bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and validation of a high throughputNeisseria gonorrhoeaegenotyping method
Authors: Komori Kohji , Aoki Kotaro , Ishii Yoshikazu , Shimuta Ken , Ohnishi Makoto , Tateda Kazuhiro 
Published: January 2023

AbstractBackgroundNeisseria gonorrhoeaegenotyping by whole-genome sequencing (WGS) is expensive for a large sample set, a less expensive and more efficient genotyping method is required. We developed a high-throughput genotyping method forN. gonorrhoeaeto improve molecular epidemiological typing and antimicrobial-resistant identification inN. gonorrhoeaeantimicrobial susceptibility surveillance.MethodsWe used multiplex-tailed PCR to amplify and sequence 15 alleles from multilocus sequence typing (MLST),N. gonorrhoeaemultiantigen sequence typing (NG-MAST), andN. gonorrhoeaesequence typing for antimicrobial resistance (NG-STAR). After indexing-PCR, we sequenced the DNA library using the MiSeq platform (Illumina). Sequencing reads werede novoassembly or constructing consensus sequences of alleles, then assigned sequence type. We used 54 previously characterized strains ofN. gonorrhoeaeand WGS data to validate our method.ResultsThe allele identification results of MLST and NG-STAR in all strains agreed with the draft WGS. However, in NG-MAST, only 35 strains agreed. Disagreement was found in the NG-MAST ofporBin 15 strains and oftbpBin seven strains. QRDR analysis perfectly predicted levofloxacin resistance. But was less successful in predicting reduced susceptibility or resistance phenotype to penicillin G, cefixime, or ceftriaxone usingpenA, porB, ponA, ormtrRalleles.ConclusionsThe successful performance in MLST and NG-STAR of our method was validated in this study. This method may be useful for large-scale genotyping forN. gonorrhoeaesurveillance in a cost- and labor-saving manner. Phenotypic prediction of antimicrobial susceptibility by combining multiple alleles may be necessary for other than fluoroquinolones.
Interleukin-1 receptor antagonist gene (IL1RN) variants modulate the cytokine release syndrome and mortality of SARS-CoV-2
Authors: Attur Mukundan , Petrilli Christopher , Adhikari Samrachana , Iturrate Eduardo , Li Xiyue , Tuminello Stephanie , Hu Nan , Chakravarti Aravinda , Beck David , Abramson Steven B. 
Published: January 2023

ABSTRACTObjectiveTo explore the regulation of the inflammatory response in acute SARS-CoV-2 infection, we examined effects of single nucleotide variants (SNVs) ofIL1RN, the gene encoding the anti-inflammatory IL-1 receptor antagonist (IL-1Ra), on the cytokine release syndrome and mortality.MethodsWe studied 2589 patients hospitalized with SARS-CoV-2 between March 2020 and March 2021 at NYU Langone’s Tisch Hospital. CTA and TTG haplotypes formed from three SNVs (rs419598, rs315952, rs9005) and the individual SNVs of theIL1RNgene were assessed for association with laboratory markers of the cytokine release syndrome (CRS) and mortality.ResultsMortality in the population was 15.3%, and was lower in women than men (13.1% vs.17.3%, p<0.0003). Carriers of the CTA-1/2IL1RNhaplotypes exhibiteddecreasedinflammatory markers andincreasedplasma IL-1Ra relative to TTG carriers. Decreased mortality among CTA-1/2 carriers was observed in male patients between the ages of 55-74 [9.2% vs. 17.9%, p=0.001]. Evaluation of individual SNVs of theIL1RNgene (rs419598, rs315952, rs9005) indicated that carriers of theIL1RNrs419598 CC SNV exhibited lower inflammatory biomarker levels, and was associated with reduced mortality compared to the CT/TT genotype in men (OR 0.49 (0.23 – 1.00); 0.052), with the most pronounced effect observed between the ages of 55-74 [5.5% vs. 18.4%, p<0.001].ConclusionTheIL1RNhaplotype CTA, and sequence variant of rs419598 are associated with attenuation of the cytokine release syndrome and decreased mortality in males with acute SARS-CoV2 infection. The data suggest thatIL1RNmodulates the COVID-19 cytokine release syndrome via endogenous “ anti-inflammatory” mechanisms.Significance statementWe provide evidence that variants ofIL1RNmodulate the severity of SARS-CoV-2 infection. TheIL1RN CTA haplotype andrs419598 CC single nucleotide variant are associated with decreased plasma levels of inflammatory markers, interleukin-1 beta (IL-1β), interleukin-6 (IL-6), interleukin-2 (IL-2), C-reactive protein (CRP), D-dimer, ferritin, and procalcitonin, in association with higher levels of IL-1Ra and IL-10, anti-inflammatory proteins. Both haplotype CTA and rs419598 CC genotype are associated with a significant reduction in the mortality of men. These data provide genetic evidence that inflammasome activation and the IL-1 pathway plays an important role in the mortality and morbidity associated with severe SARS-CoV-2 infection, and that genetic regulation of inflammatory pathways by variants ofIL1RNmerits further evaluation in severe SARS-CoV-2 infection.
The community as an active part in the implementation of interventions for the prevention and control of tuberculosis: a scoping review
Authors: Chavez-Rimache Lesly , Ugarte-Gil César , Brunette Maria J 
Published: January 2023

