bluuebunny/crossref_metadata_2025_split huggingface dataset:
SwissTargetPrediction: updated data and new features for efficient prediction of protein targets of small molecules
Authors: Daina Antoine , Michielin Olivier , Zoete Vincent 
Published: May 2019

Abstract
SwissTargetPrediction is a web tool, on-line since 2014, that aims to predict the most probable protein targets of small molecules. Predictions are based on the similarity principle, through reverse screening. Here, we describe the 2019 version, which represents a major update in terms of underlying data, backend and web interface. The bioactivity data were updated, the model retrained and similarity thresholds redefined. In the new version, the predictions are performed by searching for similar molecules, in 2D and 3D, within a larger collection of 376 342 compounds known to be experimentally active on an extended set of 3068 macromolecular targets. An efficient backend implementation allows to speed up the process that returns results for a druglike molecule on human proteins in 15–20 s. The refreshed web interface enhances user experience with new features for easy input and improved analysis. Interoperability capacity enables straightforward submission of any input or output molecule to other on-line computer-aided drug design tools, developed by the SIB Swiss Institute of Bioinformatics. High levels of predictive performance were maintained despite more extended biological and chemical spaces to be explored, e.g. achieving at least one correct human target in the top 15 predictions for >70% of external compounds. The new SwissTargetPrediction is available free of charge (www.swisstargetprediction.ch).
PubTator central: automated concept annotation for biomedical full text articles
Authors: Wei Chih-Hsuan , Allot Alexis , Leaman Robert , Lu Zhiyong 
Published: May 2019

AbstractPubTator Central (https://www.ncbi.nlm.nih.gov/research/pubtator/) is a web service for viewing and retrieving bioconcept annotations in full text biomedical articles. PubTator Central (PTC) provides automated annotations from state-of-the-art text mining systems for genes/proteins, genetic variants, diseases, chemicals, species and cell lines, all available for immediate download. PTC annotates PubMed (29 million abstracts) and the PMC Text Mining subset (3 million full text articles). The new PTC web interface allows users to build full text document collections and visualize concept annotations in each document. Annotations are downloadable in multiple formats (XML, JSON and tab delimited) via the online interface, a RESTful web service and bulk FTP. Improved concept identification systems and a new disambiguation module based on deep learning increase annotation accuracy, and the new server-side architecture is significantly faster. PTC is synchronized with PubMed and PubMed Central, with new articles added daily. The original PubTator service has served annotated abstracts for ∼300 million requests, enabling third-party research in use cases such as biocuration support, gene prioritization, genetic disease analysis, and literature-based knowledge discovery. We demonstrate the full text results in PTC significantly increase biomedical concept coverage and anticipate this expansion will both enhance existing downstream applications and enable new use cases.
Variations in VA and Medicare Use Among Veterans With Diabetes
Authors: Rose Danielle E. , Rowneki Mazhgan , Sambamoorthi Usha , Fried Dennis , Dwibedi Nilanjana , Tseng Chin-Lin , Jani Nisha , Yano Elizabeth M. , Helmer Drew A. 
Published: May 2019

Introduction:
VA and Medicare use among older Veterans has been considered fragmented care, however, it may represent access to needed care.

Methods:
The population studied were Veterans with diabetes, age 66 years and older, dually enrolled in VA and Medicare.

Data Source/Study Setting:
We conducted a dynamic retrospective cohort study with 2008, 2009, and 2010 as the outcome years (Ambulatory Care Sensitive Conditions Hospitalization (ACSC-H) or not). We analyzed administrative data to identify comorbidities; ambulatory care utilization to identify variations in use before hospitalization. We linked 2007 primary care (PC) survey data to assess if organizational factors were associated with ACSC-H.

Measures and Analysis:
We identified ACSC-Hs using a validated definition. We categorized VA/Medicare use as: single system; dual system: supplemental specialty care use; or primary care use. Using hierarchical logistic regression models, we tested for associations between VA/Medicare use, organizational characteristics, and ACSC-H controlling for patient-level, organizational-level, and area-level characteristics.

