bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparing fatal child abuse involving biological and surrogate parents
Authors: Presser Maxwell J. , Quiroz Hallie J. , Perez Eduardo A. , Sola Juan E. , Namias Nicholas , Thorson Chad M. 
Published: August 2021

BACKGROUND
Nearly half of pediatric homicides younger than 5 years are attributable to child abuse. Parents are most commonly the perpetrators, but less is known about incidents involving biological versus surrogate parents. We sought to evaluate the characteristics of fatal child abuse involving biological and surrogate parents using the Georgia National Violent Death Reporting System, which we believe may differ in demographics and incident characteristics.

METHODS
This database was used to examine all homicides of children younger than 18 years from 2011 to 2017. Demographics and incident characteristics were analyzed using the existing National Violent Death Reporting System variables and incident narratives. Nonparametric and χ2 tests were used to compare fatal child abuse incidents involving biological and surrogate parents (e.g., adoptive, foster, step-parents, intimate partners of biological parent).

RESULTS
There were 452 pediatric homicides and 219 cases of fatal child abuse. Of all cases of fatal child abuse, 60% involved biological and 29% involved surrogate parents. Compared with children killed by biological parents, children killed by surrogate parents were older (4 vs. 3 years), more often male (71% vs. 51%), more likely to survive the initial injury and present to the emergency department before death (96% vs. 69%), and less likely to have a medical comorbidity (2% vs. 11%; all p < 0.05). Surrogate parents were more likely to be male (90% vs. 48%) and use a firearm (20% vs. 13%) to inflict the injury, both p < 0.05. The race/ethnicity of the child was not associated with the parent’s relationship.

CONCLUSION
Child abuse accounts for half of all pediatric homicides. Parents are the most common perpetrators of fatal child abuse, but surrogate parent perpetrators are almost exclusively male and more likely to use firearms. Most children have a history of abuse, leaving an opportunity to intervene on potentially preventable deaths if abuse is identified in a timely fashion.

LEVEL OF EVIDENCE
Prognostic and Epidemiologic, Level III
Emulating an RCT in observational research in chest trauma: The target trial approach
Authors: Cocco Annelise M. , Jennings Fiona L. , Lockwood David 
Published: August 2021

BACKGROUND
While the concept of a “target trial”—optimizing the quality of observational studies by attempting to emulate the ideal world conditions of a randomized controlled trial—was first expounded over a decade ago, the take up of this concept in the design and analysis of trials in trauma is lacking. The target trial approach avoids common errors in observational research to increase its scientific validity as well as potentially enable causal questions to be answered without the expense and intricacies of a randomized controlled trial. This review article briefly introduces the reader to the concepts and utility of a “target trial” approach before providing demonstrations of its application in the subject area of chest trauma.

METHODS
Four articles published in the last 5 years—two case control and two cohort studies—are chosen and considered in terms of their causal question; study population; inclusion and exclusion criteria; designation of time 0; clarity of the follow-up period; study outcomes; methods to minimize confounding; results; overall issues regarding study time; and the presence of avoidable errors such as introduction of immortal time bias or information bias.

RESULTS
Two of the studies had an unclear causal question; none of the studies designated a time 0; the follow-up period was unclear for all but one of the studies; and one study had a serious issue with information bias resulting from differential misclassification.

CONCLUSION
Failure to emulate a “target trial” framework may lead to serious methodologic issues in observational research. Expansion of the awareness of this approach in trauma literature will improve the quality of our observational research and potentially translate into significant benefits for our patients.
Injection Drug use Practices and HIV infection among People Who Inject Drugs in Kigali, Rwanda
Authors: Twahirwa Rwema Jean Olivier , Nizeyimana Vianney , Menezes Neia Prata , Okonkwo Nneoma E. , Mazzei Amelia Aibina , Muhirwa Sulemani , Rukundo Athanase , Lucas Lisa , Niyigena Audace , Makuza Jean Damascene , Beyrer Chris , Baral Stefan D. , Kagaba Aflodis 
Published: August 2021

