bluuebunny/crossref_metadata_2025_split huggingface dataset:
Suicide, overdose and worker exit in a cohort of Michigan autoworkers
Authors: Eisen Ellen A , Chen Kevin T , Elser Holly , Picciotto Sally , Riddell Corinne A , Combs Mary A , Dufault Suzanne M , Goldman-Mellor Sidra , Cohen Joshua 
Published: July 2020

BackgroundIn recent decades, suicide and fatal overdose rates have increased in the US, particularly for working-age adults with no college education. The coincident decline in manufacturing has limited stable employment options for this population. Erosion of the Michigan automobile industry provides a striking case study.MethodsWe used individual-level data from a retrospective cohort study of 26 804 autoworkers in the United Autoworkers-General Motors cohort, using employment records from 1970 to 1994 and mortality follow-up from 1970 to 2015. We estimated HRs for suicide or fatal overdose in relation to leaving work, measured as active or inactive employment status and age at worker exit.ResultsThere were 257 deaths due to either suicide (n=202) or overdose (n=55); all but 21 events occurred after leaving work. The hazard rate for suicide was 16.1 times higher for inactive versus active workers (95% CI 9.8 to 26.5). HRs for suicide were elevated for all younger age groups relative to those leaving work after age 55. Those 30–39 years old at exit had the highest HR for suicide, 1.9 (95% CI 1.2 to 3.0). When overdose was included, the rate increased by twofold for both 19- to 29-year-olds and 30- to 39-year-olds at exit. Risks remained elevated when follow-up was restricted to 5 years after exit.ConclusionsAutoworkers who left work had a higher risk of suicide or overdose than active employees. Those who left before retirement age had higher rates than those who left after, suggesting that leaving work early may increase the risk.
Proteomic changes in intracranial blood during human ischemic stroke
Authors: Maglinger Benton , Frank Jacqueline A , McLouth Christopher J , Trout Amanda L , Roberts Jill Marie , Grupke Stephen , Turchan-Cholewo Jadwiga , Stowe Ann M , Fraser Justin F , Pennypacker Keith R 
Published: July 2020

BackgroundSince 2015, mechanical thrombectomy has been the standard treatment for emergent large vessel occlusion ischemic stroke.ObjectiveTo investigate, using the previously published Blood and Clot Thrombectomy Registry and Collaboration (BACTRAC) protocol (clinicaltrials.govNCT03153683), how the protein expression of a patient’s intracranial blood during ischemic stroke compares with the protein expression of their systemic arterial blood in order to better understand and treat stroke.MethodsPlasma samples from 25 subjects underwent proteomic analysis, where intracranial protein expression was compared with systemic protein levels. Data including sex, comorbidities, infarct volume, and infarct time were included for each subject.ResultsA majority of important proteins had a lower expression in intracranial blood than in systemic arterial blood. Proteins with the most significant changes in expression were: endopeptidase at −0.26 (p<0.0001), phospholipid transfer protein (PLTP) at −0.26 (p=0.0005), uromodulin (UMOD) at −0.14 (p=0.002), ficolin-2 (FCN2) at −0.46 (p=0.005), C-C motif chemokine 19 (CCL19) at −0.51 (p<0.0001), C-C motif chemokine 20 (CCL20) at −0.40 (p<0.0001), fibroblast growth factor 21 at −0.37 (p=0.0002), and C-C motif chemokine (CCL23) at −0.43 (p=0.0003).ConclusionsEvaluation of proteomic changes in the intravascular space of a cerebral infarct in progress in human subjects suggested that changes in proteins such PLTP, fetuin-B (FETUB), and FCN2 may be involved in atherosclerotic changes, and chemokines such as CCL23 are known to play a role in the Th2 autoimmune response. These data provide a scientific springboard for identifying clinically relevant biomarkers for diagnosis/prognosis, and targets for much needed neuroprotective/neuroreparative pharmacotherapies.
Role of guiding center in Landau level system and mechanical and pseudo orbital angular momenta
Authors: Kitadono Yoshio , Wakamatsu Masashi , Zou Liping , Zhang Pengming 
Published: July 2020