Results:
Our analytic population was comprised of 210,726 Medicare-eligible Veterans; more than one quarter had an ACSC-H. We found that single system users had higher odds of ACSC-H compared with dual system specialty supplemental care use (odds ratio, 1.14; 95% confidence interval, 1.09–1.20), and no significant difference between dual-system users. Veterans obtaining care at sites where PC leaders reported greater autonomy (eg, authority over personnel issues) had lower odds of ACSC-H (odds ratio, 0.74; 95% confidence interval, 0.59–0.92).

Discussion:
Our findings suggest that earlier assumptions about VA/Medicare use should be weighed against the possibility that neither VA nor Medicare may address complex Veterans’ health needs. Greater PC leader autonomy may allow for tailoring of care to match local clinical contexts.
Addressing Loneliness in Complex PTSD
Authors: Dagan Yael , Yager Joel 
Published: May 2019

Abstract
Loneliness impacts both physical and psychological health and is associated with increases of all-cause mortality and suicidal behavior. Because loneliness may result from a variety of developmental, interpersonal, and intrapersonal factors, distinguishing its components, origins, and sustaining factors as it manifests in various psychopathological states are important steps in formulating interventions to alleviate these conditions. To date, loneliness has not been widely studied in relation to complex posttraumatic stress disorder (PTSD), which is newly delineated in the International Classification of Diseases, characterized by PTSD symptoms in the context of significant early trauma, as well as “disturbances in self-organization” marked by affective dysregulation, negative self-concept, and disturbances in relationships. In this article, illustrating with case material, we suggest that loneliness plays a major role in the development of complex PTSD and in the preservation of its symptoms. Consequently, therapies for complex PTSD should include interventions that address loneliness.
Heart Rate Variability in Individual Psychotherapy
Authors: Blanck Paul , Stoffel Martin , Bents Hinrich , Ditzen Beate , Mander Johannes 
Published: May 2019

Abstract
Heart rate variability (HRV) can be conceptualized as a marker of an individual's capability to adaptively respond to its environment and has been linked with mental health. Although conceptually and empirically linked to social behavior and thus relevant in the therapeutic setting, HRV is seldom investigated directly within therapy sessions. In the present examination, we aimed at addressing this research gap by assessing patients' and therapists' HRVs both ambulatory within therapy sessions and under resting conditions. Drawing on polyvagal theory, we hypothesized that higher in-session HRV is accompanied with higher therapeutic alliance ratings. Further, we expected baseline HRV to predict symptomatic outcome and to increase over the course of therapy. In a sample of 53 outpatients receiving 25 sessions of cognitive behavioral therapy, we measured HRV, therapeutic alliance and depressive symptoms on four occasions. Multilevel modeling analyses demonstrated that patients with higher in-session high-frequency HRV rated the therapeutic alliance higher. Baseline HRV predicted symptomatic outcome and increased over the course of therapy. Possible explanations involve a link between in-session HRV and in-session behavior and should be investigated in future studies. The results highlight the usefulness of in-session HRV as a promising process variable in psychotherapy research.
WAIS-IV Performance in Patients With Schizophrenia
Authors: Fuentes-Durá Inmaculada , Ruiz Juan Carlos , Dasí Carmen , Navarro Marisa , Blasco Pilar , Tomás Pilar 
Published: May 2019

Abstract
Wechsler Adult Intelligence Scale (WAIS) is one of the most widely used instruments to measure cognitive functioning. The aims of this study were 1) to obtain the cognitive profile of Spanish patients with schizophrenia on the WAIS-IV; 2) to compare their profile to the profile of a healthy control group; and 3) to compare the cognitive profile of patients with schizophrenia to the performance observed in two separate previous studies in Canada and China. A sample of 99 outpatients and 99 healthy control participants, matched on age, sex, and educational level, were measured using the WAIS-IV, including 10 core subtests, 4 indices, and 2 general intelligence scores, to obtain their cognitive profile. Results showed that only the performance on the Verbal Comprehension Index and its subtests was similar in the patient and control groups. This pattern of cognitive impairment was similar to the pattern reported in the Canadian and Chinese studies.
Unplanned readmission after traumatic injury: A long-term nationwide analysis
Authors: Lunardi Nicole , Mehta Ambar , Ezzeddine Hiba , Varma Sanskriti , Winfield Robert D. , Kent Alistair , Canner Joseph K. , Nathens Avery B. , Joseph Bellal A. , Efron David T. , Sakran Joseph V. 
Published: May 2019

BACKGROUND
Long-term outcomes after trauma admissions remain understudied. We analyzed the characteristics of inpatient readmissions within 6 months of an index hospitalization for traumatic injury.