AbstractBackgroundIn Rwanda, epidemiological data characterizing people who inject drugs (PWID) and their burden of HIV are limited. We examined injecting drug use (IDU) history, practices, and HIV infection in a sample of PWID in Kigali.MethodsFrom October 2019–February 2020, 322 PWID aged ≥18 were enrolled in a cross-sectional study using convenience sampling in Kigali. Participants underwent a structured interview and HIV testing. We used Poisson regression with robust variance estimation to assess IDU practices associated with HIV infection.ResultsThe median age was 28 years(IQR:24-31) and 81%(248) were male. The median age at first injection was 23 years (IQR:20-27). HIV prevalence was 9.5%(95%CI:8.7-9.3).In the six months preceding the study, heroin was the primary drug of choice for 99%(303); but cocaine and methamphetamine were also reported by 10%(31) and 4%(12) respectively. Furthermore, 31%(94) and 33%(103) of participants, shared or reused needles in the previous six months, respectively. Up to 43%(133) knew someone who died from a drug-related overdose. PWID reporting sharing needles at least half the time in the previous six months had increased likelihood of HIV-infection, compared to those who did not (aPR: 2.67; 95%CI:1.23–5.78).ConclusionHIV infection was common in this sample of PWID in Kigali. The high prevalence of needle reuse and sharing practices highlight significant risk for onward transmission and acquisition of HIV and hepatitis B and C. PWID-focused harm reduction services, including needle and syringe programs, safer injection education, naloxone distribution, and substance use disorder treatment programs, are needed in Rwanda.
Automated ELISA on-chip for the detection of anti-SARS-CoV-2 antibodies
Authors: González-González Everardo , Garcia-Ramirez Ricardo , Díaz-Armas Gladys Guadalupe , Esparza Miguel , Aguilar-Avelar Carlos , Flores-Contreras Elda A. , Rodríguez-Sánchez Irám Pablo , Delgado-Balderas Jesús Rolando , Soto-García Brenda , Aráiz-Hernández Diana , Abarca-Blanco Marisol , León José R.Yee-de , Velarde-Calvillo Liza P. , Abarca-Blanco Alejandro , León Juan F. Yee-de 
Published: August 2021

AbstractThe COVID-19 pandemic has been the most critical public health issue in modern his-tory due to its highly infectious and deathly potential; and the limited access to massive, low-cost, and reliable testing has significantly worsened the crisis. The recovery and the vaccination of millions of people against COVID-19, have made serological tests highly relevant to identify the presence and levels of SARS-CoV-2 antibodies. Due to its advantages, microfluidic-based technologies represent an attractive alternative to the conventional testing methodologies used for these purposes. In this work, we describe the development of an automated ELISA on-chip capable of detecting anti-SARS-CoV-2 antibodies in serum samples from COVID-19 patients and vaccinated individuals. The colorimetric reactions were analyzed with a microplate reader. No statistically significant differences were observed when comparing the results of our automated ELISA on-chip against the ones obtained from a traditional ELISA on a microplate. Moreover, we demonstrated that it is possible to carry out the analysis of the colorimetric reaction by performing basic image analysis of photos taken with a smartphone, which constitutes a useful alternative when lacking specialized equipment or a laboratory setting. Our automated ELISA on-chip has the potential to be used in a clinical setting and mitigate some of the burden caused by testing deficiencies.
Breastfeeding Practices Among Mothers During COVID-19 in India
Authors: Akinola Ajoke Akinola , Simon N. H. , Mohamed Nasteha Abdikadir 
Published: August 2021

AbstractIntroductionThe Covid-19 pandemic is disrupting normal life globally. The COVID-19 pandemic is an emerging concern regarding the potential effects during breastfeeding. The aim of this study was to conduct a systemic review of mother-to -child transmission of COVID-19 during breastfeeding.MethodThis study systematically searched electronic databases; google scholar, PubMed, Medline, up December 2020. The study was included studies relevant to transmission breast milk and respiratory droplets during breastfeeding of mothers with COVID-19 positive. To identify the quality of data, prism standard was used and Strobe checklist scale.ResultA total of 3160 records were identified in this systemic review with eight relevant studies involving 159 mothers (63 mothers with COVID-19 positive, 55 of their breast milk samples tested negative for the-Covid-19. Twenty-one breast milk samples from 8 women tested positive for Covid-19. Of 73 infants were born to mothers with COVID-19 at the time of delivery. Two infants tested positive for Covid-19. The average mother-child separation time was 36•7 ± 21•1 days among mothers confirmed with COVID-19. Out of 22 mothers, ((37.5%) chose to breastfeed their babies after confirm covid-19 positive.ConclusionThis study shown that breastfeeding practices were extremely impacted during the COVID-19 epidemic among both confirmed positive cases and suspected mothers. However, the risk of mother-to-infant transmission of Covid-19 vertically or horizontally, in the perinatal period is very low.
BCL6-dependent TCF-1+ progenitor cells maintain effector and helper CD4 T cell responses to persistent antigen
Authors: Xia Yu , Sandor Katalin , Pai Joy A. , Daniel Bence , Raju Saravanan , Wu Renee , Hsiung Sunnie , Qi Yanyan , Yangdon Tenzin , Okamoto Mariko , Schreiber Robert D. , Murphy Kenneth M. , Satpathy Ansuman T. , Egawa Takeshi 
Published: August 2021

