluated the sensitivity of the Panbio™ COVID-19 Ag Rapid Test (Abbott) against the molecular test Aptima™ SARS-CoV-2 Assay (Hologic) which uses Transcription Mediated Amplification (TMA). TMA positive samples were further subjected to a quantitative real-time SARS-CoV-2 PCR to obtain Ct values as an indication of the viral load.Of 1101 HCWs included in the study between November 2020 and February 2021, 84 (7.6%) were TMA positive, of which 48 (57.1%) were antigen test positive. Most false negative antigen test results occurred if the duration of symptoms had been ≤1 day or ≥7 days. Sensitivities for symptom onset of ≤1, 2 or 3 days were 47.1%, 63.0% and 66.7% respectively.The Panbio™ rapid test is fast and easy to perform, but is not a suitable SARS-CoV-2 test to confirm or exclude COVID-19 in HCWs with a very recent onset of symptoms.
Evaluating the role of common risk variation in the recurrence risk of schizophrenia in multiplex schizophrenia families
Authors: Ahangari Mohammad , Gentry Amanda E. ,   Irish Schizophrenia Genomics Consortium, Nguyen Tan-Hoang , Kirkpatrick Robert , Verrelli Brian C. , Bacanu Silviu-Alin , Kendler Kenneth S. , Webb Bradley T. , Riley Brien P. 
Published: June 2021

AbstractMultiplex families have higher recurrence risk of schizophrenia compared to the families of sporadic cases, but the source of this increased recurrence risk is unknown. We used schizophrenia genome-wide association study data (N=156,509) to construct polygenic risk scores (PRS) in 1,005 individuals from 257 multiplex schizophrenia families, 2,114 ancestry-matched sporadic cases, and 2,205 population controls, to evaluate whether increased PRS can explain the higher recurrence risk of schizophrenia in multiplex families compared to ancestry-matched sporadic cases. Using mixed-effects logistic regression with family structure modeled as a random effect, we show that SCZ PRS in familial cases does not differ significantly from sporadic cases either with, or without family history (FH) of psychotic disorders (All sporadic cases p = 0.92, FH+ cases p = 0.88, FH-cases p = 0.82). These results indicate that increased burden of common schizophrenia risk variation as indexed by current SCZ PRS, is unlikely to account for the higher recurrence risk of schizophrenia in multiplex families. In the absence of elevated PRS, segregation of rare risk variation or environmental influences unique to the families may explain the increased familial recurrence risk. These findings also further validate a genetically influenced psychosis spectrum, as shown by a continuous increase of common SCZ risk variation burden from unaffected relatives to schizophrenia cases in multiplex families. Finally, these results suggest that common risk variation loading are unlikely to be predictive of schizophrenia recurrence risk in the families of index probands, and additional components of genetic risk must be identified and included in order to improve recurrence risk prediction.
Unbiased sequencing of Mycobacterium tuberculosis urinary cell-free DNA reveals extremely short fragment lengths
Authors: Oreskovic Amy , Waalkes Adam , Holmes Elizabeth A. , Rosenthal Christopher A. , Wilson Douglas P.K. , Shapiro Adrienne E. , Drain Paul K. , Lutz Barry R. , Salipante Stephen J. 
Published: June 2021

ABSTRACTUrine cell-free DNA (cfDNA) presents an attractive target for diagnosing pulmonary Mycobacterium tuberculosis (TB) infection but has not been thoroughly characterized. Here, we aimed to investigate the size and composition of TB-derived urine cfDNA with minimal bias using next-generation DNA sequencing (NGS). To enable analysis of highly fragmented urine cfDNA, we used a combination of DNA extraction (Q sepharose) and single-stranded sequence library preparation methods demonstrated to recover short, highly degraded cfDNA fragments. We examined urine cfDNA from ten HIV-positive patients with confirmed pulmonary TB (nine of which had TB cfDNA detectable by qPCR) and two TB-negative controls. TB-derived cfDNA was identifiable by NGS from all TB-positive patients. TB urine cfDNA was significantly shorter than human urine cfDNA, with median fragment lengths of ≤19–52 bp and 42–92 bp, respectively. TB cfDNA abundance increased exponentially with decreased fragment length, with a peak fragment length of ≤19 bp in most samples. Our methodology also revealed a larger fraction of short human genomic cfDNA than previously reported, with peak fragment lengths of 29–53 bp. Urine cfDNA fragments spanned the TB genome with relative uniformity, but nucleic acids derived from multicopy elements were proportionately overrepresented, providing regions of inherent signal amplification beneficial for molecular diagnosis. This study demonstrates the potential of urine cfDNA as a diagnostic biomarker for TB and will inform improved design of TB urine cfDNA assays. Methods capable of targeting the shortest cfDNA fragments possible will be critical to maximize TB urine cfDNA detection sensitivity.
Prefrontal Cortex Definitions and Their Use in Distinguishing Pornography Addicted Juveniles
Authors: Prawiroharjo Pukovisa , Edison Rizki Edmi , Ellydar Hainah , Pratama Peter , Imelda Suaidy Sitti Evangeline , Amani Nya’ Zata , Carissima Diavitri , Hatta Ghina Faradisa 
Published: June 2021