METHODS
Using the 2010 to 2015 Nationwide Readmissions Database, which captures data from up to 27 US states, we identified patients at least 15 years old admitted to a hospital through an emergency department for blunt trauma, penetrating trauma, or burns. Exclusion criteria included hospital transfers, patients who died during their index hospitalizations, and hospitals with fewer than 100 trauma patients annually. After calculating the incidences of all-cause, unplanned inpatient readmissions within 1 month, 3 months, and 6 months, we used multivariable logistic regression models to identify predictors of readmissions. Analyses adjusted for patient, clinical, and hospital factors.

RESULTS
Among 2,763,890 trauma patients, the majority had blunt injuries (92.5%), followed by penetrating injuries (6.2%) and burns (1.5%). Overall, rates of inpatient readmissions were 11.1% within 1 month, 21.6% within 6 months, and 29.8% within 6 months, with limited variability by year. After adjustment, the following were associated with all-cause 6 months inpatient readmissions: male sex (adjusted odds ratio [aOR], 1.10; 95% confidence interval [95% CI], 1.09–1.10), comorbidities (aOR, 1.21; 95% CI, 1.21–1.22), low-income quartiles (first and second) (aOR, 1.08; 95% CI, 1.07–1.10 and aOR, 1.04; 95% CI, 1.03–1.06, respectively), Medicare (aOR, 1.65; 95% CI, 1.62–1.69), Medicaid (aOR, 1.51; 95% CI, 1.48–1.53), being treated at private, investor-owned hospitals (aOR, 1.15; 95% CI, 1.12–1.18), longer hospital length of stay (aOR, 1.01; 95% CI, 1.01–1.01) and patient disposition to short-term hospital (aOR, 1.55; 95% CI, 1.49–1.62), skilled nursing facility (aOR, 1.43; 95% CI, 1.42–1.45), home health care (aOR, 1.27; 95% CI, 1.25–1.28), or leaving against medical advice (aOR, 1.85; 95% CI, 1.78–1.92).

CONCLUSION
Unplanned readmission after trauma is high and remains this way 6 months after discharge. Understanding the factors that increase the odds of readmissions within 1 month, 3 months, and 6 months offer a focus for quality improvement and have important implications for hospital benchmarking.

LEVEL OF EVIDENCE
Epidemiological study, level III.
A descriptive study of US Special Operations Command fatalities, 2001 to 2018
Authors: Kotwal Russ S. , Mazuchowski Edward L. , Stern Caryn A. , Montgomery Harold R. , Janak Jud C. , Howard Jeffrey T. , Butler Frank K. , Holcomb John B. , Eastridge Brian J. , Gurney Jennifer M. , Shackelford Stacy A. 
Published: May 2019

BACKGROUND
Studies of fatalities from injury and disease guide prevention and treatment efforts for populations at risk. Findings can inform leadership and direct clinical practice guidelines, research, and personnel, training, and equipment requirements.

METHODS
A retrospective review and descriptive analysis was conducted of United States Special Operations Command (USSOCOM) fatalities who died while performing duties from September 11, 2001, to September 10, 2018. Characteristics analyzed included subcommand, military activity, operational posture, and manner of death.

RESULTS
Of 614 USSOCOM fatalities (median age, 30 years; male, 98.5%) the leading cause of death was injury (97.7%); specifically, multiple/blunt force injury (34.5%), blast injury (30.7%), gunshot wound (GSW; 30.3%), and other (4.5%). Most died outside the United States (87.1%), during combat operations (85.3%), in the prehospital environment (91.5%), and the same day of insult (90.4%). Most fatalities were with the US Army Special Operations Command (67.6%), followed by the Naval Special Warfare Command (16.0%), Air Force Special Operations Command (9.3%), and Marine Corps Forces Special Operations Command (7.2%). Of 54.6% who died of injuries incurred during mounted operations, most were on ground vehicles (53.7%), followed by rotary-wing (37.3%) and fixed-wing (9.0%) aircrafts. The manner of death was primarily homicide (66.0%) and accident (30.5%), followed by natural (2.1%), suicide (0.8%), and undetermined (0.7%). Specific homicide causes of death were GSW (43.7%), blast injury (42.2%), multiple/blunt force injury (13.8%), and other (0.2%). Specific accident causes of death were multiple/blunt force injury (80.7%), blast injury (6.4%), GSW (0.5%), and other (12.3%). Of accident fatalities with multiple/blunt force injury, the mechanism was mostly aircraft mishaps (62.9%), particularly rotary wing (68.4%).