SummaryShortly after priming, the fate of activated CD4 T cells is segregated into BCL6+ follicular helper T (Tfh) and BCL6− effector (Teff) cells. However, it remains unknown how these subsets are sustained in the presence of chronic antigen stimulation. Using a combination of single cell- and population-based approaches, we show that in chronic viral infection, activated CD4 T cells differentiate into BCL6-dependent TCF-1+ progenitor cells with superior capacity to expand and give rise to both Teff and Tfh. They share properties with progenitor-exhausted CD8 T cells and are required for the continued generation of Teff cells as antigen persists. In response to tumors, an analogous CD4 T cell population develops in draining lymph nodes. Our study reveals the heterogeneity and plasticity of CD4 T cells upon encountering persistent antigen and highlights their population dynamics through a stable bipotent intermediate state.
Evaluation of a high-throughput deorphanization strategy to identify cytochrome p450s important for odor degradation inDrosophila
Authors: Baldwin Shane R. , Mohapatra Pratyajit , Nagalla Monica , Sindvani Rhea , Amaya Desiree , Dickson Hope A. , Menuz Karen 
Published: August 2021

AbstractMembers of the cytochrome p450 (CYP) enzyme family are abundantly expressed in insect olfactory tissues, where they are thought to act as Odorant Degrading Enzymes (ODEs). However, their contribution to olfactory signalingin vivois poorly understood. This is due in part to the challenge of identifying which of the dozens of antennal-expressed CYPs might inactivate a given odorant. Here, we tested a high-throughput deorphanization strategy inDrosophilato identify CYPs that are transcriptionally induced by exposure to a plant volatile. We discovered three CYPs selectively upregulated by the odorant using transcriptional profiling. Although these CYPs are shown to be broadly expressed in the antenna in non-neuronal cells, electrophysiological recordings from CYP mutants did not reveal any changes in olfactory neuron responses to the odorant. Neurons were desensitized by pre-exposing flies to the odorant, but this effect was similar in CYP mutants. Together, our data suggest that this transcriptomic approach may not be useful for identifying CYPs that contribute to olfactory signaling. We go on to show that some CYPs have highly restricted expression patterns in the antenna, and suggest that such CYPs may be useful candidates for further studies on olfactory CYP function.
Immunohistochemical assays for bladder cancer molecular subtyping: Optimizing parsimony and performance using Lund taxonomy
Authors: Hardy Céline , Ghaedi Hamid , Slotman Ava , Sjödahl Gottfrid , Gooding Robert J. , Berman David M. , Jackson Chelsea L. 
Published: August 2021

