bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association Between Physician Burnout and Self-reported Errors: Meta-analysis
Authors: Owoc Jakub , Mańczak Małgorzata , Jabłońska Magdalena , Tombarkiewicz Marek , Olszewski Robert 
Published: June 2020

Objectives
Burnout among physicians is an increasingly recognized phenomenon affecting different aspects of patient care and safety. This meta-analysis quantifies association of burnout and its subscales with self-reported medical errors among physicians.

Methods
This meta-analysis followed the principles formulated in the Preferred Reporting Items for Systematic Reviews and Meta-Analyses and Meta-analyses of Observational Studies. The MEDLINE, PubMed, Web of Science, PsycInfo, and Eric databases were searched until February 5, 2019, using various combinations of key terms without any language restrictions: burnout, physicians, error, safety, and quality. Reference lists of selected studies were hand searched. Data were extracted from published reports. All quantitative studies reporting prevalence of burnout and its association with self-reported errors among physicians were considered. The analyses of heterogeneity (Cochran Q, I
2), publication bias (Begg-Mazumdar and Egger), three subgroups, and sensitivity were performed. The effect of overall burnout and Maslach Burnout Inventory subscales on self-reported errors was calculated as odds ratios with 95% confidence interval.

Results
Thirteen studies on 20,643 physicians and residents were included. The overall burnout among participants was associated with a significantly increased risk of self-reported errors (odds ratio = 2.72, 95% confidence interval = 2.19–3.37). Emotional exhaustion, depersonalization, and personal accomplishment were all independently predicting factors of self-reported errors. Cochran Q test and inconsistency index I
2 were as follows: Q = 27.2; P = 0.0013, I
2 = 67% (36%–83%).

Conclusions
The results provide evidence that not only overall burnout but also its subscales independently are to be associated with a significantly increased risk of self-reported errors among physicians. As self-reported errors may translate into different types of adverse events, this strong and unequivocal association should be of major concern to healthcare organizations.
A Machine Learning Approach to Reclassifying Miscellaneous Patient Safety Event Reports
Authors: Fong Allan , Behzad Shabnam , Pruitt Zoe , Ratwani Raj M. 
Published: June 2020

Background and Objectives
Medical errors are a leading cause of death in the United States. Despite widespread adoption of patient safety reporting systems to address medical errors, making sense of the reports collected in these systems is challenging in practice. Event classification taxonomies used in many reporting systems can be complex and difficult to understand by frontline reporters, leading reporters to classify reports as “miscellaneous” as opposed to assigning a specific event-type category, which may facilitate analysis.

Methods
To assist patient safety analysts in their analysis of “miscellaneous” reports, we developed an ensemble machine learning natural language processing model to reclassify these reports. We integrated the model into a clinical workflow dashboard, evaluated user feedback, and compared differences in user thresholds for model performance.

Results and Conclusions
Integrating an ensemble model to classify “miscellaneous” event reports with an interactive visualization was helpful to patient safety analysts review “miscellaneous” reports. However, patient safety analysts have different thresholds for model reclassification depending on their role and experience with “miscellaneous” event reports.
A Novel Machine Learning-derived Radiomic Signature of the Whole Lung Differentiates Stable From Progressive COVID-19 Infection
Authors: Fu Liping , Li Yongchou , Cheng Aiping , Pang PeiPei , Shu Zhenyu 
Published: June 2020

Objective:
This study aimed to use the radiomics signatures of a machine learning-based tool to evaluate the prognosis of patients with coronavirus disease 2019 (COVID-19) infection.

Methods:
The clinical and imaging data of 64 patients with confirmed diagnoses of COVID-19 were retrospectively selected and divided into a stable group and a progressive group according to the data obtained from the ongoing treatment process. Imaging features from whole-lung images from baseline computed tomography (CT) scans were extracted and dimensionality reduction was performed. Support vector machines were used to construct radiomics signatures and to compare differences between the 2 groups. We also compared the differences of signature scores in the clinical, laboratory, and CT image feature subgroups and finally analyzed the correlation between the radiomics features of the constructed signature and the other features including clinical, laboratory, and CT imaging features.