CONCLUSION
Most USSOCOM fatalities died abroad from injury in the prehospital setting. To improve survival from military activities worldwide, leaders must continue to optimize prehospital capability and develop strategies that rapidly connect patients to advanced resuscitative and surgical care.

LEVEL OF EVIDENCE
Epidemiological, level IV; Therapeutic level IV.
Rapid point-of-care detection and classification of direct-acting oral anticoagulants with the TEG 6s: Implications for trauma and acute care surgery
Authors: Dias João D. , Lopez-Espina Carlos G. , Ippolito Jeffrey , Hsiao L. Hsiuyin , Zaman Fowzia , Muresan Adina A. , Thomas Scott G. , Walsh Mark , Jones Alexander Joseph , Grisoli Anne , Thurston Brian C. , Artang Ramin , Bilden Kevin P. , Hartmann Jan , Achneck Hardean E. 
Published: May 2019

BACKGROUNDThe trauma patient on direct oral anticoagulant (DOAC) therapy preinjury presents a challenge in trauma and acute care surgery. Our understanding of these patients is extrapolated from vitamin K antagonists. However, DOACs have different mechanisms of action, effects on laboratory coagulation assays, and reversal strategies. Rapid identification of DOACs in the blood will allow timely reversal of factor Xa inhibitors and direct thrombin inhibitors when necessary. The present study evaluated viscoelastic testing to detect and classify DOACs in patient blood samples.METHODSThis observational, prospective, open-label, multicenter study used point-of-care viscoelastic testing to analyze blood samples taken from patients with and without DOAC treatment, and healthy volunteers. Antifactor Xa and direct thrombin inhibition (DTI) assays were used to establish reference ranges for viscoelastic testing parameters on the TEG 6s system. These ranges were applied to produce a DOAC identification algorithm for patient blood samples. Internal consistency of the measurements, as well as algorithm sensitivity and specificity, was evaluated.RESULTSUsing the TEG 6s system, the R parameter reference range was 0.6 minutes to 1.5 minutes for the Antifactor Xa assay and 1.6 minutes to 2.5 minutes for the DTI assay. Our identification algorithm using these ranges for 2.5 minutes or less has sensitives of 98.3% and 100% for factor Xa inhibitor and direct thrombin inhibitor detection, respectively. Specificity was 100%. Both classes of DOAC were detectable, even when samples were collected during the “trough” between doses of medication.CONCLUSIONPoint-of-care viscoelastic testing with TEG 6s can detect and classify DOACs with high sensitivity and specificity. This tool can be used to better determine the need for reversal in trauma and acute care surgery patients and guide optimal surgical timing in the acute setting.LEVEL OF EVIDENCEPrognostic and epidemiological study, level II.
Testing for dependence on tree structures
Authors: Behr Merle , Ansari M. Azim , Munk Axel , Holmes Chris 
Published: May 2019

Tree structures, showing hierarchical relationships and the latent structures between samples, are ubiquitous in genomic and biomedical sciences. A common question in many studies is whether there is an association between a response variable measured on each sample and the latent group structure represented by some given tree. Currently this is addressed on an ad hoc basis, usually requiring the user to decide on an appropriate number of clusters to prune out of the tree to be tested against the response variable. Here we present a statistical method with statistical guarantees that tests for association between the response variable and a fixed tree structure across all levels of the tree hierarchy with high power, while accounting for the overall false positive error rate. This enhances the robustness and reproducibility of such findings.Significance StatementTree like structures are abundant in the empirical sciences as they can summarize high dimensional data and show latent structure among many samples in a single framework. Prominent examples include phylogenetic trees or hierarchical clustering derived from genetic data. Currently users employ ad hoc methods to test for association between a given tree and a response variable, which reduces reproducibility and robustness. In this paper, we introduce treeSeg, a simple to use and widely applicable methodology with high power for testing between all levels of hierarchy for a given tree and the response while accounting for the overall false positive rate. Our method allows for precise uncertainty quantification and therefore increases interpretability and reproducibility of such studies across many fields of science.
Understanding the dynamics of physical activity practice in the health context through Regulatory Focus and Self-Determination theories
Authors: Laroche Manon , Roussel Peggy , Cury François , Boiche Julie 
Published: May 2019