AbstractInterventions involving direct community stakeholders include a variety of approaches in which members take an active role in improving their health. We evaluated studies in which the community has actively participated to strengthen tuberculosis prevention and control programs. A literature search was performed in Pubmed, Scopus, ERIC, Global Index Medicus, Scielo, Cochrane Library, LILACS, Google Scholar, speciality journals, and other bibliographic references. The primary question for this review was: what is known about tuberculosis control interventions and programs in which the community has been an active part?.Two reviewers performed the search, screening and selection of studies independently. In cases of discrepancies over the eligibility of an article, it was resolved by consensus. 130 studies were selected, of which 68.47% (n=89/130) were published after 2010. The studies were conducted in Africa (44.62%), the Americas (22.31%) and Southeast Asia (19.23%). It was found that 20% (n=26/130) of the studies evaluated the participation of the community in the detection/active search of cases, 20.77% (n=27/130) in the promotion/prevention of tuberculosis; 23.07% (n=30/130) in identifying barriers to treatment, 46.15% (n=60/130) in supervision during treatment and 3.08% (n=4/130) in social support for patient. Community participation not only strengthens the capacities of health systems for the prevention and control of tuberculosis, but also allows a better understanding of the disease from the perspective of the patient and the affected community by identifying barriers and difficulties through of the tuberculosis care cascade. Engaging key community stakeholders in co-creating solutions offers a critical pathway for local governments to eradicate TB.
Estimating the impact of test-trace-isolate-quarantine systems on SARS-CoV-2 transmission in Australia
Authors: Shearer Freya M. , McCaw James M. , Ryan Gerard , Hao Tianxiao , Tierney Nicholas J , Lydeamore Michael , Ward Kate , Ellis Sally , Wood James , McVernon Jodie , Golding Nick 
Published: January 2023

ABSTRACTWe report on an analysis of Australian COVID-19 case data to estimate the impact of TTIQ systems on SARS-CoV-2 transmission in 2020–21. We estimate that in a low prevalence period in the state of New South Wales (tens of cases per day), TTIQ contributed to a 54% reduction in transmission. In a higher prevalence period in the state of Victoria (hundreds of cases per day), TTIQ contributed to a 42% reduction in transmission. Our results also suggest that case-initiated contact tracing can support timely quarantine in times of system stress. Contact tracing systems for COVID-19 in Australia were highly effective and adaptable in supporting the national suppression strategy through 2020 and 2021.
The SENSOR System: Using Standardized Data Entry and Dashboards for Review of Scientific Studies on the Utility of Blood-Based Protein Biomarkers for Patients with Mild Brain Injury
Authors: Aggerwal Salena , Safi Toufik , Beliveau Lt (N) Peter , Gupta Gaurav 
Published: January 2023

