bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical and Laboratory Predictors of In-hospital Mortality in Patients With Coronavirus Disease-2019: A Cohort Study in Wuhan, China
Authors: Wang Kun , Zuo Peiyuan , Liu Yuwei , Zhang Meng , Zhao Xiaofang , Xie Songpu , Zhang Hao , Chen Xinglin , Liu Chengyun 
Published: May 2020

AbstractBackgroundThis study aimed to develop mortality-prediction models for patients with coronavirus disease-2019 (COVID-19).MethodsThe training cohort included consecutive COVID-19 patients at the First People’s Hospital of Jiangxia District in Wuhan, China, from 7 January 2020 to 11 February 2020. We selected baseline data through the stepwise Akaike information criterion and ensemble XGBoost (extreme gradient boosting) model to build mortality-prediction models. We then validated these models by randomly collected COVID-19 patients in Union Hospital, Wuhan, from 1 January 2020 to 20 February 2020.ResultsA total of 296 COVID-19 patients were enrolled in the training cohort; 19 died during hospitalization and 277 discharged from the hospital. The clinical model developed using age, history of hypertension, and coronary heart disease showed area under the curve (AUC), 0.88 (95% confidence interval [CI], .80–.95); threshold, −2.6551; sensitivity, 92.31%; specificity, 77.44%; and negative predictive value (NPV), 99.34%. The laboratory model developed using age, high-sensitivity C-reactive protein, peripheral capillary oxygen saturation, neutrophil and lymphocyte count, d-dimer, aspartate aminotransferase, and glomerular filtration rate had a significantly stronger discriminatory power than the clinical model (P = .0157), with AUC, 0.98 (95% CI, .92–.99); threshold, −2.998; sensitivity, 100.00%; specificity, 92.82%; and NPV, 100.00%. In the subsequent validation cohort (N = 44), the AUC (95% CI) was 0.83 (.68–.93) and 0.88 (.75–.96) for the clinical model and laboratory model, respectively.ConclusionsWe developed 2 predictive models for the in-hospital mortality of patients with COVID-19 in Wuhan that were validated in patients from another center.
Functional modulation of atrio-ventricular conduction by enhanced late sodium current and calcium-dependent mechanisms in Scn5a1798insD/+ mice
Authors: Rivaud Mathilde R , Marchal Gerard A , Wolswinkel Rianne , Jansen John A , van der Made Ingeborg , Beekman Leander , Ruiz-Villalba Adrián , Baartscheer Antonius , Rajamani Sridharan , Belardinelli Luiz , van Veen Toon A B , Basso Cristina , Thiene Gaetano , Creemers Esther E , Bezzina Connie R , Remme Carol Ann 
Published: May 2020

Abstract

Aims
SCN5A mutations are associated with arrhythmia syndromes, including Brugada syndrome, long QT syndrome type 3 (LQT3), and cardiac conduction disease. Long QT syndrome type 3 patients display atrio-ventricular (AV) conduction slowing which may contribute to arrhythmogenesis. We here investigated the as yet unknown underlying mechanisms.

Methods and results
We assessed electrophysiological and molecular alterations underlying AV-conduction abnormalities in mice carrying the Scn5a1798insD/+ mutation. Langendorff-perfused Scn5a1798insD/+ hearts showed prolonged AV-conduction compared to wild type (WT) without changes in atrial and His-ventricular (HV) conduction. The late sodium current (INa,L) inhibitor ranolazine (RAN) normalized AV-conduction in Scn5a1798insD/+ mice, likely by preventing the mutation-induced increase in intracellular sodium ([Na+]i) and calcium ([Ca2+]i) concentrations. Indeed, further enhancement of [Na+]i and [Ca2+]i by the Na+/K+-ATPase inhibitor ouabain caused excessive increase in AV-conduction time in Scn5a1798insD/+ hearts. Scn5a1798insD/+ mice from the 129P2 strain displayed more severe AV-conduction abnormalities than FVB/N-Scn5a1798insD/+ mice, in line with their larger mutation-induced INa,L. Transverse aortic constriction (TAC) caused excessive prolongation of AV-conduction in FVB/N-Scn5a1798insD/+ mice (while HV-intervals remained unchanged), which was prevented by chronic RAN treatment. Scn5a1798insD/+-TAC hearts showed decreased mRNA levels of conduction genes in the AV-nodal region, but no structural changes in the AV-node or His bundle. In Scn5a1798insD/+-TAC mice deficient for the transcription factor Nfatc2 (effector of the calcium-calcineurin pathway), AV-conduction and conduction gene expression were restored to WT levels.

