bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimal Timing of Tracheostomy in Injured Adolescents*
Authors: Butler Elissa K. , Killien Elizabeth Y. , Groner Jonathan I. , Arbabi Saman , Vavilala Monica S. , Rivara Frederick P. 
Published: July 2021

OBJECTIVES:
To evaluate the optimal timing of tracheostomy for injured adolescents.

DESIGN:
Retrospective cohort study.

SETTING:
Trauma facilities in the United States.

PATIENTS:
Adolescents (age 12–17 yr) in the National Trauma Data Bank (2007–2016) who were ventilated for greater than 24 hours and survived to discharge.

INTERVENTIONS:
None.

MEASUREMENTS AND MAIN RESULTS:
After stratifying by traumatic brain injury diagnosis, we compared ICU and hospital length of stay, pneumonia, and discharge disposition of patients with tracheostomy prior to three cut points (3, 7, and 14 d after admission) to 1) patients intubated at least as long as each cut point and 2) patients with tracheostomy on or after each cut point. Of 11,045 patients, 1,391 (12.6%) underwent tracheostomy. Median time to tracheostomy was 9 days (interquartile range, 6–13 d) for traumatic brain injury and 7 days (interquartile range, 3–12 d) for nontraumatic brain injury patients. Nontraumatic brain injury patients with tracheostomy prior to 7 days had 5.6 fewer ICU days (–7.8 to –3.5 d) and 5.7 fewer hospital days (–8.8 to –2.7 d) than patients intubated greater than or equal to 7 days and had 14.8 fewer ICU days (–19.6 to –10.0 d) and 15.3 fewer hospital days (–21.7 to –8.9 d) than patients with tracheostomy greater than or equal to 7 days. Similar differences were observed at 14 days but not at 3 days for both traumatic brain injury and nontraumatic brain injury patients. At the 3- and 7-day cut points, both traumatic brain injury and nontraumatic brain injury patients with tracheostomy prior to the cut point had lower risk of pneumonia and risk of discharge to a facility than those with tracheostomy after the cut point.

CONCLUSIONS:
For injured adolescents, tracheostomy less than 7 days after admission was associated with improved in-hospital outcomes compared with those who remained intubated greater than or equal to 7 days and with those with tracheostomy greater than or equal to 7 days. Tracheostomy between 3 and 7 days may be the optimal time point when prolonged need for mechanical ventilation is anticipated; however, unmeasured consequences of tracheostomy such as long-term complications and care needs must also be considered.
The Value of 3 Tesla Field Strength for Musculoskeletal Magnetic Resonance Imaging
Authors: Khodarahmi Iman , Fritz Jan 
Published: July 2021

Abstract
Musculoskeletal magnetic resonance imaging (MRI) is a careful negotiation between spatial, temporal, and contrast resolution, which builds the foundation for diagnostic performance and value. Many aspects of musculoskeletal MRI can improve the image quality and increase the acquisition speed; however, 3.0-T field strength has the highest impact within the current diagnostic range. In addition to the favorable attributes of 3.0-T field strength translating into high temporal, spatial, and contrast resolution, many 3.0-T MRI systems yield additional gains through high-performance gradients systems and radiofrequency pulse transmission technology, advanced multichannel receiver technology, and high-end surface coils. Compared with 1.5 T, 3.0-T MRI systems yield approximately 2-fold higher signal-to-noise ratios, enabling 4 times faster data acquisition or double the matrix size. Clinically, 3.0-T field strength translates into markedly higher scan efficiency, better image quality, more accurate visualization of small anatomic structures and abnormalities, and the ability to offer high-end applications, such as quantitative MRI and magnetic resonance neurography. Challenges of 3.0-T MRI include higher magnetic susceptibility, chemical shift, dielectric effects, and higher radiofrequency energy deposition, which can be managed successfully. The higher total cost of ownership of 3.0-T MRI systems can be offset by shorter musculoskeletal MRI examinations, higher-quality examinations, and utilization of advanced MRI techniques, which then can achieve higher gains and value than lower field systems. We provide a practice-focused review of the value of 3.0-T field strength for musculoskeletal MRI, practical solutions to challenges, and illustrations of a wide spectrum of gainful clinical applications.
Pre-existing polymerase-specific T cells expand in abortive seronegative SARS-CoV-2 infection
Authors: Swadling Leo , Diniz Mariana O. , Schmidt Nathalie M. , Amin Oliver E. , Chandran Aneesh , Shaw Emily , Pade Corinna , Gibbons Joseph M. , Bert Nina Le , Tan Anthony T. , Jeffery-Smith Anna , Tan Cedric , Tham Christine Y. L. , Kucyowicz Stephanie , Aidoo-Micah Gloryanne , Rosenheim Joshua , Davies Jessica , Jensen Melanie P. , Joy George , McCoy Laura E , Valdes Ana M , van Dorp Lucy , Altmann Daniel M. , Boyton Rosemary J. , Manisty Charlotte , Treibel Thomas A. , Moon James C. ,   COVIDsortium investigators, Balloux Francois , McKnight Áine , Noursadeghi Mahdad , Bertoletti Antonio , Maini Mala K. 
Published: July 2021

