bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving mortality in older adult trauma patients: Are we doing better?
Authors: Karam Basil S. , Patnaik Rohan , Murphy Patrick , deRoon-Cassini Terri A. , Trevino Colleen , Hemmila Mark R. , Haines Krista , Puzio Thaddeus J. , Charles Anthony , Tignanelli Christopher , Morris Rachel 
Published: September 2021

BACKGROUND
Older adult trauma is associated with high morbidity and mortality. Individuals older than 65 years are expected to make up more than 21% of the total population and almost 39% of trauma admissions by 2050. Our objective was to perform a national review of older adult trauma mortality and identify associated risk factors to highlight potential areas for improvement in quality of care.

MATERIALS AND METHODS
This is a retrospective cohort study of the National Trauma Data Bank including all patients age ≥65 years with at least one International Classification of Diseases, Ninth Revision, Clinical Modification trauma code admitted to a Level I or II US trauma center between 2007 and 2015. Variables examined included demographics, comorbidities, emergency department vitals, injury characteristics, and trauma center characteristics. Multilevel mixed-effect logistic regression was performed to identify independent risk factors of in-hospital mortality.

RESULTS
There were 1,492,759 patients included in this study. The number of older adult trauma patients increased from 88,056 in 2007 to 158,929 in 2015 (p > 0.001). Adjusted in-hospital mortality decreased in 2014 to 2015 (odds ratio [OR], 0.88; 95% confidence interval [CI], 0.86–0.91) when compared with 2007 to 2009. Admission to a university hospital was protective (OR, 0.83; 95% CI, 0.74–0.93) as compared with a community hospital admission. There was no difference in mortality risk between Level II and Level I admission (OR, 1.00; 95% CI, 0.92–1.08). The strongest trauma-related risk factor for in-patient mortality was pancreas/bowel injury (OR, 2.25; 95% CI, 2.04–2.49).

CONCLUSION
Mortality in older trauma patients is decreasing over time, indicating an improvement in the quality of trauma care. The outcomes of university based hospitals can be used as national benchmarks to guide quality metrics.

LEVEL OF EVIDENCE
Therapeutic/Care Management, Level IV.
Developing a national trauma research action plan: Results from the Burn Research Gap Delphi Survey
Authors: Gibran Nicole S. , Shipper Edward , Phuong Jimmy , Braverman Max , Bixby Pam , Price Michelle A. , Bulger Eileen M. ,   on behalf of the NTRAP Burns & Reconstructive Surgery Panel Group
Published: September 2021

BACKGROUND
The 2016 National Academies of Science, Engineering and Medicine call for a national integrated, military-civilian trauma action plan to achieve zero preventable deaths and disability after injury included a proposal to establish a National Trauma Research Action Plan to “strengthen trauma research and ensure that the resources available for this research are commensurate with the importance of injury and the potential for improvement in patient outcomes.” The Department of Defense funded the Coalition for National Trauma Research to generate a comprehensive research agenda spanning the continuum of trauma/burn care from prehospital to rehabilitation. The Burn/Reconstructive Surgery group represents one focus area for this research agenda development.

METHODS
Experts in burn and reconstructive surgery research identified gaps in knowledge, generated research questions and prioritized questions using a consensus driven Delphi survey approach. Participants were identified using established Delphi recruitment guidelines to ensure heterogeneity and generalizability with military and civilian representatives. Literature reviews informed the panel. Panelists were encouraged to use a PICO format to generate research questions: Patient/Population; Intervention; Compare/Control; Outcome. Participants ranked the priority of each question on a nine-point Likert scale, which was categorized to represent low, medium, and high priority items. Consensus was defined based on ≥60% panelist agreement.

RESULTS
Subject matter experts generated 949 research questions in 29 Burn & 26 Reconstruction topics. Five hundred ninety-seven questions reached consensus. Of these, 338 (57%) were high-priority, 180 (30%), medium-priority, and 78 (13%) low-priority questions.

CONCLUSION
Many high-priority questions translate to complex wound management and outcomes. Panel recognition that significant gaps in knowledge exist in understanding functional outcomes after injury underscores the importance of long-term recovery metrics even when studying acute injury or interventions such as resuscitation or inhalation injury. Funding agencies and burn/reconstructive surgery researchers should consider these gaps when they prioritize future research.