Conclusions
Our findings indicate a detrimental role for enhanced INa,L and consequent calcium dysregulation on AV-conduction in Scn5a1798insD/+ mice, providing evidence for a functional mechanism underlying AV-conduction disturbances secondary to gain-of-function SCN5A mutations.
Loss of the Polyketide Synthase StlB Results in Stalk Cell Overproduction in Polysphondylium violaceum
Authors: Narita Takaaki B , Kawabe Yoshinori , Kin Koryu , Gibbs Richard A , Kuspa Adam , Muzny Donna M , Richards Stephen , Strassmann Joan E , Sucgang Richard , Worley Kim C , Schaap Pauline 
Published: May 2020

Abstract
Major phenotypic innovations in social amoeba evolution occurred at the transition between the Polysphondylia and group 4 Dictyostelia, which comprise the model organism Dictyostelium discoideum, such as the formation of a new structure, the basal disk. Basal disk differentiation and robust stalk formation require the morphogen DIF-1, synthesized by the polyketide synthase StlB, the des-methyl-DIF-1 methyltransferase DmtA, and the chlorinase ChlA, which are conserved throughout Dictyostelia. To understand how the basal disk and other innovations evolved in group 4, we sequenced and annotated the Polysphondylium violaceum (Pvio) genome, performed cell type-specific transcriptomics to identify cell-type marker genes, and developed transformation and gene knock-out procedures for Pvio. We used the novel methods to delete the Pvio stlB gene. The Pvio stlB− mutants formed misshapen curly sorogens with thick and irregular stalks. As fruiting body formation continued, the upper stalks became more regular, but structures contained 40% less spores. The stlB− sorogens overexpressed a stalk gene and underexpressed a (pre)spore gene. Normal fruiting body formation and sporulation were restored in Pvio stlB− by including DIF-1 in the supporting agar. These data indicate that, although conserved, stlB and its product(s) acquired both a novel role in the group 4 Dictyostelia and a role opposite to that in its sister group.
Effects of electrical anisotropy on long-offset transient electromagnetic data
Authors: Liu Yajun , Yogeshwar Pritam , Hu Xiangyun , Peng Ronghua , Tezkan Bülent , Mörbe Wiebke , Li Jianhui 
Published: May 2020

SUMMARY
Electrical anisotropy of formations has been long recognized by field and laboratory evidence. However, most interpretations of long-offset transient electromagnetic (LOTEM) data are based on the assumption of an electrical isotropic earth. Neglecting electrical anisotropy of formations may cause severe misleading interpretations in regions with strong electrical anisotropy. During a large scale LOTEM survey in a former mining area in Eastern Germany, data was acquired over black shale formations. These black shales are expected to produce a pronounced bulk anisotropy. Here, we investigate the effects of electrical anisotropy on LOTEM responses through numerical simulation using a finite-volume time-domain (FVTD) algorithm. On the basis of isotropic models obtained from LOTEM field data, various anisotropic models are developed and analysed. Numerical results demonstrate that the presence of electrical anisotropy has a significant influence on LOTEM responses. Based on the numerical modelling results, an isolated deep conductive anomaly presented in the 2-D isotropic LOTEM electric field data inversion result is identified as a possible artifact introduced by using an isotropic inversion scheme. Trial-and-error forward modelling of the LOTEM electric field data using an anisotropic conductivity model can explain the data and results in a reasonable quantitative data fit. The derived anisotropic 2-D model is consistent with the prior geological information.
High-resolution lithosphere viscosity structure and the dynamics of the 2008 Wenchuan earthquake area: new constraints from magnetotelluric imaging
Authors: Zhu Tao , Zhan Yan , Unsworth Martyn , Zhao Guoze , Sun Xiangyu 
Published: May 2020

SUMMARYEstimation of lithospheric viscosity remains challenging, especially for variations with spatial scales less than 100 km. Some recent studies have developed a method to determine viscosity structure from electrical conductivity models determined from magnetotelluric (MT) data. This method was initially applied to the extensional transition zone from the Great Basin to Colorado Plateau. Here, we use this approach to infer the effective lithospheric viscosity in a convergent setting by using an MT profile that crosses the eastern margin of the Tibetan Plateau. The profile extends from the Songpan-Ganzi block, crosses the 2008 Wenchuan earthquake epicentre region and ends in the Sichuan basin. The preferred viscosity structure is characterized by the middle-lower crustal viscosities in the range 2.42 × 1018 to 2.69 × 1021 Pa s below the Songpan-Ganzi block. In the Longmenshan fault zone and 2008 Wenchuan Ms8.0 earthquake area, the crustal viscosity is higher and in the range 4.32 × 1018 to 5.10 × 1021 Pa s with significant small-scale (&lt;100 km) lateral variations. The MT-derived viscosities are consistent with previous regional-scale estimates but reveal the viscosity structure in more detail. The preferred geodynamic model can explain both the crustal deformation velocity and the small-scale lateral variations of surface topography. It implies that the crustal deformation is driven by mantle flow that results in a weak coupling of the upper and middle-lower crust beneath the eastern Tibetan Plateau. The inferred viscosity structure may help further understand the earthquake mechanisms in the Longmenshan fault zone.
Changing Norms: A Meta-Analytic Integration of Research on Social Norms Appeals
Authors: Rhodes Nancy , Shulman Hillary C , McClaran Nikki 
Published: May 2020