ABSTRACTBackground and aimsIncreasing popularity of Internet has exposed our children pornography addiction. As in other types of addiction, it affects a brain region known as prefrontal cortex (PFC), which is important in executive functions and inhibitory control. However, this region was loosely defined, and there was no consensus for that definition. We aimed to use volumetric MRI in finding the defining region of PFC which would be suitable in distinguishing pornography addicted juveniles.MethodsWe enrolled 30 juveniles (12-16 y.o.) consisting of 15 pornography addiction and 15 non-addiction subjects. We proposed several models of PFC definition from mix-and-matched subregions, consisting of orbitofrontal (OFC), inferior frontal gyrus (IFG; pars orbitalis, opercularis, and triangularis), dorsolateral PFC (DLPFC), and anterior cingulate (ACC). Suitable PFC definition was defined as models which volume statistically different between both groups. Brain volumetric was measured using 3D-T1 3T MRI images and analyzed using FreeSurfer® for automatic cortical reconstruction and brain segmentation (recon-all command).ResultsWe found significant differences between groups in 6 models, which mainly included OFC, ACC, and DLPFC, with models devoid of DLPFC had lowest mean differences.ConclusionThe most suitable definition of PFC for pornography addiction study should consist of OFC, ACC, and especially DLPFC. Inferior frontal gyrus pars orbitalis was not necessary for this purpose, but may increase effect size if it is included.
Into the thirteenth Month: A Case Study on the Outbreak Analytics and Modeling the spread of SARS-CoV-2 Infection in Pune City, India
Authors: Monteiro Joy , Pujari Bhalchandra , Bhattacharrya Sarika Maitra , Raghunathan Anu , Keskar Ashwini , Shaikh Arsh , Bogam Prasad , Kadu Shweta , Raut Nikita , Vavale Devendra , Mishra Rupa , Kembhavi Ajit , Shashidhara L.S. , Mave Vidya 
Published: June 2021

AbstractWith more than 140 million people infected globally and 3 million deaths, the COVID 19 pandemic has left a lasting impact. A modern response to a pandemic of such proportions needs to focus on exploiting all available data to inform the response in real-time and allow evidence-based decision-making. The intermittent lockdowns in the last 13 months have created economic adversity to prevent anticipated large-scale mortality and relax the lockdowns have been an attempt at recovering and balancing economic needs and public health realities. This article is a comprehensive case study of the outbreak in the city limits of Pune, Maharashtra, India, to understand the evolution of the disease and transmission dynamics starting from the first case on March 9, 2020. A unique collaborative effort between the Pune Municipal Corporation (PMC), a government entity, and the Pune knowledge Cluster (PKC) allowed us to layout a context for outbreak response and intervention. We report here how access to granular data for a metropolitan city with pockets of very high-density populations will help analyze, in real-time, the dynamics of the pandemic and forecasts for better management and control of SARS-CoV-2. Outbreak data analytics resulted in a real-time data visualization dashboard for accurate information dissemination for public access on the epidemic’s progress. As government agencies craft testing and vaccination policies and implement intervention strategies to mitigate a second wave, our case study underscores the criticality of data quality and analytics to decode community transmission of COVID-19.
Association between SARS-Cov-2 infection during pregnancy and adverse pregnancy outcomes: a re-analysis of data from Wei et al. (2021)
Authors: Ludwig Serge Aho Glele , Simon Emmanuel , Bouit Camille , Serrand Maeva , Filipuzzi Laurence , Astruc Karine , Kadhel Philippe , Sagot Paul 
Published: June 2021