There is an interesting but not-so-popular quantity called pseudo orbital angular momentum (OAM) in the Landau-level system, besides the well-known canonical and mechanical OAMs. The pseudo OAM can be regarded as a gauge-invariant extension of the canonical OAM, which is formally gauge invariant and reduces to the canonical OAM in a certain gauge. Since both of the pseudo OAM and the mechanical OAM are gauge invariant, it is impossible to judge which of those is superior to the other solely from the gauge principle. However, these two OAMs have totally different physical meanings. The mechanical OAM shows manifest observability and clear correspondence with the classical OAM of the cyclotron motion. On the other hand, we demonstrate that the standard canonical OAM as well as the pseudo OAM in the Landau problem is the concept which crucially depend on the choice of the origin of the coordinate system. We try to reveal the relation between the pseudo OAM and the mechanical OAM as well as their observability by paying special attention to the role of guiding-center operator in the Landau problem.
Extracellular ATP and CD39 Activate cAMP-Mediated Mitochondrial Stress Response to Promote Cytarabine Resistance in Acute Myeloid Leukemia
Authors: Aroua Nesrine , Boet Emeline , Ghisi Margherita , Nicolau-Travers Marie-Laure , Saland Estelle , Gwilliam Ryan , de Toni Fabienne , Hosseini Mohsen , Mouchel Pierre-Luc , Farge Thomas , Bosc Claudie , Stuani Lucille , Sabatier Marie , Mazed Fetta , Larrue Clément , Jarrou Latifa , Gandarillas Sarah , Bardotti Massimiliano , Picard Muriel , Syrykh Charlotte , Laurent Camille , Gotanègre Mathilde , Bonnefoy Nathalie , Bellvert Floriant , Portais Jean-Charles , Nicot Nathalie , Azuaje Francisco , Kaoma Tony , Joffre Carine , Tamburini Jérome , Récher Christian , Vergez François , Sarry Jean-Emmanuel 
Published: July 2020

Abstract

Relapses driven by chemoresistant leukemic cell populations are the main cause of mortality for patients with acute myeloid leukemia (AML). Here, we show that the ectonucleotidase CD39 (ENTPD1) is upregulated in cytarabine-resistant leukemic cells from both AML cell lines and patient samples in vivo and in vitro. CD39 cell-surface expression and activity is increased in patients with AML upon chemotherapy compared with diagnosis, and enrichment in CD39-expressing blasts is a marker of adverse prognosis in the clinics. High CD39 activity promotes cytarabine resistance by enhancing mitochondrial activity and biogenesis through activation of a cAMP-mediated adaptive mitochondrial stress response. Finally, genetic and pharmacologic inhibition of CD39 ecto-ATPase activity blocks the mitochondrial reprogramming triggered by cytarabine treatment and markedly enhances its cytotoxicity in AML cells in vitro and in vivo. Together, these results reveal CD39 as a new residual disease marker and a promising therapeutic target to improve chemotherapy response in AML.

Significance:
Extracellular ATP and CD39–P2RY13–cAMP–OxPHOS axis are key regulators of cytarabine resistance, offering a new promising therapeutic strategy in AML.
This article is highlighted in the In This Issue feature, p. 1426
Racial Differences in Diuretic Efficiency, Plasma Renin, and Rehospitalization in Subjects With Acute Heart Failure
Authors: Morris Alanna A. , Nayak Aditi , Ko Yi-An , D’Souza Melroy , Felker G. Michael , Redfield Margaret M. , Tang W.H. Wilson , Testani Jeffrey M. , Butler Javed 
Published: July 2020

Background:
Black patients have higher rates of hospitalization for acute heart failure than other race/ethnic groups. We sought to determine whether diuretic efficiency is associated with racial differences in risk for rehospitalization after acute heart failure.

Methods:
A post hoc analysis was performed on 721 subjects (age, 68±13 years; 22% black) enrolled in 3 acute heart failure clinical trials: ROSE-AHF (Renal Optimization Strategies Evaluation in Acute Heart Failure), DOSE-AHF (Diuretic Optimization Strategy Evaluation in Acute Decompensated Heart Failure), and CARRESS-HF (Cardiorenal Rescue Study in Acute Decompensated Heart Failure). Repeated-measures ANOVA was used to test for a race×time effect on measures of decongestion. Diuretic efficiency was calculated as net fluid balance per total furosemide equivalents. In a subset of subjects, Cox regression was used to examine the association between race and rehospitalization according to plasma renin activity (PRA).