AbstractBackgroundThere is no objective way of diagnosing or prognosticating acute traumatic brain injuries (TBIs). A systematic review conducted byMondello et al. reviewed studies looking at blood based protein biomarkers in the context of acute mild traumatic brain injuries and correlation to results of computed tomography scanning. This paper provides a summary of this same literature using the SENSOR system.MethodsAn existing review written byMondello et al. was selected to apply the previously described SENSOR system (Kamal et al.) that uses a systematic process made up of a Google Form for data intake, Google Drive for article access, and Google Sheets for the creation of the dashboard. The dashboard consisted of a map, bubble graphs, multiple score charts, and a pivot table to facilitate the presentation of data.ResultsA total of 29 entries were inputted by two team members. Sensitivities, specificities, positive predictive values (PPVs), negative predictive values (NPVs), demographics, cut-off levels, biomarker levels, and assay ranges were analyzed and presented in this study. S100B and GFAP biomarkers may provide good clinical utility, whereas UCH-L1, C-Tau, and NSE do not.DiscussionThis study determined the feasibility and reliability of multiple biomarkers (S100B, UCH-L1, GFAP, C-tau, and NSE) in predicting traumatic brain lesions on CT scans, in mTBI patients, using the SENSOR system. Many potential limitations exist for the existing literature including controlling for known confounders for mild traumatic brain injuries.ConclusionThe SENSOR system is an adaptable, dynamic, and graphical display of scientific studies that has many benefits, which may still require further validation. Certain protein biomarkers may be helpful in deciding which patients with mTBIs require CT scans, but impact on prognosis is still not clear based on the available literature.
The same but different. Multidimensional assessment of depression in students of natural science and music
Authors: Korte Michaela , Cerci Deniz , Wehry Roman , Timmers Renee , Williamson Victoria J. 
Published: January 2023

AbstractDepression is one of the most common and debilitating health problems, however, its heterogeneity makes a diagnosis challenging. Thus far the restriction of depression variables explored within groups, the lack of comparability between groups, and the heterogeneity of depression as a concept limit a meaningful interpretation, especially in terms of predictability. Research established students in late adolescence to be particularly vulnerable, especially those with a natural science or musical study main subject. This study used a predictive design, observing the change in variables between groups as well as predicting which combinations of variables would likely determine depression prevalence. 102 under- and postgraduate students from various higher education institutions participated in an online survey. Students were allocated into three groups according to their main study subject and type of institution: natural science students, music college students and a mix of music and natural science students at university with comparable levels of musical training and professional musical identity. Natural science students showed significantly higher levels of anxiety prevalence and pain catastrophizing prevalence, while music college students showed significantly higher depression prevalence compared to the other groups. A hierarchical regression and a tree analysis found that depression for all groups was best predicted with a combination of variables: high anxiety prevalence and low burnout of students with academic staff. The use of a larger pool of depression variables and the comparison of at-risk groups provide insight into how these groups experience depression and thus allow initial steps towards personalized support structures.
Military sexual trauma-related posttraumatic stress disorder service-connection award denial across gender and race
Authors: Webermann Aliya R. , Gianoli Mayumi O. , Rosen Marc I. , Portnoy Galina A. , Haskell Sally G. , Runels Tessa , Black Anne C. 
Published: January 2023