ABSTRACTThis research aimed to associate for the first time in the literature the Regulatory Focus and Self-Determination theories to understand the dynamics of physical activity practice in the health context. Two cross-sectional studies were conducted with 603 (Study 1) and 395 (Study 2) French volunteer participants aged from 18 to 69 and 19 to 71 respectively, and healthy or concerned by a health condition. The main results of structural equation modeling analyses demonstrated that across the two studies, health promotion focus was positively associated with intrinsic motivation (.44 < β < .74, p < .001), integrated regulation (.47 < β < .72, p < .001), identified regulation (.40 < β < .69, p < .001) and introjected regulation (.41 < β < .53, p < .001), whereas health prevention focus was positively related with external regulation (.31 < β < .45, p < .001) and amotivation (.32 < β < .38, p < .001). Bootstrapping analyses main results in Study 2 showed that health promotion focus was indirectly associated with physical activity through intrinsic motivation (95% CI [.02 to .11]), integrated regulation (95% CI [.00 to .08]), identified regulation (95% CI [.00 to .09]) and introjected regulation (95% CI [.04 to .12]), whereas health prevention focus was indirectly associated with physical activity through external regulation (95% CI [.00 to .12]). These studies reveal meaningful associations between Regulatory Focus and Self-Determination theories’ variables which support the relevance of associating these two models to understand the processes underlying the physical activity practice.
IL-1RA controls the development of esophageal cancer by inhibition of VEGF via PI3K/NF-κB signaling pathway
Authors: Shen Zhimin , Yu Shaobin , Gao Lei , Liu Zhun , Zhang Peipei , Chai Tianci , Chen Sui , Kang Mingqiang 
Published: May 2019

AbstractIL-1RA has been reported to function as tumor suppressor in a variety of tumors, but its function and mechanism in esophageal cancer remains largely unknown. Our previous studies have shown that IL-1RA is downregulated in primary esophageal cancer(EC), and this downregulation of IL-1RA is closely related to TNM staging and survival prognosis. In this study, we observed that over-expression of IL-1RA inhibits proliferation, migration, and tumor growth in esophageal cancer cells(ESCC), inhibits the expression and secretion of VEGF, and inhibits tumor angiogenesis. Further studies have shown the overexpression of IL-1RA inhibits the transmission of PI3K/NF-kappaB. Taken together, this study shows that IL-1RA can regulating the development of esophageal cancer by inhibiting VEGF expression and secretion via inhibiting PI3K/NF-kappaB signaling, and it may serve as a potential prognostic marker and therapeutic target for EC.
Deep sequencing of 3 cancer cell lines on 2 sequencing platforms
Authors: Arora Kanika , Shah Minita , Johnson Molly , Sanghvi Rashesh , Shelton Jennifer , Nagulapalli Kshithija , Oschwald Dayna M. , Zody Michael C. , Germer Soren , Jobanputra Vaidehi , Carter Jade , Robine Nicolas 
Published: May 2019

AbstractTo test the performance of a new sequencing platform, develop an updated somatic calling pipeline and establish a reference for future benchmarking experiments, we sequenced 3 common cancer cell lines along with their matched normal cell lines to great sequencing depths (up to 278X coverage) on both Illumina HiSeqX and NovaSeq sequencing instruments. Somatic calling was generally consistent between the two platforms despite minor differences at the read level. We designed and implemented a novel pipeline for the analysis of tumor-normal samples, using multiple variant callers. We show that coupled with a high-confidence filtering strategy, it improves the accuracy of somatic calls. We also demonstrate the utility of the dataset by creating an artificial purity ladder to evaluate the somatic pipeline and benchmark methods for estimating purity and ploidy from tumor-normal pairs. The data and results of the pipeline are made accessible to the cancer genomics community.