Results:

Compared with nonblack patients, black patients were younger and more likely to have nonischemic heart failure. During the first 72 to 96 hours, there was greater fluid loss (
P
=0.001), decrease in NT-proBNP (N-terminal pro-B-type natriuretic peptide;
P
=0.002), and lower levels of PRA (
P
<0.0001) in black patients. Diuretic efficiency was higher in black than in nonblack patients (403 [interquartile range, 221–795] versus 325 [interquartile range, 154–698];
P
=0.014). However, adjustment for baseline PRA attenuated the association between black race and diuretic efficiency. Over a median follow-up of 68 (interquartile range, 56–177) days, there was an increased risk of all-cause and heart failure–specific rehospitalization in nonblack patients with increasing levels of PRA, while the risk of rehospitalization was relatively constant across levels of PRA in black patients.

Conclusions:
Higher diuretic efficiency in black patients with acute heart failure may be related to racial differences in activity of the renin-angiotensin-aldosterone system.
Impact of Genetically Predicted Red Blood Cell Traits on Venous Thromboembolism: Multivariable Mendelian Randomization Study Using UK Biobank
Authors: Luo Shan , Au Yeung Shiu Lun , Zuber Verena , Burgess Stephen , Schooling Catherine Mary 
Published: July 2020

Background
Red blood cell (RBC) transfusion and erythropoiesis‐stimulating agent administration are cornerstones of clinical practice, yet concerns exist as to potential increased risk of thrombotic events. This study aims to identify RBC traits most relevant to venous thromboembolism (VTE) and assess their genetically predicted effects on VTE in the general population.

Methods and Results
We used multivariable mendelian randomization with bayesian model averaging for exposure selection. We obtained genetic variants predicting any of 12 RBC traits from the largest genome‐wide association study of hematological traits (173 480 participants of European ancestry) and applied them to the UK Biobank (265 424 white British participants). We used univariable mendelian randomization methods as sensitivity analyses for validation. Among 265 424 unrelated participants in the UK Biobank, there were 9752 cases of VTE (4490 men and 5262 women). Hemoglobin was selected as the plausible important RBC trait for VTE (marginal inclusion probability=0.91). The best‐fitting model across all RBC traits contained hemoglobin only (posterior probability=0.46). Using the inverse variance–weighted method, genetically predicted hemoglobin was positively associated (odds ratio, 1.21 per g/dL unit of hemoglobin; 95% CI, 1.05–1.41) with VTE. Sensitivity analyses (mendelian randomization–Egger, weighted median, and mendelian randomization pleiotropy residual sum and outlier test) gave consistent estimates.

Conclusions
Endogenous hemoglobin is the key RBC trait causing VTE, with a detrimental effect in the general population on VTE. Given men have higher hemoglobin than women, this finding may help explain the sexual disparity in VTE rates. The benefits of therapies and other factors that raise hemoglobin need to be weighed against their risks.
Traumatic Brain Injury in the Elderly: Can We Reduce Readmissions?
Authors: Wasfie Tarik , Maxwell Jordan , Parsons Andrea , Hille Jennifer , Yapchai Raquel , Hella Jennifer , Cwalina N , Barber Kimberly R. , Shapiro Brian 
Published: July 2020

Background Traumatic brain injury (TBI) is a leading cause of mortality and long-term morbidity in trauma patients, with a growing incidence among the elderly. Injury-related disability has many costs, and rehospitalization is a significant part of that. The current study was carried out in an elderly population with TBI to identify risk factors and measures associated with rehospitalization. Methods We performed a retrospective analysis of 299 patients with a primary diagnosis of TBI admitted between 2016 and 2018. Variables selected for analysis encompassed the following: patient age, sex, comorbidities, diagnosis, length of stay, use of anticoagulants, 6-month readmission rate, and diagnosis for readmission. Chi-square analysis was used to identify potential risk factors, and multiple regression analysis was conducted to model the relationship. Results 209 patients met inclusion criteria, with a mean age of 69 years (SD ± 18.6 years), with (51.5%) males and (48.5%) females. 188 (62.9%) patients were on anticoagulant therapy. 120 patients were discharged to home (40.1%). 79 patients (26.4%) were readmitted within 6 months of discharge, the majority of whom (48 patients, 60.8%) presented with a subdural hematoma (SDH). 38 readmitted patients (49%) came from home, and 57 patients (80%) were on anticoagulant therapy. Conclusion In elderly patients with TBI, discharge to a home setting correlates with a higher risk of readmission within 6 months, a majority with a diagnosis of recurrent SDH. Anticoagulant therapy and frequent past readmissions also correlated with a higher risk of subsequent readmission.
Low C4 as a risk factor for severe neuropsychiatric flare in patients with systemic lupus erythematosus
Authors: Aso Kuniyuki , Kono Michihito , Kono Michihiro , Watanabe Toshiyuki , Shimizu Yuka , Ogata Yusuke , Fujieda Yuichiro , Kato Masaru , Oku Kenji , Amengual Olga , Yasuda Shinsuke , Atsumi Tatsuya 
Published: July 2020