AbstractThe current study characterizes a cohort of veteran claims filed with the Veterans Benefits Administration for posttraumatic stress disorder secondary to experiencing military sexual trauma, compares posttraumatic stress disorder service-connection award denial for military sexual trauma-related claims versus combat-related claims, and examines military sexual trauma -related award denial across gender and race. We conducted analyses on a retrospective national cohort of veteran claims submitted and rated between October 2017-May 2022, including 102,404 combat-related claims and 31,803 military sexual trauma-related claims. Descriptive statistics were calculated, logistic regressions assessed denial of service-connection across stressor type and demographics, and odds ratios were calculated as effect sizes. Military sexual trauma-related claims were submitted primarily by White women Army veterans, and had a two times higher odds of being denied (27.6%) than combat claims (18.2%). When controlling for demographics including age, race, and gender, men veterans had a 1.77 times higher odds of having military sexual trauma-related claims denied compared to women veterans (36.6% vs. 25.4%), and Black veterans had a 1.39 times higher odds of having military sexual trauma-related claims denied compared to White veterans (32.4% vs. 25.3%). Three-fourths of military sexual trauma-related claims were awarded in this cohort, however, there were disparities in awarding of claims across gender and race for men and Black veterans, which suggest the possibility of systemic barriers for veterans from underserved backgrounds and/or who may underreport military sexual trauma.
Female Saudi nursing students’ perspectives on pursuing a career in home healthcare: A qualitative study
Authors: Almegewly Wafa Hamad , Karavasileiadou Savvato , Alotaibi Taghreed Samel 
Published: January 2023

AbstractBackgroundWhile the number of patients requiring home healthcare in Saudi Arabia is increasing, there is insufficient data on what attracts nurses to work in this field.ObjectiveThis qualitative study investigates how nursing students practicing in home healthcare perceive it as a future career.MethodsA purposive sample was used to recruit fourth-year nursing students enrolled in an older adult nursing care course and trained in home healthcare settings. Data were gathered using five focus groups of five students each (a total of 25 students) and analyzed using thematic analysis.ResultsIt was found that the majority of students did not perceive home healthcare as a viable career option compared to working in a hospital. They vacillated due to the nature of the work, safety concerns, working demands, invariability of health cases, and lack of opportunities for professional development. Nevertheless, some nursing students were amenable to pursuing a career in home healthcare due to the less working hours, sense of autonomy, and the ability to provide holistic care and educate patients and their families.ConclusionPopulation awareness programs are needed to overcome cultural barriers, increase student motivation and ultimately bolster the number of certified nurses working in home healthcare.
Addressing spatial misalignment in population health research: a case study of US congressional district political metrics and county health data
Authors: Nethery Rachel C. , Testa Christian , Tabb Loni P. , Hanage William P. , Chen Jarvis T. , Krieger Nancy 
Published: January 2023

AbstractAreal spatial misalignment, which occurs when data on multiple variables are collected using mismatched boundary definitions, is a ubiquitous obstacle to data analysis in public health and social science research. As one example, the emerging sub-field studying the links between political context and health in the United States faces significant spatial misalignment-related challenges, as the congressional districts (CDs) over which political metrics are measured and administrative units, e.g., counties, for which health data are typically released, have a complex misalignment structure. Standard population-weighted data realignment procedures can induce measurement error and invalidate inference, which has prompted the development of fully model-based approaches for analyzing spatially misaligned data. One such approach, atom-based regression models (ABRM), holds particular promise but has scarcely been used in practice due to the lack of appropriate software or examples of implementation. ABRM use “atoms”, the areas created by intersecting all sets of units on which variables of interest are measured, as the units of analysis and build models for the atom-level data, treating the atom-level variables (generally unmeasured) as latent variables. In this paper, we demonstrate the feasibility and strengths of the ABRM in a case study of the association between political representatives’ voting behavior (CD-level) and COVID-19 mortality rates (county-level) in a post-vaccine period. The adjusted ABRM results suggest that more conservative voting record is associated with an increase in COVID-19 mortality rates, with estimated associations smaller in magnitude but consistent in direction with those of standard realignment methods. The results also indicate that ABRM may enable more robust confounding adjustment and more realistic uncertainty estimates, properly representing the uncertainties arising from all analytic procedures. We also implement the ABRM in modern optimized Bayesian computing programs and make our code publicly available, which may enable these methods to be more widely adopted.
SURFBAT: a surrogate family-based association test building on large imputation reference panels
Authors: Herzig AF , Rubinacci S , Marenne G , Perdry H ,   FrEx Consortium,   FranceGenRef Consortium, Dina C , Redon R , Delaneau O , Génin E 
Published: January 2023