AbstractBackgroundWei et al. have published a meta-analysis (MA) which aimed to “evaluate the association between SARS-CoV-2 infection during pregnancy and adverse pregnancy outcomes”.Using classical random-effects model, they found that SARS-CoV-2 infection was associated with preeclampsia, preterm birth and stillbirth.Performing MA with low event rates or with few studies may be challenging as MA relies on several within and between study distributional assumptions.Methodsto assess the robustness of the results provided by Wei et al., we performed a sensitivity analysis using several frequentist and Bayesian meta-analysis methods. We also estimated fragility indexes.ResultsFor eclampsia (patients with Covid-19 vs without), the confidence intervals of most frequentist models contain 1. All beta-binomial models (Bayesian) lead to credible intervals containing 1. The prediction interval, based on DL method ranges from 0.75 to 2.38. The fragility index is 2 for the DL method.For preterm, the confidence (credible) intervals exclude 1. The prediction interval is broad, ranging from 0.84 to 20.61. The fragility index ranges from 27 to 10.For stillbirth, the confidence intervals of most frequentist models contain 1. Six Bayesian MA models lead to credible intervals containing 1.The prediction interval ranges from 0.52 to 8.49. The fragility index is 3.InterpretationGiven the available data and the results of our broad sensitivity analysis, we can only suggest that SARS-CoV-2 infection during pregnancy is associated to preterm, and may be associated to preeclampsia. For stillbirth, more data are needed as none of the Bayesian analyses are conclusive.
GRADING prognostic factors for severe and recurrentClostridioides difficileinfection: expected and unexpected findings. A systematic review
Authors: van Rossen Tessel M. , Ooijevaar Rogier E. , Vandenbroucke-Grauls Christina M.J.E. , Dekkers Olaf M. , Kuijper Ed. J. , Keller Josbert J. , van Prehn Joffrey 
Published: June 2021

AbstractBackgroundClostridioides difficileinfection (CDI), its subsequent recurrences (rCDI), and severe CDI (sCDI) provide a significant burden for both patients and the healthcare system. Treatment consists of oral antibiotics. Fidaxomicin, bezlotoxumab and fecal microbiota transplantion (FMT) reduce the number of recurrences compared to vancomycin, but are more costly. Identifying patients diagnosed with initial CDI who are at increased risk of developing sCDI/rCDI could lead to more cost-effective therapeutic choices.ObjectivesIn this systematic review we aimed to identify clinical prognostic factors associated with an increased risk of developing sCDI or rCDI.MethodsPubMed, Embase, Emcare, Web of Science and COCHRANE Library databases were searched from database inception through March, 2021. Study selection was performed by two independent reviewers on the basis of predefined selection criteria; conflicts were resolved by consensus. Cohort and case-control studies providing an analysis of clinical or laboratory data to predict sCDI/rCDI in patients ≥18 years diagnosed with CDI, were included. Risk of bias was assessed with the Quality in Prognostic Research (QUIPS) tool and the quality of evidence by the Grading of Recommendations Assessment, Development and Evaluation (GRADE) tool, modified for prognostic studies. Overview tables of prognostic factors were constructed to assess the number of studies and the respective direction of an association (positive, negative, or no association).Results and conclusions136 studies were included for final analysis. Higher age and the presence of multiple comorbidities were prognostic factors for sCDI. Identified risk factors for rCDI were higher age, healthcare-associated CDI, prior hospitalization, PPIs started during/after CDI diagnosis and previous rCDI. Some variables that were found as risk factors for sCDI/rCDI in previous reviews were not confirmed in the current review, which can be attributed to differences in methodology. Risk stratification for sCDI/rCDI may contribute to a more personalized and optimal treatment for patients with CDI.
Can Auxiliary Indicators Improve COVID-19 Forecasting and Hotspot Prediction?
Authors: McDonald Daniel J. , Bien Jacob , Green Alden , Hu Addison J. , DeFries Nat , Hyun Sangwon , Oliveira Natalia L. , Sharpnack James , Tang Jingjing , Tibshirani Robert , Ventura Valérie , Wasserman Larry , Tibshirani Ryan J. 
Published: June 2021