Objective This study aimed to explore the risk factors for ‘severe’ neuropsychiatric (NP) flare in patients with systemic lupus erythematosus (SLE). Methods This retrospective study comprised newly diagnosed 184 adult SLE patients who visited Hokkaido University Hospital between 2006 and 2017. In this study, severe NP flare was defined as the occurrence of at least one newly developed British Isles Lupus Assessment Group A score in the neurological domain. Overall severe NP flare-free survival was estimated by Kaplan–Meier analysis. Clinical and demographic profiles at SLE diagnosis were assessed as potential risk items in the adjusted multivariate Cox regression model. Results The median follow-up period was 7.9 years (interquartile range (IQR) 4.6–12.3) years. A total of 28 (15.2%) patients had one or more severe NP flares during the observation period. The median time from patient enrolment date to severe NP flare occurrence was 3.1 years (IQR 0.9–6.3 year). The 2- and 10-year severe NP flare-free survival rates were 92.7% and 86.0%, respectively. Among the manifestations of severe NP flare, psychosis was the most frequent (19.1%). In the multivariate model, low serum levels of C4 (hazard ratio (HR) = 3.67, p = 0.013) and severe NP manifestations at SLE diagnosis (HR = 7.11, p < 0.001) emerged as independent risk factors for developing severe NP flare. Conclusion The first severe NP flare presented early in the course of SLE. Low C4 level and severe NP manifestations at SLE diagnosis could predict the development of severe NP flare.
Pathology and pathogenicity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
Authors: Afewerky Henok Kessete 
Published: July 2020

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a beta coronavirus that causes infectious respiratory disease, named as coronavirus disease of 2019 (COVID-19). While extensive studies have provided basic information on clinical characteristics of COVID-19, the disease pathology is not fully known. The SARS-CoV-2 virus structural studies and biochemical experiments have also indicated that the virus receptor-binding domain (RBD) binds with a high affinity to angiotensin-converting enzyme-2 (ACE-2) receptor from humans; however, the mechanism remains unclear. Hereunder, a summary of relevant findings in the SARS-CoV-2 virus pathology and major pathogenicity mechanisms are discussed. This review of studies provides additional enlightenments on the way forward to prevent further spread or even cure for the SARS-CoV-2 virus-caused COVID-19 disease, either-or should a similar viral plague occur in the future. Impact statement The current survey of studies outlines the direct and indirect effects of SARS-CoV-2 on the specific body systems and summarizes the SARS-CoV-2 main pathogenicity mechanisms that require attention during patient hospitalization and for further research.
Anaemia in patients undergoing major bowel surgery – Prevalence and current practice: A public and private institution experience
Authors: Poon Edgar , Pache David , Delaforce Alana , Abdalla Lemya , McGuire Treasure 
Published: July 2020

Aim The study aimed to compare the frequency and alignment of preoperative anaemia screening and treatment with Australian guidelines in elective bowel surgery and determine the impact on clinical outcomes. Methods We performed a retrospective observational study, with an audit of 559 adult patients who underwent major elective bowel surgery in an Australian metropolitan hospital, January 2016–December 2018. Outcome measures included rate of anaemia, guideline compliance, hospital length of stay, and transfusion rate. Results Preoperative anaemia assessment occurred in 82.6% of patients. However, only 5.2% received recommended biochemical tests at least one week before surgery. Only 25.2% of anaemic patients received preoperative treatment; they experienced a longer hospital length of stay (9.93 days versus 7.88 days, p < 0.001) and an increased rate of transfusion (OR: 3.186, p < 0.05). Conclusion The gaps between current preoperative anaemia screening, management and national guidelines may place patients at higher risk of poor surgical outcome.
Pulmonary alveolar proteinosis: from classification to therapy
Authors: Salvaterra Elena , Campo Ilaria 
Published: July 2020