AbstractGenotype-phenotype association tests are typically adjusted for population stratification using principal components that are estimated genome-wide. This lacks resolution when analysing populations with fine structure and/or individuals with fine levels of admixture. This can affect power and precision, and is a particularly relevant consideration when control individuals are recruited using geographic selection criteria. Such is the case in France where we have recently created reference panels of individuals anchored to different geographic regions. To make correct comparisons against case groups, who would likely be gathered from large urban areas, new methods are needed.We present SURFBAT (a SURrogate Family Based Association Test) which performs an approximation of the transmission-disequilibrium test. Our method hinges on the application of genotype imputation algorithms to match similar haplotypes between the case and control groups. This permits us to approximate local ancestry informed posterior probabilities of un-transmitted parental alleles of each case individual. SURFBAT provides an association test that is inherently robust to fine-scale population stratification and opens up the possibility of efficiently using large imputation reference panels as control groups for association testing. The method is suitable when the control panel spans the local ancestry spectrum of the case-group population and each control has similar paternal and maternal ancestries. This is the case for our reference panels where individuals have their four grand-parents born in the same geographic area. In contrast to other methods for association testing that incorporate local-ancestry inference, SURFBAT does not require a set of ancestry groups to be defined, nor for local ancestry to be explicitly estimated.We demonstrate the interest of our tool on simulated datasets created from the 1000 Genomes project and the FranceGenRef project, as well as on a real-data example for a group of case individuals affected by Brugada syndrome.
dentist: Computing uncertainty by sampling points around maximum likelihood estimates
Authors: Boyko James D. , O’Meara Brian C. 
Published: January 2023

AbstractIt is standard statistical practice to provide measures of uncertainty around parameter estimates. Unfortunately, this very basic and necessary enterprise is often absent in macroevolutionary studies.dentist is an R package allows an estimate of confidence intervals around parameter estimates without an analytic solution to likelihood equations or an approximation based on local curvature at a peak. This package works by “denting” the likelihood surface by sampling points a specified distance around the maximum likelihood estimate following what is essentially a Metropolis-Hastings walk.We describe the importance of estimating uncertainty around parameter estimates as well as demonstrate the ability of dentist to accurately estimate confidence intervals.We introduce several plotting tools to visualize the results of a dentist analysis. dentist is freely available fromhttps://github.com/bomeara/dentist, written in the R language, and can be used for any given likelihood function.
Improved enzymatic labeling of fluorescent in situ hybridization probes applied to the visualization of retained introns in cells
Authors: Xiao Wen , Yeom Kyu-Hyeon , Lin Chia-Ho , Black Douglas L. 
Published: January 2023

AbstractFluorescence In Situ Hybridization (FISH) is a widely used tool for quantifying gene expression and determining the location of RNA molecules in cells. Here, we present an improved method for FISH probe production that yields high purity probes with a wide range of fluorophores using standard laboratory equipment at low cost. The method modifies an earlier protocol that uses terminal deoxynucleotidyl transferase to add fluorescently labeled nucleotides to synthetic deoxyoligonucleotides. In our protocol, Amino-11-ddUTP is joined to an oligonucleotide pool prior to its conjugation to a fluorescent dye, thereby generating pools of probes ready for a variety of modifications. This order of reaction steps allows for high labeling efficiencies regardless of the GC content or terminal base of the oligonucleotides. The Degree Of Labeling (DOL) for spectrally distinct fluorophores (Quasar, ATTO and Alexa dyes) was mostly greater than 90%, comparable to commercial probes. The ease and low cost of production allowed generation of probe-sets targeting a wide variety of RNA molecules. Using these probes, FISH assays in C2C12 cells showed the expected subcellular localization of mRNAs and pre-mRNAs forPolr2a(RNA polymerase II subunit 2a) andGapdh, and of the long noncoding RNAsMalat1andNeat1. Developing FISH probe sets for several transcripts containing retained introns, we found that retained introns in theGabbr1andNoc2ltranscripts are present in subnuclear foci separate from their sites of synthesis and partially coincident with nuclear speckles. This labeling protocol should have many applications in RNA biology.