Abstract
Social norm appeals attempt to change behavior by modifying the prevailing view that a particular, usually harmful, behavior is less prevalent or less approved of in certain social contexts. These messages have been widely used, such as in safe-drinking campaigns targeted towards college students, but reviews of such efforts have been mixed. The present review used meta-analytic techniques to clarify the effects of social norm manipulations by synthesizing findings from 110 articles. We found consistent support for the effectiveness of social norm manipulations across various outcomes, although effect sizes overall tended to be small. There was also evidence that injunctive norms, though underutilized, may be more effective in changing behavior than previously considered. Moderator analyses demonstrated effects for methodological, sample, and message variables that offer insights into how norms function. The analysis also revealed significant heterogeneity, which underscores the need for more standardization in this area.
The effect of paternal exposure to immunosuppressive drugs on sexual function, reproductive hormones, fertility, pregnancy and offspring outcomes: a systematic review
Authors: Perez-Garcia L F , Dolhain R J E M , Vorstenbosch S , Bramer W , van Puijenbroek E , Hazes J M W , te Winkel B 
Published: May 2020

AbstractBACKGROUNDInformation regarding the possible influence of immunosuppressive drugs on male sexual function and reproductive outcomes is scarce. Men diagnosed with immune-mediated diseases and a wish to become a father represent an important neglected population since they lack vital information to make balanced decisions about their treatment.OBJECTIVE AND RATIONALEThe aim of this research was to systematically review the literature for the influence of paternal immunosuppressive drug use on many aspects of male sexual health, such as sexual function, fertility, pregnancy outcomes and offspring health outcomes.SEARCH METHODSA systematic literature search was performed in the bibliographic databases: Embase (via Elsevier embase.com), MEDLINE ALL via Ovid, Cochrane Central Register of Trials (via Wiley) and Web of Science Core Collection. Additionally, Google Scholar and the Clinical trial registries of Europe and the USA were searched. The databases were searched from inception until 31 August 2019. The searches combined keywords regarding male sexual function and fertility, pregnancy outcomes and offspring health with a list of immunosuppressive drugs. Studies were included if they were published in English and if they included original data on male human exposure to immunosuppressive drugs. A meta-analysis was not possible to perform due to the heterogeneity of the data.OUTCOMESA total of 5867 references were identified, amongst which we identified 161 articles fulfilling the eligibility criteria. Amongst these articles, 50 included pregnancy and offspring outcomes and 130 included sexual health outcomes. Except for large Scandinavian cohorts, most of the identified articles included a small number of participants. While a clear negative effect on sperm quality was evident for sulfasalazine and cyclophosphamide, a dubious effect was identified for colchicine, methotrexate and sirolimus. In three articles, exposure to tumour necrosis factor-α inhibitors in patients diagnosed with ankylosing spondylitis resulted in improved sperm quality. The information regarding pregnancy and offspring outcomes was scant but no large negative effect associated with paternal immunosuppressive drug exposure was reported.WIDER IMPLICATIONSEvidence regarding the safety of immunosuppressive drugs in men with a wish to become a father is inconclusive. The lack of standardisation on how to evaluate and report male sexual function, fertility and reproduction as study outcomes in men exposed to immunosuppressive drugs is an important contributor to this result. Future research on this topic is needed and should be preferably done using standardised methods.
The Promises and the Challenges of Integrating Multi-Omics and Systems Biology in Comparative Stress Biology
Authors: Schwartz Tonia S 
Published: May 2020