AbstractTranscriptomic and proteomic profiling reliably classifies bladder cancers into luminal and basal molecular subtypes. Based on their prognostic and predictive associations, these subtypes may improve clinical management of bladder cancers. However, the complexity of published subtyping algorithms has limited their translation into practice. Here we optimize and validate compact subtyping algorithms based on the Lund taxonomy. We reanalyzed immunohistochemistry (IHC) expression data of muscle-invasive bladder cancer samples from Lund 2017 (n=193) and 2012 (n=76) cohorts. We characterized and quantified IHC expression patterns, and determined the simplest, most accurate decision tree models to identify subtypes. We tested the utility of a previously published algorithm using routine antibody assays commonly available in surgical pathology laboratories (GATA3, KRT5 and p16) to identify basal/luminal subtypes and to distinguish between luminal subtypes, Urothelial-Like (Uro) and Genomically Unstable (GU). We determined the dominant decision tree classifiers using four-fold cross-validation with separate uniformly distributed train (75%) and validation (25%) sets. Using the three-antibody algorithm resulted in 86-95% accuracy across training and validation sets for identifying basal/luminal subtypes, and 67-86% accuracy for basal/Uro/GU subtypes. Although antibody assays for KRT14 and RB1 are not routinely used in pathology practice, these features achieved the simplest and most accurate models to identify basal/luminal and Uro/GU/basal subtypes, achieving 93-96% and 85-86% accuracies, respectively. When translated to a more complex model using eight antibody assays, accuracy was comparable to simplified models, with 86% (train) and 82% (validation). We conclude that a simple immunohistochemical classifier can accurately identify luminal (Uro, GU) and basal subtypes and pave the way for clinical implementation.
Quantification of live cell membrane compartmentalization with high-speed single lipid tracking through interferometric Scattering Microscopy
Authors: Reina Francesco , Eggeling Christian , Lagerholm B. Christoffer 
Published: August 2021

AbstractThe specific details of the lateral diffusion dynamics in cellular plasma membrane are an open topic in modern biophysics. Many studies have documented several different behaviours, including free (Brownian) motion, confined diffusion, transiently confined (hop) diffusion, anomalous diffusion, and combinations thereof. Here we have employed Interferometric Scattering Microscopy (ISCAT) to explore the lateral diffusion dynamics in the plasma membrane of living cells of a biotinylated lipid analogue that had been labelled with streptavidin-coated gold nanoparticles (20 and 40nm in diameter) at a sampling rate of 2kHz. The data was analysed with an unbiased statistics-driven mean squared displacement analysis pipeline that was designed to identify both the most likely diffusion mode for a specific data set, and the best fit parameters of the most likely model. We found that the prevalent diffusion mode of the tracked lipids, independent of the particle size, is compartmentalized diffusion, although the use of the larger tags resulted in tighter confinement and reduced diffusion rates. Through our analysis and comparison with simulated data, we quantify significant physical parameters, such as average compartment size, dynamic localization uncertainty, and the diffusion rates. We hereby further demonstrate the use of a confinement strength metric that makes it possible to compare diffusivity measurements across techniques and experimental conditions.Statement of SignificanceThis work offers new details on the data analysis of lipid diffusion on cellular membranes in vitro, through Interferometric Scattering microscopy. With this technique, we performed single particle tracking (SPT) experiments at 2kHz sampling rate. We analyzed the data through an unbiased statistics-driven protocol. The data shows that the diffusion motion of the tracked lipids follows mainly the “hopping” diffusion behaviour, whereby transient confinement zones hinder the particle dynamics. Matching the experimental data with diffusion simulations, we have been able to verify the physical parameters inferred by the experimental data analysis. Finally, we showcase a framework to compare SPT data with other techniques, to offer a complete overview of plasma membrane dynamics.
The Global Virome in One Network (VIRION): an atlas of vertebrate-virus associations
Authors: Carlson Colin J. , Gibb Rory J. , Albery Gregory F. , Brierley Liam , Connor Ryan P. , Dallas Tad A. , Eskew Evan A. , Fagre Anna C. , Farrell Maxwell J. , Frank Hannah K. , Muylaert Renata L. , Poisot Timothée , Rasmussen Angela L. , Ryan Sadie J. , Seifert Stephanie N. 
Published: August 2021

AbstractData cataloguing viral diversity on Earth have been fragmented across sources, disciplines, formats, and various degrees of open collation, posing challenges for research on macroecology, evolution, and public health. Here, we solve this problem by establishing a dynamically-maintained database of vertebrate-virus associations, called The Global Virome in One Network (VIRION). The VIRION database has been assembled through both reconciliation of static datasets and integration of dynamically-updated databases. These data sources are all harmonized against one taxonomic backbone, including metadata on host and virus taxonomic validity and higher classification; additional metadata on sampling methodology and evidence strength are also available in a harmonized format. In total, the VIRION database is the largest open-source, open-access database of its kind, with roughly half a million unique records that include 9,521 resolved virus “species” (of which 1,661 are ICTV ratified), 3,692 resolved vertebrate host species, and 23,147 unique interactions between taxonomically-valid organisms. Together, these data cover roughly a quarter of mammal diversity, a tenth of bird diversity, and ~6% of the estimated total diversity of vertebrates, and a much larger proportion of their virome than any previous database. We show how these data can be used to test hypotheses about microbiology, ecology, and evolution, and make suggestions for best practices that address the unique mix of evidence that coexists in these data.
SARS-CoV-2 Breakthrough Infections among the Healthcare Workers Post-Vaccination with ChAdOx1 nCoV-19 Vaccine in the South Indian State of Kerala
Authors: Issac Aleena , Kochuparambil Jose J , Elizabeth Linu 
Published: August 2021