LEVEL OF EVIDENCE
Expert consensus, Level IV.
The derivation of an International Classification of Diseases, Tenth Revision–based trauma-related mortality model using machine learning
Authors: Tran Zachary , Zhang Wenhao , Verma Arjun , Cook Alan , Kim Dennis , Burruss Sigrid , Ramezani Ramin , Benharash Peyman 
Published: September 2021

BACKGROUND
Existing mortality prediction models have attempted to quantify injury burden following trauma-related admissions with the most notable being the Injury Severity Score (ISS). Although easy to calculate, it requires additional administrative coding. International Classification of Diseases (ICD)–based models such as the Trauma Mortality Prediction Model (TMPM-ICD10) circumvent these limitations, but they use linear modeling, which may not adequately capture the intricate relationships of injuries on mortality. Using ICD-10 coding and machine learning (ML) algorithms, the present study used the National Trauma Data Bank to develop mortality prediction models whose performance was compared with logistic regression, ISS, and TMPM-ICD10.

METHODS
The 2015 to 2017 National Trauma Data Bank was used to identify adults following trauma-related admissions. Of 8,021 ICD-10 codes, injuries were categorized into 1,495 unique variables. The primary outcome was in-hospital mortality. eXtreme Gradient Boosting (XGBoost), a ML technique that uses iterations of decision trees, was used to develop mortality models. Model discrimination was compared with logistic regression, ISS, and TMPM-ICD10 using receiver operating characteristic curve and probabilistic accuracy with calibration curves.

RESULTS
Of 1,611,063 patients, 54,870 (3.41%) experienced in-hospital mortality. Compared with those who survived, those who died more frequently suffered from penetrating trauma and had a greater number of injuries. The XGBoost model exhibited superior receiver operating characteristic curve (0.863 [95% confidence interval (CI), 0.862–0.864]) compared with logistic regression (0.845 [95% CI, 0.844–0.846]), ISS (0.828 [95% CI, 0.827–0.829]), and TMPM-ICD10 (0.861 [95% CI, 0.860–0.862]) (all p < 0.001). Importantly, the ML model also had significantly improved calibration compared with other methodologies (XGBoost, coefficient of determination (R
2) = 0.993; logistic regression, R
2 = 0.981; ISS, R
2 = 0.649; TMPM-ICD10, R
2 = 0.830).

CONCLUSION
Machine learning models using XGBoost demonstrated superior performance and calibration compared with logistic regression, ISS, and TMPM-ICD10. Such approaches in quantifying injury severity may improve its utility in mortality prognostication, quality improvement, and trauma research.

LEVEL OF EVIDENCE
Prognostic and Epidemiologic; level III.
Karawun: assisting evaluation of advances in multimodal imaging for neurosurgical planning and intraoperative neuronavigation
Authors: Beare Richard , Alexander Bonnie , Warren Aaron , Kean Michael , Seal Marc , Wray Alison , Maixner Wirginia , Yang Joseph Yuan-Mou 
Published: September 2021

AbstractSubmitted toMagnetic Resonance in MedicinePurposeTo introduce a tool allowing neurosurgeons to evaluate the results of research tractography workflows for presurgical planning and intraoperative image-guidance, using standard neurosurgical navigation platforms.Theory and MethodsImproving communication between neurosurgeons and researchers developing new image acquisition and processing methods is critical for rapid translation of research to surgical practice. Presenting research outputs within existing clinical workflows is one approach that can assist such interdisciplinary communication. Neurosurgical navigation platforms can display and manipulate a wide range of medical image data and associated delineations and thus allow clinicians to evaluate the impact of new imaging research on their work. Currently, it is extremely difficult to integrate research-based image processing outputs into standard neurosurgical navigation platforms.ResultsIn this note we introduceKarawun, an open-source software tool for converting outputs from research imaging pipelines, especially diffusion MRI tractography reconstructions using advanced methodologies currently unavailable on commercial navigation platforms, into forms that can be imported into theBrainlabneurosurgical navigation platform (Brainlab AG, Munich, Germany). The externally created tractography images and delineations can be viewed and manipulated as if they were created byBrainlab. We illustrate how two surgical workups, created using open-source tools and different processing choices can be presented to the neurosurgeon who can evaluate the impact of the differences between the two workups on surgical decisions.ConclusionKarawunallows researchers developing novel imaging methodologies to display their results in environments that are familiar to clinical end-users, especially neurosurgeons, thus assisting translation of research into clinical practice.
Two doses of the mRNA BNT162b2 vaccine reduce severe outcomes, viral load and secondary attack rate: evidence from a SARS-CoV-2 Alpha outbreak in a nursing home in Germany, January-March 2021
Authors: Meyer Emily Dorothee , Sandfort Mirco , Bender Jennifer , Matysiak-Klose Dorothea , Dörre Achim , Bojara Gerhard , Beyrer Konrad , Hellenbrand Wiebke 
Published: September 2021