Results:
The signature has a good classification effect for the stable group and the progressive group, with area under curve, sensitivity, and specificity of 0.833, 80.95%, and 74.42%, respectively. Signature score differences in laboratory and CT imaging features between subgroups were not statistically significant (P>0.05); cough was negatively correlated with GLCM Entropy_angle 90_offset4 (r=−0.578), but was positively correlated with ShortRunEmphhasis_AllDirect_offset4_SD (r=0.454); C-reactive protein was positively correlated with Cluster Prominence_ AllDirect_offset 4_ SD (r=0.47).

Conclusion:
The radiomics signature of the whole lung based on machine learning may reveal the changes of lung microstructure in the early stage and help to indicate the progression of the disease.
Stable isotopes of fatty acids: current and future perspectives for advancing trophic ecology
Authors: Twining Cornelia W. , Taipale Sami J. , Ruess Liliane , Bec Alexandre , Martin-Creuzburg Dominik , Kainz Martin J. 
Published: June 2020

To understand consumer dietary requirements and resource use across ecosystems, researchers have employed a variety of methods, including bulk stable isotope and fatty acid composition analyses. Compound-specific stable isotope analysis (CSIA) of fatty acids combines both of these tools into an even more powerful method with the capacity to broaden our understanding of food web ecology and nutritional dynamics. Here, we provide an overview of the potential that CSIA studies hold and their constraints. We first review the use of fatty acid CSIA in ecology at the natural abundance level as well as enriched physiological tracers, and highlight the unique insights that CSIA of fatty acids can provide. Next, we evaluate methodological best practices when generating and interpreting CSIA data. We then introduce three cutting-edge methods: hydrogen CSIA of fatty acids, and fatty acid isotopomer and isotopologue analyses, which are not yet widely used in ecological studies, but hold the potential to address some of the limitations of current techniques. Finally, we address future priorities in the field of CSIA including: generating more data across a wider range of taxa; lowering costs and increasing laboratory availability; working across disciplinary and methodological boundaries; and combining approaches to answer macroevolutionary questions.This article is part of the theme issue ‘The next horizons for lipids as ‘trophic biomarkers’: evidence and significance of consumer modification of dietary fatty acids’.
Fatty acid bioconversion in harpacticoid copepods in a changing environment: a transcriptomic approach
Authors: Boyen Jens , Fink Patrick , Mensens Christoph , Hablützel Pascal I. , De Troch Marleen 
Published: June 2020

By 2100, global warming is predicted to significantly reduce the capacity of marine primary producers for long-chain polyunsaturated fatty acid (LC-PUFA) synthesis. Primary consumers such as harpacticoid copepods (Crustacea) might mitigate the resulting adverse effects on the food web by increased LC-PUFA bioconversion. Here, we present a high-quality de novo transcriptome assembly of the copepodPlatychelipus littoralis, exposed to changes in both temperature (+3°C) and dietary LC-PUFA availability. Using this transcriptome, we detected multiple transcripts putatively coding for LC-PUFA-bioconverting front-end fatty acid (FA) desaturases and elongases, and performed phylogenetic analyses to identify their relationship with sequences of other (crustacean) taxa. While temperature affected the absolute FA concentrations in copepods, LC-PUFA levels remained unaltered even when copepods were fed an LC-PUFA-deficient diet. While this suggests plasticity of LC-PUFA bioconversion withinP. littoralis, none of the putative front-end desaturase or elongase transcripts was differentially expressed under the applied treatments. Nevertheless, the transcriptome presented here provides a sound basis for future ecophysiological research on harpacticoid copepods.This article is part of the theme issue ‘The next horizons for lipids as ‘trophic biomarkers’: evidence and significance of consumer modification of dietary fatty acids'.
Dietary fat concentrations influence fatty acid assimilation patterns in Atlantic pollock (Pollachius virens)
Authors: Budge Suzanne M. , Townsend Kathryn , Lall Santosh P. , Bromaghin Jeffrey F. 
Published: June 2020