Abstract
Comparative stress biology is inherently a systems biology approach with the goal of integrating the molecular, cellular, and physiological responses with fitness outcomes. In this way, the systems biology approach is expected to provide a holistic understanding of how different stressors result in different fitness outcomes, and how different individuals (or populations or species) respond to stressors differently. In this perceptive article, I focus on the use of multiple types of -omics data in stress biology. Targeting students and those researchers who are considering integrating -omics approaches in their comparative stress biology studies, I discuss the promise of the integration of these measures for furthering our holistic understanding of how organisms respond to different stressors. I also discuss the logistical and conceptual challenges encountered when working with -omics data and the current hurdles to fully utilize these data in studies of stress biology in non-model organisms.
Leading Terms of SL3 Web Invariants
Authors: Bazier-Matte Véronique , Douville Guillaume , Garver Alexander , Patrias Rebecca , Thomas Hugh , Yıldırım Emine 
Published: May 2020

Abstract
We use Khovanov and Kuperberg’s web growth rules to identify the leading term in the invariant associated to an $\textrm{SL}_3$ web diagram, with respect to a particular term order.
Methamphetamine Injection Among Young Men Who Have Sex With Men: Risk for Human Immunodeficiency Virus Transmission in a Los Angeles Cohort
Authors: Gorbach Pamina M , Javanbakht Marjan , Ragsdale Amy , Bolan Robert B , Flynn Risa , Mandler Raul , Shoptaw Steven 
Published: May 2020

Abstract

Background
Prevalence of methamphetamine (meth) injection and associated human immunodeficiency virus (HIV) risks among men who have sex with men (MSM) are unclear.

Methods
A total of 532 MSM completed 1880 mSTUDY study visits between August 2014 and June 2018 in Los Angeles, California. Assessments every 6 months included computer-assisted self-interviews and testing for sexually transmitted infections. Analyses by person and across visits adjusted for repeated measures.

Results
Of 532 participants, 51% (n = 276) reported meth use (past 6 months). Across 1880 visits, mutually exclusive substance use categories were as follows: 5% meth injection (5%), meth use without injection (33%), other substance use excluding meth (36%), and no substance use (26%). Comparisons across these categories respectively found that meth injectors reported higher prevalence of new sex partners (89%, 70%, 68%, and 51%, respectively), more were HIV positive (83%, 65%, 34%, and 50%), fewer were virally suppressed (53%, 48%, 61%, and 67%), and more had sexually transmitted infections (31%, 22%, 15%, and 15% (all P &lt;.01).

Conclusions
Among the young MSM reporting meth injection in this Los Angeles cohort, elevated risks of acquiring or transmitting HIV suggest that they contribute significantly to sustaining the local HIV epidemic. Preventing transition to injection use has potential for HIV prevention.
UMLS users and uses: a current overview
Authors: Amos Liz , Anderson David , Brody Stacy , Ripple Anna , Humphreys Betsy L 
Published: May 2020

Abstract
The US National Library of Medicine regularly collects summary data on direct use of Unified Medical Language System (UMLS) resources. The summary data sources include UMLS user registration data, required annual reports submitted by registered users, and statistics on downloads and application programming interface calls. In 2019, the National Library of Medicine analyzed the summary data on 2018 UMLS use. The library also conducted a scoping review of the literature to provide additional intelligence about the research uses of UMLS as input to a planned 2020 review of UMLS production methods and priorities. 5043 direct users of UMLS data and tools downloaded 4402 copies of the UMLS resources and issued 66 130 951 UMLS application programming interface requests in 2018. The annual reports and the scoping review results agree that the primary UMLS uses are to process and interpret text and facilitate mapping or linking between terminologies. These uses align with the original stated purpose of the UMLS.
TREC-COVID: rationale and structure of an information retrieval shared task for COVID-19
Authors: Roberts Kirk , Alam Tasmeer , Bedrick Steven , Demner-Fushman Dina , Lo Kyle , Soboroff Ian , Voorhees Ellen , Wang Lucy Lu , Hersh William R 
Published: May 2020

Abstract
TREC-COVID is an information retrieval (IR) shared task initiated to support clinicians and clinical research during the COVID-19 pandemic. IR for pandemics breaks many normal assumptions, which can be seen by examining 9 important basic IR research questions related to pandemic situations. TREC-COVID differs from traditional IR shared task evaluations with special considerations for the expected users, IR modality considerations, topic development, participant requirements, assessment process, relevance criteria, evaluation metrics, iteration process, projected timeline, and the implications of data use as a post-task test collection. This article describes how all these were addressed for the particular requirements of developing IR systems under a pandemic situation. Finally, initial participation numbers are also provided, which demonstrate the tremendous interest the IR community has in this effort.
Real-world use of osimertinib for epidermal growth factor receptor T790M-positive non-small cell lung cancer in Japan
Authors: Ohe Yuichiro , Kato Terufumi , Sakai Fumikazu , Kusumoto Masahiko , Endo Masahiro , Saito Yoshinobu , Baba Tomohisa , Sata Masafumi , Yamaguchi Ou , Sakamoto Kei , Sugeno Masatoshi , Tamura Reiko , Tokimoto Toshimitsu , Shimizu Wataru , Gemma Akihiko 
Published: May 2020

Abstract

Objective
Adverse drug reactions (ADRs) during real-world osimertinib use were investigated in Japan.