AbstractObjectiveThe national COVID-19 vaccination campaigns in India, prioritized healthcare workers to be vaccinated with ChAdOx1 nCoV-19 (AZD1222). So, we aimed to ascertain the effectiveness of ChAdOx1 nCoV-19 vaccine among the healthcare workers by characterizing the breakthrough infections which occurred 14 days after the second dose of the vaccine.MethodsWe prospectively evaluated the ‘Institutional Covid Vaccination Database’ to categorize the SARS-CoV-2 positive healthcare workers into 2 cohorts: infected vaccinated and infected unvaccinated cohort. Along with comparing the descriptive statistics of the cohorts, the relative risk (RR), relative risk reduction (RRR), and the vaccine effectiveness were calculated. The study population was compared for the significant difference by using the parametric model (binary logistic regression) for the Odds ratio and the non-parametric model (cox proportionality model) for the Hazard ratio.ResultsOut of the 324 healthcare workers employed in our institution 243 (75%) were vaccinated. When 6.58% (16) of the vaccinated healthcare workers were tested positive, 43.75% (35) were infected in the unvaccinated cohort and the median time of infection in the vaccinated cohort was 65 days (range 20 -91 days). While the cox proportionality model reveals that the age, sex, and the contact exposure status of the cohort are not significant factors for getting infected after being vaccinated, binary logistic regression proves that a significant relationship exists between the incidence of infection and the unvaccinated status (p = 0.001, OR = 4.278). Completing the two-dose of vaccination decreased the hazard of testing positive for the SARS-CoV-2 by 84.96 % when compared with the unvaccinated individuals, which is the effectiveness of the ChAdOx1 nCoV-19 vaccine.ConclusionThere is an increased risk of the third wave of COVID-19 infection in the upcoming months. So, primary infection control measures should be followed even if vaccinated, to prevent the risk of breakthrough infections.
Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters
Authors: Gallego-García Pilar , Varela Nair , Estévez-Gómez Nuria , De Chiara Loretta , Fernández-Silva Iria , Valverde Diana , Sapoval Nicolae , Treangen Todd , Regueiro Benito , Cabrera-Alvargonzález Jorge Julio , del Campo Víctor , Pérez Sonia , Posada David 
Published: August 2021

AbstractA detailed understanding of how and when SARS-CoV-2 transmission occurs is crucial for designing effective prevention measures. Other than contact tracing, genome sequencing provides information to help infer who infected whom. However, the effectiveness of the genomic approach in this context depends on both (high enough) mutation and (low enough) transmission rates. Today, the level of resolution that we can obtain when describing SARS-CoV-2 outbreaks using just genomic information alone remains unclear. In order to answer this question, we sequenced 49 SARS-CoV-2 patient samples from ten local clusters for which partial epidemiological information was available, and inferred transmission history using genomic variants. Importantly, we obtained high-quality genomic data, sequencing each sample twice and using unique barcodes to exclude cross-sample contamination. Phylogenetic and cluster analyses showed that consensus genomes were generally sufficient to discriminate among independent transmission clusters. However, levels of intrahost variation were low, which prevented in most cases the unambiguous identification of direct transmission events. After filtering out recurrent variants across clusters, the genomic data were generally compatible with the epidemiological information but did not support specific transmission events over possible alternatives. We estimated the effective transmission bottleneck size to be 1-2 viral particles for sample pairs whose donor-recipient relationship was likely. Our analyses suggest that intrahost genomic variation in SARS-CoV-2 might be generally limited and that homoplasy and recurrent errors complicate identifying shared intrahost variants. Reliable reconstruction of direct SARS-CoV-2 transmission based solely on genomic data seems hindered by a slow mutation rate, potential convergent events, and technical artifacts. Detailed contact tracing seems essential in most cases to study SARS-CoV-2 transmission at high resolution.