A key aspect in the use of fatty acids (FA) to estimate predator diets using quantitative FA signature analysis (QFASA) is the ability to account for FA assimilation through the use of calibration coefficients (CC). Here, we tested the assumption that CC are independent of dietary fat concentrations by feeding Atlantic pollock (Pollachius virens) three formulated diets with very similar FA proportions but different fat concentrations (5–9% of diet) for 20 weeks. CC calculated using FA profiles of diet and triacylglycerols in pollock liver were significantly different for the three diets. To test the robustness of diet estimates to these differences, we used the CC set derived from feeding the diet with the lowest fat concentration, published prey FA profiles and realistic diet estimates of pollock to construct ‘pseudo-predators'. Application of QFASA to each pseudo-predator using the three sets of CC and the same prey FA profiles resulted in diet estimate biases of twofold for major prey items and approximately fivefold for minor prey items. This work illustrates the importance of incorporating diets with fat concentrations that are similar to natural prey when conducting feeding experiments to calculate CC.This article is part of the theme ‘The next horizons for lipids as ‘trophic biomarkers': evidence and significance of consumer modification of dietary fatty acids'.
Shifting systems: prerequisites for the application of quantitative fatty acid signature analysis in soil food webs
Authors: Kühn Jakob , Tobias Kevin , Jähngen Alexander , Ruess Liliane 
Published: June 2020

Quantitative fatty acid signature analysis (QFASA) is widely used to investigate trophic interactions in marine ecosystems, as nutritionally importantω3 long-chain polyunsaturated fatty acids at the food web base allow tracing of their trophic transfer in the food chain. By contrast, the basal resources in soil food webs comprise a wider array of trophic markers, including branched-chain, cyclopropane as well as several mono- and polyunsaturated fatty acids. These diverse markers allow distinguishing between the three dominant soil carbon and energy channels, the root, bacterial and fungal pathway. QFASA has not been applied yet to soil ecosystems owing to the lack ofa prioridata to fit the model. The present work investigates the transfer of absolute and relative trophic marker fatty acids into Collembola as dominant representatives of the soil mesofauna. Three different species were fed on a variety of single diets characteristic for the green and brown food chain. Calibration coefficients were calculated and diet estimation trials for mixed diet set-ups were performed, using a library comprising 50 different resources. However, estimation of Collembola diet was only partially successful, identifying the main components, but not the correct relative proportions. Adjustments by fat content or diet group exclusion did not improve the results. Nonetheless, this work provides, to our knowledge, a first comprehensive dataset to translate the application of QFASA from marine to soil ecosystems.This article is part of the theme issue ‘The next horizons for lipids as ‘trophic biomarkers’: evidence and significance of consumer modification of dietary fatty acids’.
Juvenile Dungeness crabs (Metacarcinus magister) selectively integrate and modify the fatty acids of their experimental diets
Authors: Thomas Michael D. , Schram Julie B. , Clark-Henry Zade F. , Yednock Bree K. , Shanks Alan L. , Galloway Aaron W. E. 
Published: June 2020

Dungeness crabs (Metacarcinus magister) are ecologically and economically important in the coastal Northeast Pacific, yet relatively little is currently known about their feeding behaviour in the wild or their natural diet. Trophic biomarkers, such as fatty acids (FA), can be used to reveal trophic interactions. We used two feeding experiments to assess differences in FA composition of juvenile crabs fed different known foods to evaluate how they modify and integrate dietary FA into their own tissues and determine whether crab FA reflect diet changes over a six-week period. These experimental results were then compared with the FA signatures of wild caught juvenile crab with undetermined diets. We found that juvenile Dungeness crabs fed different foods assimilated dietary FA into their tissues and were distinct in their FA signatures when analysed with multivariate statistics. Experimentally fed juvenile crabs contained greater proportions of the most abundant long-chain polyunsaturated fatty acids (LCPUFA, >C20) than their foods. Crabs fed foods lacking in LCPUFA, particularly DHA (22:6ω3, docosahexaenoic acid), did not survive or grew slower than crabs fed other foods. This suggests that LCPUFA are physiologically important for this species and indicates biosynthesis of these FA does not occur or is not sufficient to meet their needs.This article is part of the theme issue ‘The next horizons for lipids as ‘trophic biomarkers’: evidence and significance of consumer modification of dietary fatty acids’.
Asip(Agouti-signaling protein) aggression gene regulate auditory processing genes in mice
Authors: Mickael Alexandra , Klimovich Pavel , Henckel Patrick , Kubick Norwin , Mickael Michel E 
Published: June 2020