AbstractShort-term forecasts of traditional streams from public health reporting (such as cases, hospitalizations, and deaths) are a key input to public health decision-making during a pandemic. Since early 2020, our research group has worked with data partners to collect, curate, and make publicly available numerous real-time COVID-19 indicators, providing multiple views of pandemic activity in the U.S. This paper studies the utility of five such indicators—derived from de-identified medical insurance claims, self-reported symptoms from online surveys, and COVID-related Google search activity—from a forecasting perspective. For each indicator, we ask whether its inclusion in an autoregressive (AR) model leads to improved predictive accuracy relative to the same model excluding it. Such an AR model, without external features, is already competitive with many top COVID-19 forecasting models in use today. Our analysis reveals that (a) inclusion of each of these five indicators improves on the overall predictive accuracy of the AR model; (b) predictive gains are in general most pronounced during times in which COVID cases are trending in “flat” or “down” directions; (c) one indicator, based on Google searches, seems to be particularly helpful during “up” trends.
Pembrolizumab and Decitabine for Refractory or Relapsed Acute Myeloid Leukemia
Authors: Goswami Meghali , Gui Gege , Dillon Laura W. , Lindblad Katherine E. , Thompson Julie , Valdez Janet , Kim Dong-Yun , Ghannam Jack Y. , Oetjen Karolyn A. , Destefano Christin B. , Smith Dana M. , Tekleab Hanna , Li Yuesheng , Dagur Pradeep K. , Hughes Thomas , Marte Jennifer L. , del Rivero Jaydira , Klubo-Gwiezdzinksa Joanna , Gulley James L. , Calvo Katherine R. , Lai Catherine , Hourigan Christopher S. 
Published: June 2021

AbstractThe powerful “graft versus leukemia” effect thought partly responsible for the therapeutic effect of allogeneic hematopoietic cell transplantation in acute myeloid leukemia (AML) provides rationale for investigation of immune-based therapies in this high-risk blood cancer. There is considerable pre-clinical evidence for potential synergy between PD-1 immune checkpoint blockade and the hypomethylating agents already commonly used for this disease. We report here the results of 17-H-0026 (PD-AML, NCT02996474), an investigator sponsored, single-institution, single-arm open-label ten-subject pilot study to test the feasibility of the first-in-human combination of pembrolizumab and decitabine in adult patients with refractory or relapsed AML (R-AML). In this cohort of previously treated patients, this novel combination of anti-PD-1 and hypomethylating therapy was feasible and associated with a best response of stable disease or better in 6 of 10 patients. Considerable immunological changes were identified using TCRβ sequencing as well as single-cell immunophenotypic and RNA expression analyses on sorted CD3+ T cells in patients who developed immune-related adverse events (irAEs) during treatment. Clonal T cell expansions occurred at irAE onset; single-cell sequencing demonstrated that these expanded clones were predominately CD8+ effector memory T cells with high cell surface PD-1 expression and transcriptional profiles indicative of activation and cytotoxicity. In contrast, no such distinctive immune changes were detectable in those experiencing a measurable anti-leukemic response during treatment. Addition of pembrolizumab to ten-day decitabine therapy was clinically feasible in patients with R-AML, with immunological changes from PD-1 blockade observed in patients experiencing irAEs.One Sentence SummaryAML patients receiving a novel combination of a PD-1 immune checkpoint inhibitor with a hypomethylating agent demonstrated clear evidence of induced immunological responses in those developing autoimmune toxicity during treatment but not in those demonstrating an anti-leukemic response.
Averting an outbreak of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in a university residence hall through wastewater surveillance
Authors: Corchis-Scott Ryland , Geng Qiudi , Seth Rajesh , Ray Rajan , Beg Mohsan , Biswas Nihar , Charron Lynn , Drouillard Kenneth D. , D’Souza Ramsey , Heath Daniel D. , Houser Chris , Lawal Felicia , McGinlay James , Menard Sherri Lynne , Porter Lisa A. , Rawlings Diane , Tong Yufeng , Scholl Matthew L. , Siu K.W. Michael , Weisener Christopher G. , Wilhelm Steven. W. , McKay R. Michael L. 
Published: June 2021

AbstractA wastewater surveillance program targeting a university residence hall was implemented during the spring semester 2021 as a proactive measure to avoid an outbreak of COVID-19 on campus. Over a period of 7 weeks from early February through late March 2021, wastewater originating from the residence hall was collected as grab samples 3 times per week. During this time, there was no detection of SARS-CoV-2 by RT-qPCR in the residence hall wastewater stream. Aiming to obtain a sample more representative of the residence hall community, a decision was made to use passive samplers beginning in late March onwards. Adopting a Moore Swab approach, SARS-CoV-2 was detected in wastewater samples on just two days after passive samplers were activated. These samples were also positive for the B.1.1.7 (Alpha) Variant of Concern (VOC) by RT-qPCR. The positive result triggered a public health case finding response including a mobile testing unit deployed to the residence hall the following day with testing of nearly 200 students and staff, which identified two laboratory-confirmed cases of B.1.1.7 variant COVID-19. These individuals were re-located to a separate quarantine facility averting an outbreak on campus. Aggregating wastewater and clinical data, the campus wastewater surveillance program has yielded the first estimates of fecal shedding rates of the B.1.1.7 VOC of SARS-CoV-2 in individuals from a non-clinical setting.