Pulmonary alveolar proteinosis (PAP) is a rare respiratory syndrome characterised by the accumulation of surfactant lipoproteins within the alveoli. According to various pathogenetic mechanisms and aetiologies, PAP is classified as primary, secondary or congenital. Primary PAP is led by a granulocyte–macrophage colony-stimulating factor (GM-CSF) signalling disruption; the autoimmune form is driven by the presence of anti GM-CSF autoantibodies and represents 90% of all the PAP cases; and the hereditary form is the result of mutations in genes encoding GM-CSF receptor. Secondary PAP is associated with various diseases causing a reduction in function and/or number of alveolar macrophages. Congenital PAP emerges as a consequence of corrupted surfactant production, due to mutations in surfactant proteins or lipid transporter, or mutations affecting lung development. The clinical manifestations are various, ranging from insidious onset to acute or progressive respiratory failure, including premature death within the first days of life in neonates with congenital surfactant production disorders. The diagnostic workup includes clinical and radiological assessment (respiratory function test, high-resolution chest computed tomography), laboratory tests (anti-GM-CSF autoantibodies dosage, GM-CSF serum level and GM-CSF signalling test), and genetic tests. Whole-lung lavage is the current gold standard of care of PAP; however, the therapeutic approach depends on the pathogenic form and disease severity, including GM-CSF augmentation strategies in autoimmune PAP and other promising new treatments.Educational aimsTo update knowledge about a rare respiratory syndrome, pulmonary alveolar proteinosis, in order to promote early diagnosis and correct management.To highlight recent treatment options based on pathogenesis and disease severity.
Bioinformatics recipes: creating, executing and distributing reproducible data analysis workflows
Authors: Aberra Natay , Sebastian Aswathy , Maloy Aaron P. , Rees Christopher B. , Bartron Meredith L. , Albert Istvan 
Published: July 2020

Abstract
Background
Bioinformaticians collaborating with life scientists need software that allows them to involve their collaborators in the process of data analysis.

Results
We have developed a web application that allows researchers to publish and execute data analysis scripts. Within the platform bioinformaticians are able to deploy data analysis workflows (recipes) that their collaborators can execute via point and click interfaces. The results generated by the recipes are viewable via the web interface and consist of a snapshot of all the commands, printed messages and files that have been generated during the recipe run.
A demonstration version of our software is available at https://www.bioinformatics.recipes/.
Detailed documentation for the software is available at: https://bioinformatics-recipes.readthedocs.io.
The source code for the software is distributed through GitHub at https://github.com/ialbert/biostar-central.

Conclusions
Our software platform supports collaborative interactions between bioinformaticians and life scientists. The software is presented via a web application that provides a high utility and user-friendly approach for conducting reproducible research. The recipes developed and shared through the web application are generic, with broad applicability and may be downloaded and executed on other computing platforms.
SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem
Authors: Calvelo Javier , Juan Hernán , Musto Héctor , Koziol Uriel , Iriarte Andrés 
Published: July 2020

AbstractBackgroundSpliced Leader trans-splicing is an important mechanism for the maturation of mRNAs in several lineages of eukaryotes, including several groups of parasites of great medical and economic importance. Nevertheless, its study across the tree of life is severely hindered by the problem of identifying the SL sequences that are being trans-spliced.ResultsIn this paper we present SLFinder, a four-step pipeline meant to identify de novo candidate SL sequences making very few assumptions regarding the SL sequence properties. The pipeline takes transcriptomic de novo assemblies and a reference genome as input and allows the user intervention on several points to account for unexpected features of the dataset. The strategy and its implementation were tested on real RNAseq data from species with and without SL Trans-Splicing.ConclusionsSLFinder is capable to identify SL candidates with good precision in a reasonable amount of time. It is especially suitable for species with unknown SL sequences, generating candidate sequences for further refining and experimental validation.