AbstractIndividuals with likely exposure to the highly infectious SARS-CoV-2 do not necessarily develop PCR or antibody positivity, suggesting some may clear sub-clinical infection before seroconversion. T cells can contribute to the rapid clearance of SARS-CoV-2 and other coronavirus infections1–5. We hypothesised that pre-existing memory T cell responses, with cross-protective potential against SARS-CoV-26–12, would expand in vivo to mediate rapid viral control, potentially aborting infection. We studied T cells against the replication transcription complex (RTC) of SARS-CoV-2 since this is transcribed first in the viral life cycle13–15and should be highly conserved. We measured SARS-CoV-2-reactive T cells in a cohort of intensively monitored healthcare workers (HCW) who remained repeatedly negative by PCR, antibody binding, and neutralisation for SARS-CoV-2 (exposed seronegative, ES). 16-weeks post-recruitment, ES had memory T cells that were stronger and more multispecific than an unexposed pre-pandemic cohort, and more frequently directed against the RTC than the structural protein-dominated responses seen post-detectable infection (matched concurrent cohort). The postulate that HCW with the strongest RTC-specific T cells had an abortive infection was supported by a low-level increase in IFI27 transcript, a robust early innate signature of SARS-CoV-2 infection16. We showed that the RNA-polymerase within RTC was the largest region of high sequence conservation across human seasonal coronaviruses (HCoV) and was preferentially targeted by T cells from UK and Singapore pre-pandemic cohorts and from ES. RTC epitope-specific T cells capable of cross-recognising HCoV variants were identified in ES. Longitudinal samples from ES and an additional validation cohort, showed pre-existing RNA-polymerase-specific T cells expanded in vivo following SARS-CoV-2 exposure, becoming enriched in the memory response of those with abortive compared to overt infection. In summary, we provide evidence of abortive seronegative SARS-CoV-2 infection with expansion of cross-reactive RTC-specific T cells, highlighting these highly conserved proteins as targets for future vaccines against endemic and emerging Coronaviridae.
Reliability and Validity of Bifactor Models of Dimensional Psychopathology in Youth from three Continents
Authors: Hoffmann Maurício Scopel , Moore Tyler Maxwell , Axelrud Luiza Kvitko , Tottenham Nim , Zuo Xi-Nian , Rohde Luis Augusto , Milham Michael Peter , Satterthwaite Theodore Daniel , Abrahão Salum Giovanni 
Published: July 2021