AbstractCovid-19 strategy of lockdown has affected the lives of millions. The strict actions to enclose the epidemic have exposed many households to inner tensions. Domestic violence has been reported to increase during the lockdown. However, the reasons for this phenomenon have not been thoroughly investigated. Melanocortin GPCRs family contribution to aggression is well documented. ASIP (nonagouti) gene plays a vital role in regulating the melanocortin GPCRs family function, and it is responsible for regulating aggression in mice. We conducted a selection analysis of ASIP. We found that it negatively purified from Shark to humans. In order to better asses the effect of this gene in mammals, we performed RNA-seq analysis of a knockout of an ASIP crisper-cas mouse model. We found that ASIP KO in mice upregulates several genes controlling auditory function, includingPhox2b,Mpk13,Fat2, Neurod2, Slc18a3, Gon4l Gbx2, Slc6a3(Dat1) Aldh1a7 Tyrp1 and Lbx1. Interestingly, we found thatSlc6a5, andLamp5as well asIL33, which are associated with startle disease, are also upregulated in response to knocking out ASIP. These findings are indicative of a direct autoimmune effect between aggression-associated genes and startle disease. Furthermore, in order to validate the link between aggression and auditory inputs processing. We conducted psychological tests of persons who experienced lockdown. We found that aggression has risen by 16 % during the lockdown. Furthermore, 3% of the subjects interviewed reported a change in their hearing abilities. Our data shed light on the importance of the auditory input in aggression and open perceptions to interpret how hearing and aggression interact at the molecular neural circuit level.
Fungal dual-domain LysM effectors undergo chitin-induced intermolecular, and not intramolecular, dimerization
Authors: Tian Hui , Fiorin Gabriel L. , Kombrink Anja , Mesters Jeroen R. , Thomma Bart P.H.J. 
Published: June 2020

SUMMARYChitin is a homopolymer of β-(1,4)-linkedN-acetyl-D-glucosamine (GlcNAc) and a major structural component of fungal cell walls. In plants, chitin acts as a microbe-associated molecular pattern (MAMP) that is recognized by lysin motif (LysM)-containing plant cell surface-localized pattern recognition receptors (PRRs) that activate a plethora of downstream immune responses. In order to deregulate chitin-induced plant immunity and successfully establish infection, many fungal pathogens secrete LysM domain-containing effector proteins during host colonization. It was previously shown that the LysM effector Ecp6 from the tomato leaf mould fungusCladosporium fulvumcan outcompete plant PRRs for chitin binding because two of its three LysM domains cooperate to form a composite groove with ultra-high (pM) chitin-binding affinity. However, most functionally characterized LysM effectors contain only two LysMs, includingMagnaporthe oryzaeMoSlp1,Verticillium dahliaeVd2LysM, andColletotrichum higginsianumChElp1 and ChElp2. Here, we performed modelling, structural and functional analyses to investigate whether such dual-domain LysM effectors can also form ultra-high chitin-binding affinity grooves through intramolecular LysM dimerization. However, our study suggests that intramolecular LysM dimerization does not occur. Rather, our data support the occurrence of intermolecular LysM dimerization for these effectors, associated with a significantly lower chitin binding affinity than monitored for Ecp6. Interestingly, the intermolecular LysM dimerization allows for the formation of polymeric complexes in the presence of chitin. Possibly, such polymers may precipitate at infection sites in order to eliminate chitin oligomers, and thus suppress the activation of chitin-induced plant immunity.
E-cigarette, combustible, and smokeless tobacco product use combinations among youth in the United States, 2014-2019
Authors: Tam Jamie 
Published: June 2020