Methods
Patients with epidermal growth factor receptor (EGFR) T790M-positive non-small cell lung cancer treated with second-line or later oral osimertinib per the Japanese package insert (80 mg once daily) were included. Data were collected between 28 March 2016 and 31 August 2018.

Results
The median observation period in the safety analysis population (n = 3578) was 343.0 days. ADRs (defined as adverse events whose causality to osimertinib could not be denied by the attending physicians or manufacturer) were reported in 58.1% (2079/3578) of patients. ADRs of interstitial lung disease events were reported in 6.8% (245/3578; Grade ≥ 3, 2.9% [104/3578]) of patients, of whom 29 (11.8%) died (0.8% of patients overall). ADRs of QT interval prolonged, liver disorder and haematotoxicity were reported in 1.3% (45/3578; Grade ≥ 3, 0.1% [5/3578]), 5.9% (212/3578; Grade ≥ 3, 1.0% [35/3578]) and 11.4% (409/3578; Grade ≥ 3, 2.9% [104/3578]) of patients, respectively. In the efficacy analysis population (n = 3563), 119 (3.3%) patients had complete responses, 2373 (66.6%) had partial responses and 598 (16.8%) had stable disease. The objective response rate was 69.9%; disease control rate was 86.7%; and median progression-free survival (PFS) was 12.3 months. At 6 and 12 months, PFS rates were 77.4% (95% confidence interval [CI], 75.9–78.9) and 53.2% (95% CI, 51.3–55.1) and overall survival rates were 88.3% (95% CI, 87.2–89.4) and 75.4% (95% CI, 73.8–77.0), respectively.

Conclusions
These data support the currently established benefit-risk assessment of osimertinib in this patient population.
3D-Printing to Address COVID-19 Testing Supply Shortages
Authors: Cox Jesse L , Koepsell Scott A 
Published: May 2020

Abstract
The recent SARS-CoV-2 outbreak has placed immense pressure on supply chains, including shortages in nasopharyngeal (NP) swabs. Here, we report our experience of using 3D-printing to rapidly develop and deploy custom-made NP swabs to address supply shortages at our healthcare institution.
Comparative accuracy of 1,3 beta-D glucan and galactomannan for diagnosis of invasive fungal infections in pediatric patients: a systematic review with meta-analysis
Authors: Singh Shreya , Singh Manvi , Verma Nipun , Sharma Minakshi , Pradhan Pranita , Chauhan Anil , Jaiswal Nishant , Chakrabarti Arunaloke , Singh Meenu 
Published: May 2020

Abstract
Invasive fungal infections (IFI) cause considerable morbidity and mortality in pediatric patients. Serum biomarkers such as 1,3-beta-D glucan (BDG) and galactomannan (GM) have been evaluated for the IFI diagnosis. However, most evidence regarding their utility is derived from studies in adult oncology patients. This systematic review aimed to compare the diagnostic accuracy of BDG and GM individually or in combination for diagnosing IFI in pediatric patients. PubMed, CINAHL, Embase, and Cochrane Library were searched until March 2019 for diagnostic studies evaluating both serum GM and BDG for diagnosing pediatric IFI. The pooled diagnostic odds ratio (DOR), specificity and sensitivity were computed. Receiver operating characteristics (ROC) curve and area under the curve (AUC) were used for summarizing overall assay performance. Six studies were included in the meta-analysis. The summary estimates of sensitivity, specificity, pooled DOR, AUC of the GM assay for proven or probable IFI were 0.74, 0.76, 13.25, and 0.845. The summary estimates of sensitivity, specificity, pooled DOR, AUC of the BDG assay were 0.70, 0.69, 4.3, and 0.722. The combined predictive ability of both tests was reported in two studies (sensitivity: 0.67, specificity: 0.877). Four studies were performed in hematology-oncology patients, while two were retrospective studies from pediatric intensive care units (ICUs). In the subgroup of hematology-oncology patients, DOR of BDG remained similar at 4.25 but increased to 40.28 for GM. We conclude that GM and BDG have a modest performance for identifying IFI in pediatric patients. GM has a better accuracy over BDG. Combining both improves the specificity at the cost of sensitivity.