bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene Graphics: a genomic neighborhood data visualization web application
Authors: Harrison Katherine J , Crécy-Lagard Valérie de , Zallot Rémi 
Published: December 2017

Abstract

Summary
The examination of gene neighborhood is an integral part of comparative genomics but no tools to produce publication quality graphics of gene clusters are available. Gene Graphics is a straightforward web application for creating such visuals. Supported inputs include National Center for Biotechnology Information gene and protein identifiers with automatic fetching of neighboring information, GenBank files and data extracted from the SEED database. Gene representations can be customized for many parameters including gene and genome names, colors and sizes. Gene attributes can be copied and pasted for rapid and user-friendly customization of homologous genes between species. In addition to Portable Network Graphics and Scalable Vector Graphics, produced representations can be exported as Tagged Image File Format or Encapsulated PostScript, formats that are standard for publication. Hands-on tutorials with real life examples inspired from publications are available for training.

Availability and implementation
Gene Graphics is freely available at https://katlabs.cc/genegraphics/ and source code is hosted at https://github.com/katlabs/genegraphics.

Supplementary information
Supplementary data are available at Bioinformatics online.
Matrix factorization-based data fusion for the prediction of lncRNA–disease associations
Authors: Fu Guangyuan , Wang Jun , Domeniconi Carlotta , Yu Guoxian 
Published: December 2017

AbstractMotivationLong non-coding RNAs (lncRNAs) play crucial roles in complex disease diagnosis, prognosis, prevention and treatment, but only a small portion of lncRNA–disease associations have been experimentally verified. Various computational models have been proposed to identify lncRNA–disease associations by integrating heterogeneous data sources. However, existing models generally ignore the intrinsic structure of data sources or treat them as equally relevant, while they may not be.ResultsTo accurately identify lncRNA–disease associations, we propose a Matrix Factorization based LncRNA–Disease Association prediction model (MFLDA in short). MFLDA decomposes data matrices of heterogeneous data sources into low-rank matrices via matrix tri-factorization to explore and exploit their intrinsic and shared structure. MFLDA can select and integrate the data sources by assigning different weights to them. An iterative solution is further introduced to simultaneously optimize the weights and low-rank matrices. Next, MFLDA uses the optimized low-rank matrices to reconstruct the lncRNA–disease association matrix and thus to identify potential associations. In 5-fold cross validation experiments to identify verified lncRNA–disease associations, MFLDA achieves an area under the receiver operating characteristic curve (AUC) of 0.7408, at least 3% higher than those given by state-of-the-art data fusion based computational models. An empirical study on identifying masked lncRNA–disease associations again shows that MFLDA can identify potential associations more accurately than competing models. A case study on identifying lncRNAs associated with breast, lung and stomach cancers show that 38 out of 45 (84%) associations predicted by MFLDA are supported by recent biomedical literature and further proves the capability of MFLDA in identifying novel lncRNA–disease associations. MFLDA is a general data fusion framework, and as such it can be adopted to predict associations between other biological entities.Availability and implementationThe source code for MFLDA is available at: http://mlda.swu.edu.cn/codes.php? name = MFLDA.Supplementary informationSupplementary data are available at Bioinformatics online.
Does Podcast Use Enhance Critical Thinking in Nursing Education?
Authors: Blum Cynthia A. 
Published: December 2017

Abstract
The purpose of this pilot interventional study was to examine relationships between adjunctive podcast viewing and nursing students' critical thinking (CT) abilities. Participants were last semester/preceptorship nursing students. The intervention group was given unrestricted access to a CT podcast. There was no statistical significance between Health Sciences Reasoning Test pretest and posttest scores, the number of times the podcast was viewed, and specific demographic factors. The results suggest that CT podcast viewing did not improve CT abilities. However, Likert scale results indicated students liked this method of learning. Demographic factors and sample size were limited, and further research is recommended.
Primary care management of ulcerative colitis
Authors: Davis Stephanie C. , Robinson Brittani L. , Vess Joy , Lebel Joseph S. 
Published: December 2017

Abstract:
Ulcerative colitis (UC) is an inflammatory bowel disease marked by mucosal inflammation. UC has an impact on quality of life and places a financial burden on the healthcare system. This article focuses on the impact, presentation, diagnosis and classification, systemic manifestations, complications, management, and treatment associated with UC.
Descriptive Analysis of State and Federal Spine Surgery Malpractice Litigation in the United States
Authors: Agarwal Nitin , Gupta Raghav , Agarwal Prateek , Matthew Pravin , Wolferz Richard , Shah Aakash , Adeeb Nimer , Prabhu Arpan V. , Kanter Adam S. , Okonkwo David O. , Hamilton David Kojo 
Published: December 2017

Study Design.
A retrospective review.