AbstractBifactor models are a promising strategy to parse general from specific aspects of psychopathology in youth. Currently, there are multiple configurations of bifactor models originating from different theoretical and empirical perspectives. Our aim is to identify and test the reliability, validity, measurement invariance, and the correlation of different bifactor models of psychopathology using the Child Behavior Checklist (CBCL). We used data from the Reproducible Brain Charts (RBC) initiative (N=7,011, ages 5 to 22 years, 40.2% females). Factor models were tested using the baseline data. To address our aim, we a) mapped the published bifactor models using the CBCL; b) tested their global model fit; c) calculated model-based reliability indices. d) tested associations with symptoms’ impact in everyday life; e) tested measurement invariance across many characteristics and f) analyzed the observed factor correlation across the models. We found 11 bifactor models ranging from 39 to 116 items. Their global model fit was broadly similar. Factor determinacy and H index were acceptable for the p-factors, internalizing, externalizing and somatic specific factors in most models. However, only p- and attention factors were predictors of symptoms’ impact in all models. Models were broadly invariant across different characteristics. P-factors were highly correlated across models (r = 0.88 to 0.99). Homotypic specific factors were also highly correlated. Regardless of item selection and strategy to compose CBCL bifactor models, results suggest that they all assess very similar constructs. Our results provide support for the robustness of the bifactor of psychopathology and distinct study characteristics.General Scientific SummariesThis study supports the notion that models of psychopathology that separate what is general from what is specific in mental health problems have little impact from item selection and types of specific dimensions. The general dimensions are highly correlated among different models, valid to predict symptom impact in daily life and are not influenced by demographic and clinical characteristics, time and information.
Multi-Sequence Average Templates for Aging and Neurodegenerative Disease Populations
Authors: Dadar Mahsa , Camicioli Richard , Duchesne Simon ,   For the CCNA Group
Published: July 2021

AbstractMagnetic resonance image (MRI) processing pipelines use average templates to enable standardization of individual MRIs in a common space. MNI-ICBM152 is currently used as the standard template by most MRI processing tools. However, MNI-ICBM152 represents an average of 152 healthy young adult brains and is vastly different from brains of patients with neurodegenerative diseases. In those populations, extensive atrophy might cause inevitable registration errors when using an average template of young healthy individuals for standardization. Disease-specific templates that represent the anatomical characteristics of the populations can reduce such errors and improve downstream driven estimates.We present multi-sequence average templates for Alzheimer’s Dementia (AD), Fronto-temporal Dementia (FTD), Lewy Body Dementia (LBD), Mild Cognitive Impairment (MCI), cognitively intact and impaired Parkinson’s Disease patients (PD-CIE and PD-CI, respectively), individuals with Subjective Cognitive Impairment (SCI), AD with vascular contribution (V-AD), Vascular Mild Cognitive Impairment (V-MCI), Cognitively Intact Elderly (CIE) individuals, and a human phantom. We also provide separate templates for males and females to allow better representation of the diseases in each sex group.
Redefining tissue specificity of genetic regulation of gene expression in the presence of allelic heterogeneity
Authors: Arvanitis Marios , Tayeb Karl , Strober Benjamin J. , Battle Alexis 
Published: July 2021

AbstractUnderstanding the mechanisms that underlie genetic regulation of gene expression is crucial to explaining the diversity that governs complex traits. Large scale expression quantitative trait locus (eQTL) studies have been instrumental in identifying genetic variants that influence the expression of target genes. However, a large fraction of disease-associated genetic variants have not been clearly explained by current eQTL data, frustrating attempts to use these data to comprehensively characterize disease loci. One notable observation from recent studies is that cis-eQTL effects are often shared across different cell types and tissues. This would suggest that common genetic variants impacting steady-state, adult gene expression are largely tolerated, shared across tissues, and less relevant to disease. However, allelic heterogeneity and complex patterns of linkage disequilibrium (LD) within each locus may skew the quantification of sharing of genetic effects between tissues, impede our ability to identify causal variants, and hinder the identification of regulatory effects for disease-associated genetic variants. Indeed, recent research suggests that multiple causal variants are often present in many eQTL and complex trait associated loci. Here, we re-analyze tissue-specificity of genetic effects in the presence of LD and allelic heterogeneity, proposing a novel method, CAFEH, that improves the identification of causal regulatory variants across tissues and their relationship to disease loci.
Rotation-based schedules in elementary schools to prevent COVID-19 spread: A simulation study
Authors: Brom Cyril , Diviák Tomáš , Drbohlav Jakub , Korbel Václav , Levínský René , Neruda Roman , Suchopárová Gabriela , Šlerka Josef , Šmíd Martin , Trnka Jan , Vidnerová Petra 
Published: July 2021

SummaryBackgroundRotations of schoolchildren on a weekly basis is one of the nonpharmaceutical interventions often considered in the covid-19 pandemic. This study aims to investigate the impact of different types of rotations in various testing contexts.MethodsWe built an agent-based model of interactions among pupils and teachers based on an online survey in an elementary school in Prague, Czechia. This model contains 624 schoolchildren and 55 teachers (679 nodes) and about 27 thousands social contacts (edges) in 10 layers. The layers reflect different types of contacts (in classroom, cafeteria etc.) as described in the survey. On this multi-graph structure we run a modified SEIR model of the covid-19 dynamics. The parameters of the model are calibrated on data from the outbreak in the Czech Republic in the period March to June 2020.FindingsThere are three main findings in our paper.Weekly rotations of in-class and distance learning reduce the spread of covid-19 by 75–81% and thus represent an effective preventative measure in school setting.Regular antigen testing twice a week, or weekly PCR testing, significantly reduces infections even when using tests with a lower sensitivity: tests with a 40% sensitivity reduce infections by more than 50 percent.The density of revealed contact graphs for older pupils is 1.5 times higher than the younger pupils graph, the teachers network is yet an order of magnitude denser. Consequently, the infection transmission between teachers is highly overproportional in our school. Moreover, teachers act as bridges connecting clusters of classes, especially in the secondary grade where they are responsible for 14–18% of infections, in comparison to 8–11% in primary grade.InterpretationWeekly rotations with regular testing are a highly effective non-pharmaceutical intervention for the prevention of covid-19 spread in schools and a way to keep schools open during an epidemic or to reopen them as the epidemiological situation improves.
Correlation between the environmental parameters with outbreak pattern of COVID-19: A district level investigation based on yearlong period in India
Authors: Gupta Amitesh , Saha Laboni 
Published: July 2021

AbstractThe present study has investigated the role of regional meteorology and air quality parameters in the outbreak pattern of COVID-19 pandemic in India. Using the remote sensing based dataset of 12 environmental variables we correlated infective case counts at a district level in India. Our investigation carried out on the circumstantial data from more than 300 major affected districts in India and found that air quality parameters are playing very crucial role in this outbreak. Among the air pollutants, O3 was better correlating with infection counts followed by AOD, CO, NO2, BC and SO2. We also observed that among the weather parameters air temperature, incoming shortwave radiation, wind speed are positively and significantly associate with outbreak pattern and precipitation and humidity are negatively correlated with confirmed cases; only cloud cover has no significant relation. We noted that coastal districts in the both coast of India and districts located in the plain and low-lying areas have experienced bitter situation during this pandemic. Our study suggests that improving air quality with proper strict regulations and complete lockdown during the peak of pandemic could reduce the misfortune in all over India.
The Gendered Implications of Energy Gaps in Health Care: A Comparative Analysis of Haiti, Senegal, and the Democratic Republic of Congo
Authors: Shastry Vivek , Morse Sophie M. 
Published: July 2021

AbstractThe World Health Organization recently articulated a number of challenges faced by health systems due to unreliable access to energy services. Reliable energy availability at rural health facilities is understood to be an enabler of access to quality healthcare, owing to its potential impacts on medical services, health and safety, disease prevention and treatment, staff recruitment and retention, and administration and logistics. However, little is known empirically about the intersections of energy and healthcare, often due to the lack of availability of facility level data. Moreover, the gender implications of energy access (or lack thereof) for women as providers and seekers of primary healthcare have not been investigated. In this study, using a gender lens, we explore the linkages between energy and healthcare in three Francophone countries in the Caribbean and sub-Saharan Africa: Democratic Republic of the Congo (DRC), Haiti and Senegal. All three countries have faced serious challenges to the provision of quality health services, including infrastructure problems and specifically unreliable access to electricity. We use Demographic Health Survey data from all three countries to present detailed descriptions of the association between (a) the availability and reliability of electricity sources, and (b) availability of health services, equipment and medical personnel at different levels of the respective health systems. We find that the unavailability and unreliability of electricity is associated with lower availability of medical equipment and basic health services, especially among facilities at the primary care level in DRC and Haiti. Our findings highlight the opportunity to create more dependable and sustainable health systems by integrating decentralized clean energy technologies into health infrastructure, which can facilitate providers in female-dominated cadres such as nursing the ability to provide the care they are tasked with.
Infectivity and immune escape of the new SARS-CoV-2 variant of interest Lambda
Authors: Acevedo Mónica L. , Alonso-Palomares Luis , Bustamante Andrés , Gaggero Aldo , Paredes Fabio , Cortés Claudia P. , Valiente-Echeverría Fernando , Soto-Rifo Ricardo 
Published: July 2021

ABSTRACTBackgroundThe newly described SARS-CoV-2 lineage C.37 was recently classified as a variant of interest by the WHO (Lambda variant) based on its high circulation rates in South American countries and the presence of critical mutations in the spike protein. The impact of such mutations in infectivity and immune escape from neutralizing antibodies are entirely unknown.MethodsWe performed a pseudotyped virus neutralization assay and determined the impact of the Lambda variant on infectivity and immune escape using plasma samples from healthcare workers (HCW) from two centers in Santiago, Chile who received the two-doses scheme of the inactivated virus vaccine CoronaVac.ResultsWe observed an increased infectivity mediated by the Lambda spike protein that was even higher than that of the D614G (lineage B) or the Alpha and Gamma variants. Compared to the Wild type (lineage A), neutralization was decreased by 3.05-fold for the Lambda variant while it was 2.33-fold for the Gamma variant and 2.03-fold for the Alpha variant.ConclusionsOur results indicate that mutations present in the spike protein of the Lambda variant of interest confer increased infectivity and immune escape from neutralizing antibodies elicited by CoronaVac. These data reinforce the idea that massive vaccination campaigns in countries with high SARS-CoV-2 circulation must be accompanied by strict genomic surveillance allowing the identification of new isolates carrying spike mutations and immunology studies aimed to determine the impact of these mutations in immune escape and vaccines breakthrough.
Characterization of DNA extrusion scenarios underlying aggregate Hi-C patterns by a new computational framework
Authors: Zhang Xizhe , Gogoshin Grigoriy , Branciamore Sergio 
Published: July 2021

1AbstractAggregate Hi-C maps centered on several genetic elements show significant DNA extrusion features. However, these features are missing from the component Hi-C images. To resolve this discrepancy, we present a new computational framework that reconstructs DNA extrusion scenarios (DESs) and explains the enhancement of DNA extrusion features by aggregation. We showed that the reconstructed DES is essential to understand the site interactions of the relevant genetic elements. For example, CCCTC-binding factor (CTCF) binding elements (CBE) with a specific motif direction are only affected by DNA extrusion activities initiated from one side, manifested as a directional bias. About half of promoters search for enhancers in a specific direction, as indicated by the corresponding DES. Moreover, since DNA extrusion does not pause at promoter or enhancer elements, direct promoter-enhancer contacts are not long-lasting; rather, promoters and enhancers are brought in proximity by continuous, dynamic DNA extrusion.
The recent range expansion of Great Cormorants (Phalacrocorax carbo hanedae) in Hokkaido, Japan
Authors: Squires Theodore E. , Aoki Daisuke , Hasegawa Osamu 
Published: July 2021

AbstractThough the Japanese subspecies of Great Cormorant (Phalacrocorax carbo hanedae) has increased its population in recent decades, information on its spread to the northern island of Hokkaido has not been reported outside of Japan. The purpose of this paper is to update the scientific community about the breeding and range ecology of P. carbo, and to provide comparative information on the abundant and similar looking resident Japanese Cormorant (P. capillatus). Several ornithological groups and researchers were contacted in order to gather information about the current distribution and breeding activities of P. carbo in the region. Here the findings of Japanese research groups, translated publications, and direct observations are made available.