AbstractA SARS-CoV-2 Alpha outbreak was detected in a nursing home after residents and staff had completed vaccination with BNT162b. In a retrospective cohort study, we estimated an age-adjusted vaccine effectiveness of 88% [95% confidence interval (95%CI) 41-98%] against hospitalization/death. Ct values at diagnosis were higher with longer intervals since the second vaccination [>21 vs. ≤21 days: 4.82 cycles, 95%CI: 0.06-9.58]. Secondary attack rates were 67% lower in households of vaccinated [2/9 (22.2%)] than unvaccinated infected staff [12/18 (66.7%); p=0.046]. Vaccination reduced the risk of severe outcomes, Ct values and transmission, but not fully. Non-pharmaceutical interventions remain important for vaccinated individuals.
Subtyping of common complex diseases and disorders by integrating heterogeneous data. Identifying clusters among women with lower urinary tract symptoms in the LURN study
Authors: Andreev Victor P. , Helmuth Margaret E. , Liu Gang , Smith Abigail R. , Merion Robert M. , Yang Claire C. , Cameron Anne P. , Jelovsek J. Eric , Amundsen Cindy L. , Helfand Brian T. , Bradley Catherine S. , DeLancey John O. L. , Griffith James W. , Glaser Alexander P. , Gillespie Brenda W. , Clemens J. Quentin , Lai H. Henry ,   the LURN Study Group
Published: September 2021

ABSTRACTWe present a novel methodology for subtyping of persons with a common clinical symptom complex by integrating heterogeneous continuous and categorical data. We illustrate it by clustering women with lower urinary tract symptoms (LUTS), who represent a heterogeneous cohort with overlapping symptoms and multifactorial etiology. Identifying subtypes within this group would potentially lead to better diagnosis and treatment decision-making. Data collected in the Symptoms of Lower Urinary Tract Dysfunction Research Network (LURN), a multi-center prospective observational cohort study, included self-reported urinary and non-urinary symptoms, bladder diaries, and physical examination data for 545 women. Heterogeneity in these multidimensional data required thorough and non-trivial preprocessing, including scaling by controls and weighting to mitigate data redundancy, while the various data types (continuous and categorical) required novel methodology using a weighted Tanimoto indices approach. Data domains only available on a subset of the cohort were integrated using a semi-supervised clustering approach. Novel contrast criterion for determination of the optimal number of clusters in consensus clustering was introduced and compared with existing criteria. Distinctiveness of the clusters was confirmed by using multiple criteria for cluster quality, and by testing for significantly different variables in pairwise comparisons of the clusters. Cluster dynamics were explored by analyzing longitudinal data at 3- and 12-month follow-up. Five distinct clusters of women with LUTS were identified using the developed methodology. The clinical relevance of the identified clusters is discussed and compared with the current conventional approaches to the evaluation of LUTS patients. Rationale and thought process are described for selection of procedures for data preprocessing, clustering, and cluster evaluation. Suggestions are provided for minimum reporting requirements in publications utilizing clustering methodology with multiple heterogeneous data domains.
Concerted changes in the pediatric single-cell intestinal ecosystem before and after anti-TNF blockade
Authors: Zheng Hengqi Betty , Doran Benjamin A. , Kimler Kyle , Yu Alison , Tkachev Victor , Niederlova Veronika , Cribbin Kayla , Fleming Ryan , Bratrude Brandi , Betz Kayla , Cagnin Lorenzo , McGuckin Connor , Keskula Paula , Albanese Alexandre , Sacta Maria , de Sousa Casal Joshua , van Esch Ruben , Kwong Andrew C. , Kummerlowe Conner , Taliaferro Faith , Fiaschi Nathalie , Kou Baijun , Coetzee Sandra , Jalal Sumreen , Yabe Yoko , Dobosz Michael , Wipperman Matthew F. , Hamon Sara , Kalliolias George D. , Hooper Andrea , Lim Wei Keat , Haxhinasto Sokol , Wei Yi , Ford Madeline , Ambartsumyan Lusine , Suskind David L. , Lee Dale , Deutsch Gail , Deng Xuemei , Collen Lauren V. , Mitsialis Vanessa , Snapper Scott B. , Wahbeh Ghassan , Shalek Alex K. , Ordovas-Montanes Jose , Kean Leslie S. 
Published: September 2021

AbstractCrohn’s disease is an inflammatory bowel disease (IBD) commonly treated through anti-TNF blockade. However, most patients still relapse and inevitably progress. Comprehensive single-cell RNA-sequencing (scRNA-seq) atlases have largely sampled patients with established treatment-refractory IBD, limiting our understanding of which cell types, subsets, and states at diagnosis anticipate disease severity and response to treatment. Here, through combining clinical, flow cytometry, histology, and scRNA-seq methods, we profile diagnostic human biopsies from the terminal ileum of treatment-naïve pediatric patients with Crohn’s disease (pediCD; n=14), matched repeat biopsies (pediCD-treated; n=8) and from non-inflamed pediatric controls with functional gastrointestinal disorders (FGID; n=13). To resolve and annotate epithelial, stromal, and immune cell states among the 201,883 baseline single-cell transcriptomes, we develop a principled and unbiased tiered clustering approach, ARBOL. Through flow cytometry and scRNA-seq, we observe that treatment-naïve pediCD and FGID have similar broad cell type composition. However, through high-resolution scRNA-seq analysis and microscopy, we identify significant differences in cell subsets and states that arise during pediCD relative to FGID. By closely linking our scRNA-seq analysis with clinical meta-data, we resolve a vector of T cell, innate lymphocyte, myeloid, and epithelial cell states in treatment-naïve pediCD (pediCD-TIME) samples which can distinguish patients along the trajectory of disease severity and anti-TNF response. By using ARBOL with integration, we position repeat on-treatment biopsies from our patients between treatment-naïve pediCD and on-treatment adult CD. We identify that anti-TNF treatment pushes the pediatric cellular ecosystem towards an adult, more treatment-refractory state. Our study jointly leverages a treatment-naïve cohort, high-resolution principled scRNA-seq data analysis, and clinical outcomes to understand which baseline cell states may predict Crohn’s disease trajectory.
Unusual SARS-CoV-2 intra-host diversity reveals lineages superinfection
Authors: Dezordi Filipe Zimmer , Resende Paola Cristina , Naveca Felipe Gomes , do Nascimento Valdinete Alves , de Souza Victor Costa , Paixão Anna Carolina Dias , Appolinario Luciana , Lopes Renata Serrano , Mendonça Ana Carolina da Fonseca , da Rocha Alice Sampaio Barreto , Venas Taina Moreira Martins , Pereira Elisa Cavalcante , Salvato Richard Steiner , Gregianini Tatiana Schäffer , Martins Leticia Garay , Pereira Felicidade Mota , Rovaris Darcita Buerger , Fernandes Sandra Bianchini , Ribeiro-Rodrigues Rodrigo , Costa Thais Oliveira , Sousa Joaquim Cesar , Miyajima Fabio , Delatorre Edson , Gräf Tiago , Bello Gonzalo , Siqueira Marilda Mendonça , Wallau Gabriel da Luz 
Published: September 2021

AbstractThe SARS-CoV-2 has infected almost 200 million people worldwide by July 2021 and the pandemic has been characterized by infection waves of viral lineages showing distinct fitness profiles. The simultaneous infection of a single individual by two distinct SARS-CoV-2 lineages provides a window of opportunity for viral recombination and the emergence of new lineages with differential phenotype. Several hundred SARS-CoV-2 lineages are currently well characterized but two main factors have precluded major coinfection/codetection analysis thus far: i) the low diversity of SARS-CoV-2 lineages during the first year of the pandemic which limited the identification of lineage defining mutations necessary to distinguish coinfecting viral lineages; and the ii) limited availability of raw sequencing data where abundance and distribution of intrasample/intrahost variability can be accessed. Here, we have put together a large sequencing dataset from Brazilian samples covering a period of 18 May 2020 to 30 April 2021 and probed it for unexpected patterns of high intrasample/intrahost variability. It enabled us to detect nine cases of SARS-CoV-2 coinfection with well characterized lineage-defining mutations. In addition, we matched these SARS-CoV-2 coinfections with spatio-temporal epidemiological data confirming their plausibility with the co-circulating lineages at the timeframe investigated. These coinfections represent around 0.61% of all samples investigated. Although our data suggests that coinfection with distinct SARS-CoV-2 lineages is a rare phenomenon, it is likely an underestimation and coinfection rates warrants further investigation.DATA SUMMARYThe raw fastq data of codetection cases are deposited on gisaid.org and correlated to gisaid codes: EPI_ISL_1068258, EPI_ISL_2491769, EPI_ISL_2491781, EPI_ISL_2645599, EPI_ISL_2661789, EPI_ISL_2661931, EPI_ISL_2677092, EPI_ISL_2777552, EPI_ISL_3869215. Supplementary data are available on https://doi.org/10.6084/m9.figshare.16570602.v1. The workflow code used in this study is publicly available on: https://github.com/dezordi/IAM_SARSCOV2.
Understanding the pathways leading to socioeconomic inequalities in HIV testing uptake in 18 sub-Saharan African countries: a mediation analysis
Authors: Ante-Testard Pearl Anne , Hamidouche Mohamed , Apouey Bénédicte , Baggaley Rachel , Larmarange Joseph , Benmarhnia Tarik , Temime Laura , Jean Kévin 
Published: September 2021

AbstractIntroductionAlthough socioeconomic inequalities in HIV prevention, testing and treatment services have been well documented, their drivers remain poorly understood. Understanding the different pathways between socioeconomic position and HIV testing across different countries could help designing tailored programs aimed at reducing such inequalities.MethodsWe analysed data from Demographic and Health Surveys conducted between 2010 and 2018 in 18 sub-Saharan African countries (Burkina Faso, Cameroon, Côte d’Ivoire, Congo DR, Ethiopia, Guinea, Kenya, Lesotho, Liberia, Malawi, Mali, Niger, Rwanda, Senegal, Sierra Leone, Tanzania, Zambia and Zimbabwe). Using a potential outcomes framework and the product method, we decomposed the total effect linking wealth and recent (< 12 months) HIV testing into i) direct effects, and ii) indirect effects, via demand-related (related to individual’s ability to perceive need for care and inclination to seek care) or supply-related (related to individual’s ability to reach, pay for and engage in health care) mediators. Multivariable gender-specific modified Poisson models were fitted to estimate proportions mediated, while accounting for exposure-mediator interaction when present.ResultsA total of 392,044 participants were included in the analysis. Pro-rich wealth-related inequalities were observed in a majority of countries, with nine countries with high levels of inequalities among women and 15 countries among men.The indirect effects of each mediator varied greatly across countries. The proportion mediated tended to be higher for demand-related than for supply-related mediators. For instance, among women, HIV-related knowledge was estimated to mediate up to 12.1% of inequalities in Côte d’Ivoire; this proportion was up to 31.5% for positive attitudes toward people living with HIV (PLHIV) in Senegal. For the four supply-related mediators, the proportion mediated was systematically below 7%. Similar conclusions were found when repeating analyses on men for the demand-related mediators, with higher proportions mediated by positive attitudes toward PLHIV (up to 39.9% in Senegal).ConclusionsOur findings suggest that socioeconomic inequalities in HIV testing may be mediated by the demand-side more than supply-side characteristics, with important variability across countries. Overall, the important inter-country heterogeneity in pathways of socioeconomic inequalities in HIV testing illustrates that addressing inequalities requires tailored efforts as well as upstream interventions.A French version of the abstract is available upon request from the corresponding author.