Objective.
This study aimed to determine the factors associated with malpractice litigation in cases involving spine surgery in the United States.

Summary of Background Data.
Medical malpractice is of substantial interest to the medical community due to concerns of increased health care costs and medical decision-making for the sole purpose of reducing legal liability.

Methods.
The Westlaw online legal database (Thomson Reuters, New York, NY) was searched for verdict and settlement reports pertaining to spine surgery from 2010 to 2015. Data were collected regarding type of procedure, patient age and gender, defendant specialty, outcome, award, alleged cause of malpractice, and factors involved in the plaintiff's decision to file. Initial search queried 187 cases, after which exclusion criteria were applied to eliminate duplicates and cases unrelated to spine surgery, yielding a total of 98 cases for analysis.

Results.
The verdict was in favor of the defendant in 62 cases (63.3%). Neurosurgeons and orthopedic surgeons were the most common defendants in 29 (17.3%) and 40 (23.8%) of the cases, respectively. A perceived lack of informed consent was noted as a factor in 24 (24.4%) of the cases. A failure to diagnose or a failure to treat was noted in 31 (31.6%) and 32 (32.7%) cases, respectively. Median payments for plaintiff verdicts were nearly double those of settlements ($2,525,000 vs. $1,300,000). A greater incidence of plaintiff verdicts was noted in cases in which a failure to treat (P < 0.05) was cited, a patient death occurred (P < 0.05), or an emergent surgery had been performed (P < 0.01).

Conclusion.
Overall, physicians were not found liable in the majority of spine surgery malpractice cases queried.

Level of Evidence: 4
Comparing Health-Related Quality of Life Outcomes in Patients Undergoing Either Primary or Revision Anterior Cervical Discectomy and Fusion
Authors: Schroeder Gregory D. , Boody Barrett S. , Kepler Christopher K. , Kurd Mark F. , Silva Stephen , Nicholson Kristen , Wilson Jefferson R. , Woods Barret I. , Radcliff Kris E. , Anderson David Greg , Hilibrand Alan S. , Vaccaro Alexander R. , Rihn Jeffery A. 
Published: December 2017

Study Design.
A retrospective review of prospectively collected data.

Objective.
Compare health-related quality of life (HRQOL) outcome metrics in patients undergoing primary and revision anterior cervical discectomy and fusion (ACDF).

Summary of Background Data.
ACDF is associated with significant improvements in HRQOL outcome metrics. However, 2.9% of patients per year will develop symptomatic adjacent segment disease and there is a paucity of literature on HRQOL outcomes after revision ACDF.

Methods.
Patients were identified who underwent either a primary or revision ACDF, and who had both preoperative and a minimum of 1-year postoperative HRQOL outcome data. Pre- and postoperative Short Form 12 Physical Component Score (SF12 PCS), Short Form 12 Mental Component Score (SF12 MCS) Visual Analog Scale for neck pain (VAS-Neck), VAS-Arm, and Neck Disability Index (NDI) scores were compared.

Results.
A total of 360 patients (299 primary, 61 revision) were identified. Significant improvement in SF12 PCS, NDI, VAS-Neck, and VAS-Arm was seen in both groups; however, only a significant improvement in SF12 MCS was seen in the primary group. When comparing the results of a primary versus a revision surgery, the SF12 PCS score was the only outcome with a significantly different net improvement in the primary group (7.23 ± 9.72) compared to the revision group (2.9 ± 11.07; P = 0.006) despite similar baseline SF12 PCS scores. The improvement in each of the other reported HRQOL outcomes did not significantly vary between surgical groups.

Conclusion.
A revision ACDF for cervical radiculopathy or myelopathy leads to a significant improvement in the HRQOL outcome, and with the exception of the SF12 PCS, these results are similar to those of patients undergoing a primary ACDF.

Level of Evidence: 2
Postoperative Deep Vein Thrombosis, