bluuebunny/crossref_metadata_2025_split huggingface dataset:
Perceptions of Equity and Inclusion in Acute Care Surgery
Authors: Tseng Esther S. , Zakrison Tanya L. , Williams Brian , Bernard Andrew C. , Martin Matthew J. , Zebib Laura , Soklaridis Sophie , Kaafarani Haytham M. , Zarzaur Ben L. , Crandall Marie , Seamon Mark J. , Winfield Robert D. , Bruns Brandon 
Published: October 2020

Objectives and Background:
The aim of this study was to characterize equity and inclusion in acute care surgery (ACS) with a survey to examine the demographics of ACS surgeons, the exclusionary or biased behaviors they witnessed and experienced, and where those behaviors happen. A major initiative of the Equity, Quality, and Inclusion in Trauma Surgery Practice Ad Hoc Task Force of the Eastern Association for the Surgery of Trauma was to characterize equity and inclusion in ACS. To do so, a survey was created with the above objectives.

Methods:
A cross-sectional, mixed-methods anonymous online survey was sent to all EAST members. Closed-ended questions are reported as percentages with a cutoff of α = 0.05 for significance. Quantitative results were analyzed focusing on mistreatment and bias.

Results:
Most respondents identified as white, non-Hispanic and male. In the past 12 months, 57.5% of females witnessed or experienced sexual harassment, whereas 48.6% of surgeons of color witnessed or experienced racial/ethnic discrimination. Sexual harassment, racial/ethnic prejudice, or discrimination based on sexual orientation/sex identity was more frequent in the workplace than at academic conferences or in ACS. Females were more likely than males to report unfair treatment due to age, appearance or sex in the workplace and ACS (P ≤ 0.002). Surgeons of color were more likely than white, non-Hispanics to report unfair treatment in the workplace and ACS due to race/ethnicity (P < 0.001).

Conclusions:
This is the first survey of ACS surgeons on equity and inclusion. Perceptions of bias are prevalent. Minorities reported more inequity than their white male counterparts. Behavior in the workplace was worse than at academic conferences or ACS. Ensuring equity and inclusion may help ACS attract and retain the best and brightest without fear of unfair treatment.
New Persistent Opioid Use After Inguinal Hernia Repair
Authors: Howard Ryan , Gunaseelan Vidhya , Brummett Chad , Waljee Jennifer , Englesbe Michael , Telem Dana 
Published: October 2020

Objective:
To describe the incidence of new persistent opioid use after inguinal hernia repair as well as its associated risk factors.

Summary of Background Data:
The development of new persistent opioid use after surgery is a common complication; however, its incidence following inguinal hernia repair has not been described. Given that roughly 800,000 inguinal hernia repairs are performed annually in the USA, any incidence could have profound implications for patients.

Methods:
A retrospective cross-sectional study of the incidence of new persistent opioid use after inguinal hernia repair using a national database of de-identified administrative health claims of opioid-naïve patients undergoing surgery from 2008 to 2016.

Results:
During the study period, 59,795 opioid-naïve patients underwent inguinal hernia repair and met inclusion criteria. Mean (SD) age was 57.8 (16.1) years and 55,014 (92%) patients were male. Nine hundred twenty-two (1.5%) patients continued filling opioids prescriptions for at least 3 months after surgery. The most significant risk factor for developing new persistent opioid use after surgery was filling an opioid prescription in the 30 days before surgery (odds ratio 4.34, 95% confidence interval 3.75–5.01). These prescriptions were provided by surgeons in 52% of cases and primary care physicians in 16% of cases. Other risk factors for new persistent opioid use included receiving a larger opioid prescription, having more comorbidities, having a major postoperative complication, and certain mental health disorders and pain disorders.

Conclusions:
After undergoing inguinal hernia repair, 1.5% of patients developed new persistent opioid use. Filling an opioid prescription in the 30 days before surgery had the strongest association with this complication.
Evidence-Based and Clinically Relevant Outcomes for Hemorrhage Control Trauma Trials
Authors: Holcomb John B. , Moore Ernest E. , Sperry Jason L. , Jansen Jan O. , Schreiber Martin A. , del Junco Deborah J. , Spinella Philip C. , Sauaia Angela , Brohi Karim , Bulger Eileen M. , Cap Andrew P. , Hess John R. , Jenkins Donald , Lewis Roger J. , Neal Matthew D. , Newgard Craig , Pati Shibani , Pusateri Anthony E. , Rizoli Sandro , Russell Robert T. , Shackelford Stacy A. , Stein Deborah M. , Steiner Marie E. , Wang Henry , Ward Kevin R. , Young Pampee 
Published: October 2020

Objective:
To address the clinical and regulatory challenges of optimal primary endpoints for bleeding patients by developing consensus-based recommendations for primary clinical outcomes for pivotal trials in patients within 6 categories of significant bleeding, (1) traumatic injury, (2) intracranial hemorrhage, (3) cardiac surgery, (4) gastrointestinal hemorrhage, (5) inherited bleeding disorders, and (6) hypoproliferative thrombocytopenia.

Background:
A standardized primary outcome in clinical trials evaluating hemostatic products and strategies for the treatment of clinically significant bleeding will facilitate the conduct, interpretation, and translation into clinical practice of hemostasis research and support alignment among funders, investigators, clinicians, and regulators.

Methods:
An international panel of experts was convened by the National Heart Lung and Blood Institute and the United States Department of Defense on September 23 and 24, 2019. For patients suffering hemorrhagic shock, the 26 trauma working-group members met for almost a year, utilizing biweekly phone conferences and then an in-person meeting, evaluating the strengths and weaknesses of previous high quality studies. The selection of the recommended primary outcome was guided by goals of patient-centeredness, expected or demonstrated sensitivity to beneficial treatment effects, biologic plausibility, clinical and logistical feasibility, and broad applicability.

Conclusions:
For patients suffering hemorrhagic shock, and especially from truncal hemorrhage, the recommended primary outcome was 3 to 6-hour all-cause mortality, chosen to coincide with the physiology of hemorrhagic death and to avoid bias from competing risks. Particular attention was recommended to injury and treatment time, as well as robust assessments of multiple safety related outcomes.
LuftiBus in the school (LUIS): a population-based study on respiratory health in schoolchildren
Authors: Mozun Rebeca , Kuehni Claudia E. , Pedersen Eva S. L. , Goutaki Myrofora , Kurz Johanna M. , de Hoogh Kees , Usemann Jakob , Singer Florian , Latzin Philipp , Moeller Alexander 
Published: October 2020

SummaryRespiratory disease is common in children and strongly associated with lifestyle and environmental exposures. Thus, it is important to study the epidemiology locally. LuftiBus in the school (LUIS) was set up to assess the respiratory health of schoolchildren in the canton of Zurich, Switzerland.LUIS is a cross-sectional population-based study that was carried out 2013 to 2016. Children aged 6-17 years living in the canton of Zurich were eligible to participate. All schools in the canton were approached and the school head decided whether the school would participate and with which classes. Consenting parents answered a standardized questionnaire at home and assenting children completed a shorter questionnaire by interview at school. Trained technicians measured children’s lung function including spirometry, double tracer gas single-breath washout (DTG-SBW) and fractional exhaled nitric oxide (FeNO). Address histories of participants were geocoded to be linked with area-based socioeconomic measures and environmental exposures like spatiotemporal air pollution estimates for specific time periods and locations. A subgroup was seen again 12 months later using the same procedures to collect longitudinal data.The study included 3870 children at baseline and 655 at the one-year follow-up. Median age was 12.7 years; 281 (8%) had wheezed in the past year. At baseline we collected 3457 (89%) parental and 3546 (92%) children’s questionnaires, and 3393 (88%) FeNO, 3446 (89%) spirometry, and 1795 (46%) DTG-SBW measurements.LUIS is a rich resource of health-related data, with information on lung function, environmental exposures and respiratory health on Swiss schoolchildren.Take home messageLuftiBus in the school (LUIS) is a population-based study with detailed lung function data and rich information on respiratory health in Swiss schoolchildren.
Estimating incidence of infection from diverse data sources: Zika virus in Puerto Rico, 2016
Authors: Quandelacy Talia M. , Healy Jessica M. , Greening Bradford , Rodriguez Dania M. , Chung Koo-Whang , Kuehnert Matthew J. , Biggerstaff Brad J. , Dirlikov Emilio , Mier-y-Teran-Romero Luis , Sharp Tyler M. , Waterman Stephen , Johansson Michael A. 
Published: October 2020

AbstractEmerging epidemics are challenging to track. Only a subset of cases is recognized and reported, as seen with the Zika virus (ZIKV) epidemic where large proportions of infection were asymptomatic. However, multiple imperfect indicators of infection provide an opportunity to estimate the underlying incidence of infection. We developed a modeling approach that integrates a generic Time-series Susceptible-Infected-Recovered epidemic model with assumptions about reporting biases in a Bayesian framework and applied it to the 2016 Zika epidemic in Puerto Rico using three indicators: suspected arboviral cases, suspected Zika-associated Guillain-Barré Syndrome cases, and blood bank data. Using this combination of surveillance data, we estimated the peak of the epidemic occurred during the week of August 15, 2016 (the 33rdweek of year), and 120 to 140 (50% credible interval [CrI], 95% CrI: 97 to 170) weekly infections per 10,000 population occurred at the peak. By the end of 2016, we estimated that approximately 890,000 (95% CrI: 660,000 to 1,100,000) individuals were infected in 2016 (26%, 95% CrI: 19% to 33%, of the population infected). Utilizing multiple indicators offers the opportunity for real-time and retrospective situational awareness to support epidemic preparedness and response.
On Modeling of COVID-19 for the Indian Subcontinent using Polynomial and Supervised Learning Regression
Authors: Neve Dishita , Patel Honey , Dhiman Harsh S. 
Published: October 2020

AbstractCOVID-19, a recently declared pandemic by WHO has taken the world by storm causing catastrophic damage to human life. The novel cornonavirus disease was first incepted in the Wuhan city of China on 31st December 2019. The symptoms include fever, cough, fatigue, shortness of breath or breathing difficulties, and loss of smell and taste. Since the devastating phenomenon is essentially a time-series representation, accurate modeling may benefit in identifying the root cause and accelerate the diagnosis. In the current analysis, COVID-19 modeling is done for the Indian subcontinent based on the data collected for the total cases confirmed, daily recovered, daily deaths, total recovered and total deaths. The data is treated with total confirmed cases as the target variable and rest as feature variables. It is observed that Support vector regressions yields accurate results followed by Polynomial regression. Random forest regression results in overfitting followed by poor Bayesian regression due to highly correlated feature variables. Further, in order to examine the effect of neighbouring countries, Pearson correlation matrix is computed to identify geographic cause and effect.
SM-Omics: An automated platform for high-throughput spatial multi-omics
Authors: Vickovic Sanja , Lötstedt Britta , Klughammer Johanna , Segerstolpe Åsa , Rozenblatt-Rosen Orit , Regev Aviv 
Published: October 2020

AbstractThe spatial organization of cells and molecules plays a key role in tissue function in homeostasis and disease. Spatial Transcriptomics (ST) has recently emerged as a key technique to capture and positionally barcode RNAs directly in tissues. Here, we advance the application of ST at scale, by presenting Spatial Multiomics (SM-Omics) as a fully automated high-throughput platform for combined and spatially resolved transcriptomics and antibody-based proteomics.
C9orf72- derived proline:arginine poly-dipeptides disturb cytoskeletal architecture
Authors: Shiota Tomo , Nagata Riko , Kikuchi Sotaro , Nanaura Hitoki , Matsubayashi Masaya , Nakanishi Mari , Kobashigawa Shinko , Nagayama Kazuaki , Sugie Kazuma , Yamashiro Yoshito , Mori Eiichiro 
Published: October 2020

AbstractAmyotrophic lateral sclerosis (ALS) is an irreversible neurodegenerative disease caused by the degeneration of motor neurons, and cytoskeletal instability is considered to be involved in neurodegeneration. A hexanucleotide repeat expansion of theC9orf72, one of the most common causes of familial ALS, produces toxic proline:arginine (PR) poly-dipeptides. PR poly-dipeptides binds polymeric forms of low complexity sequences and intracellular puncta, thereby altering intermediate filaments (IFs). However, how PR poly-dipeptides affect the cytoskeleton, including IFs, microtubules and actin filaments, remains unknown. Here we performed a synthetic PR poly-dipeptide treatment on mammalian cells and investigated how it affects morphology of cytoskeleton and cell behaviors. We observed that PR poly-dipeptide treatment induce the degradation of vimentin bundles at perinucleus and dissociation of β-tubulin network. PR poly-dipeptides also lead to alteration of actin filaments toward to cell contours and strength cortical actin filaments via activation of ERM (ezrin/radixin/moesin) proteins. In addition, we found that PR poly-dipeptides promote phosphorylation of paxillin and recruitment of vinculin on focal adhesions, which lead to maturation of focal adhesions. Finally, we evaluated the effects of PR poly-dipeptides on mechanical property and stress response. Interestingly, treatment of PR poly-dipeptides increased the elasticity of the cell surface, leading to maladaptive response to cyclic stretch. These results suggest that PR poly-dipeptides cause mechanically sensitive structural reorganization and disrupt the cytoskeleton architecture.
Evidence of antigenic imprinting in sequential Sarbecovirus immunization
Authors: Lv Huibin , So Ray T. Y. , Yuan Meng , Liu Hejun , Lee Chang-Chun D. , Yip Garrick K. , Ng Wilson W. , Wilson Ian A. , Peiris Malik , Wu Nicholas C. , Mok Chris K. P. 
Published: October 2020

SUMMARYAntigenic imprinting, which describes the bias of antibody response due to previous immune history, can influence vaccine effectiveness and has been reported in different viruses. Give that COVID-19 vaccine development is currently a major focus of the world, there is a lack of understanding of how background immunity influence antibody response to SARS-CoV-2. This study provides evidence for antigenic imprinting inSarbecovirus, which is the subgenus that SARS-CoV-2 belongs to. Specifically, we sequentially immunized mice with two antigenically distinctSarbecovirusstrains, namely SARS-CoV and SARS-CoV-2. We found that the neutralizing antibodies triggered by the sequentially immunization are dominantly against the one that is used for priming. Given that the impact of the background immunity on COVID-19 is still unclear, our results will provide important insights into the pathogenesis of this disease as well as COVID-19 vaccination strategy.
Multiplexed proteomics and imaging of resolving and lethal SARS-CoV-2 infection in the lung
Authors: Kalocsay Marian , Maliga Zoltan , Nirmal Ajit J. , Eisert Robyn J. , Bradshaw Gary A. , Solomon Isaac H , Chen Yu-An , Pelletier Roxanne J. , Jacobson Connor A. , Mintseris Julian , Padera Robert F. , Martinot Amanda J. , Barouch Dan H. , Santagata Sandro , Sorger Peter K. 
Published: October 2020

ABSTRACTNormal tissue physiology and repair depends on communication with the immune system. Understanding this communication at the molecular level in intact tissue requires new methods. The consequences of SARS-CoV-2 infection, which can result in acute respiratory distress, thrombosis and death, has been studied primarily in accessible liquid specimens such as blood, sputum and bronchoalveolar lavage, all of which are peripheral to the primary site of infection in the lung. Here, we describe the combined use of multiplexed deep proteomics with multiplexed imaging to profile infection and its sequelae directly in fixed lung tissue specimens obtained from necropsy of infected animals and autopsy of human decedents. We characterize multiple steps in disease response from cytokine accumulation and protein phosphorylation to activation of receptors, changes in signaling pathways, and crosslinking of fibrin to form clots. Our data reveal significant differences between naturally resolving SARS-CoV-2 infection in rhesus macaques and lethal COVID-19 in humans. The approach we describe is broadly applicable to other tissues and diseases.SummaryProteomics of infected tissue reveals differences in inflammatory and thrombotic responses between resolving and lethal COVID-19.
A Common Methodological Phylogenomics Framework for intra-patient heteroplasmies to infer SARS-CoV-2 sublineages and tumor clones
Authors: Utro Filippo , Levovitz Chaya , Rhrissorrakrai Kahn , Parida Laxmi 
Published: October 2020

AbstractWe present a common methodological framework to infer the phylogenomics from genomic data, be it reads of SARS-CoV-2 of multiple COVID-19 patients or bulk DNAseq of the tumor of a cancer patient. The commonality is in the phylogenetic retrodiction based on the genomic reads in both scenarios. While there is evidence of heteroplasmy, i.e., multiple lineages of SARS-CoV-2 in the same COVID-19 patient; to date, there is no evidence of sublineages recombining within the same patient. The heterogeneity in a patient’s tumor is analogous to intra-patient heteroplasmy and the absence of recombination in the cells of tumor is a widely accepted assumption. Just as the different frequencies of the genomic variants in a tumor presupposes the existence of multiple tumor clones and provides a handle to computationally infer them, we postulate that so do the different variant frequencies in the viral reads, offering the means to infer the multiple co-infecting sublineages. We describe the Concerti computational framework for inferring phylogenies in each of the two scenarios. To demonstrate the accuracy of the method, we reproduce some known results in both scenarios. We also make some additional discoveries. We uncovered new potential parallel mutation in the evolution of the SARS-CoV-2 virus. In the context of cancer, we uncovered new clones harboring resistant mutations to therapy from clinically plausible phylogenetic tree in a patient.
From amazing work to I beg to differ - analysis of bioRxiv preprints that received one public comment till September 2019
Authors: Malički Mario , Costello Joseph , Alperin Juan Pablo , Maggio Lauren A. 
Published: October 2020

AbstractWhile early commenting on studies is seen as one of the advantages of preprints, the nature of such comments, and the people who post them, have not been systematically explored. We analysed comments posted between 21 May 2015 and 9 September 2019 for 1,983 bioRxiv preprints that received only one comment. Sixty-nine percent of comments were posted by non-authors (n=1,366), and 31% by preprint authors (n=617). Twelve percent of non-author comments (n=168) were full review reports traditionally found during journal review, while the rest most commonly contained praises (n=577, 42%), suggestions (n=399, 29%), or criticisms (n=226, 17%). Authors’ comments most commonly contained publication status updates (n=354, 57%), additional study information (n=158, 26%), or solicited feedback for the preprints (n=65, 11%). Our study points to the value of preprint commenting, but further studies are needed to determine the role that comments play in shaping preprint versions and eventual journal publications.
Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data
Authors: Zhang Junpeng , Liu Lin , Xu Taosheng , Zhang Wu , Zhao Chunwen , Li Sijing , Li Jiuyong , Rao Nini , Le Thuc Duy 
Published: October 2020

AbstractBackgroundExisting computational methods for studying miRNA regulation are mostly based on bulk miRNA and mRNA expression data. However, bulk data only allows the analysis of miRNA regulation regarding a group of cells, rather than the miRNA regulation unique to individual cells. Recent advance in single-cell miRNA-mRNA co-sequencing technology has opened a way for investigating miRNA regulation at single-cell level. However, as currently single-cell miRNA-mRNA co-sequencing data is just emerging and only available at small-scale, there is a strong need of novel methods to exploit existing single-cell data for the study of cell-specific miRNA regulation.ResultsIn this work, we propose a new method,CSmiR(Cell-SpecificmiRNA regulation) to use single-cell miRNA-mRNA co-sequencing data to identify miRNA regulatory networks at the resolution of individual cells. We applyCSmiRto the miRNA-mRNA co-sequencing data in 19 K562 single-cells to identify cell-specific miRNA-mRNA regulatory networks for understanding miRNA regulation in each K562 single-cell. By analyzing the obtained cell-specific miRNA-mRNA regulatory networks, we observe that the miRNA regulation in each K562 single-cell is unique. Moreover, we conduct detailed analysis on the cell-specific miRNA regulation associated with the miR-17/92 family as a case study. Finally, through exploring cell-cell similarity matrix characterized by cell-specific miRNA regulation,CSmiRprovides a novel strategy for clustering single-cells to help understand cell-cell crosstalk.ConclusionsTo the best of our knowledge,CSmiRis the first method to explore miRNA regulation at a single-cell resolution level, and we believe that it can be a useful method to enhance the understanding of cell-specific miRNA regulation.
Mechanical competition alters the cellular interpretation of an endogenous genetic programme
Authors: Bhide Sourabh , Gombalova Denisa , Mönke Gregor , Stegmaier Johannes , Zinchenko Valentyna , Kreshuk Anna , Belmonte Julio M , Leptin Maria 
Published: October 2020

AbstractThe intrinsic genetic programme of a cell is not sufficient to explain all of the cell’s activities. External mechanical stimuli are increasingly recognized as determinants of cell behaviour. In the epithelial folding event that constitutes the beginning of gastrulation inDrosophila, the genetic programme of the future mesoderm leads to the establishment of a contractile actomyosin network that triggers apical constriction of cells, and thereby, tissue folding. However, some cells do not constrict but instead stretch, even though they share the same genetic programme as their constricting neighbours. We show here that tissue-wide interactions force these cells to expand even when an otherwise sufficient amount of apical, active actomyosin is present. Models based on contractile forces and linear stress-strain responses do not reproduce experimental observations, but simulations in which cells behave as ductile materials with non-linear mechanical properties do. Our models show that this behaviour is a general emergent property of actomyosin networks [in a supracellular context, in accordance with our experimental observations of actin reorganisation within stretching cells.