ABSTRACTIntroductionYouth e-cigarette use has been rising, however U.S. prevalence data are generally reported without disaggregating by individuals’ use of other tobacco products. It is not clear how the proportion of youth e-cigarette users naïve to all combustible tobacco is changing.MethodsAnnual prevalence estimates of ever and current (defined as past 30-day use) tobacco use prevalence by school type are reported using the 2014-2019 National Youth Tobacco Surveys (NYTS) with mutually exclusive categories of e-cigarette, smokeless tobacco, and/or combustible tobacco product use. T-tests were used to compare annual estimates with the preceding year. The annual percent change (APC) for each category from 2014-2018 were analyzed using JoinPoint regression. Data for 2019 were reported separately due to the change in survey format from paper to electronic.ResultsCurrent use of only e-cigarettes among HS students who never used combustible tobacco increased significantly from 2014-2018 (APC = +42.4%, 95% CI: 0.7, 101.3); by 2019, prevalence peaked at 9.2% (95% CI: 8.2, 10.2) among never combustible users and 8.3% (95% CI: 7.3, 9.3) among former combustible users. This coincided with significant declines in use of only combustible tobacco (APC=-14.5%, 95% CI: −18.3, −10.5).ConclusionsUse of only e-cigarettes among US youth with no history of combustible tobacco use has increased substantially over time, even as combustible tobacco use continues to plummet. Of the 17.5% (95% CI: 15.7, 19.0) of HS students who currently used only e-cigarettes (but not other tobacco) in 2019, more than half have no history of combustible tobacco use.
Critical Questions when Interpreting Coronavirus PCR Diagnostics
Authors: Durner Jürgen , Burggraf Siegfried , Czibere Ludwig , Fleige Tobias , Spannagel Michael , Watts David C , Becker Marc 
Published: June 2020

AbstractThe results of PCR measurements are regarded as unquestionable. This statement must be put into perspective. This relativization is particularly important in connection with the interpretation of SARS-CoV-2 results. Members of the critical infrastructure, such as nurses, may be quarantined although this is not necessary and are therefore missing from patient care. With our small but impressive comparison of methods and transport media for SARS-CoV-2, we not only show the different sensitivity of common routine systems and media in laboratory medicine. Further, we would like to inform clinically working physicians, who are not familiar with the technical weaknesses of the PCR investigation, about gaps and present solutions for their daily work.
Genome sequencing of the first SARS-CoV-2 reported from patients with COVID-19 in Ecuador
Authors: Márquez Sully , Prado-Vivar Belén , José Guadalupe Juan , Gutierrez Bernardo , Jibaja Manuel , Tobar Milton , Mora Francisco , Gaviria Juan , García María , Espinosa Franklin , Ligña Edison , Reyes Jorge , Barragán Verónica , Rojas-Silva Patricio , Trueba Gabriel , Grunauer Michelle , Cárdenas Paúl 
Published: June 2020

AbstractSARS-CoV-2, the etiological agent of COVID-19 was first described in Wuhan in December 2019 and has now spread globally. Ecuador was the second country in South America to report confirmed cases. The first case reported in Quito, the capital city of Ecuador, was a tourist who came from the Netherlands and presented symptoms on March 10th, 2020 (index case). In this work we used the MinION platform (Oxford Nanopore Technologies) to sequence the metagenome of the bronchoalveolar lavage (BAL) from this case reported, and subsequently we sequenced the whole genome of the index case and other three patients using the ARTIC network protocols. Our data from the metagenomic approach confirmed the presence of SARS-CoV-2 coexisting with pathogenic bacteria suggesting coinfection. Relevant bacteria found in the BAL metagenome were Streptococcus pneumoniae, Mycobacterium tuberculosis, Staphylococcus aureus and Chlamydia spp. Lineage assignment of the four whole genomes revealed three different origins. The variant HEE-01 was imported from the Netherlands and was assigned to B lineage, HGSQ-USFQ-018, belongs to the B.1 lineage showing nine nucleotide differences with the reference strain and grouped with sequences from the United Kingdom, and HGSQ-USFQ-007 and HGSQ-USFQ-010 belong to the B lineage and grouped with sequences from Scotland. All genomes show mutations in their genomes compared to the reference strain, which could be important to understand the virulence, severity and transmissibility of the virus. Our findings also suggest that there were at least three independent introductions of SARS-CoV-2 to Ecuador.IMPORTANCECOVID-19, an infectious disease caused by SARS-CoV-2, has spread globally including Latin American countries including Ecuador. The first strain of SARS-CoV-2 sequenced was from Wuhan, which is considered as the reference strain. There were no data about the SARS-CoV-2 lineages in Ecuador, and the purpose of this study was to find out the origin of the different lineages circulating in the population. We also were interested in the mutations present in these genomes as they can influence virulence, transmission and infectivity.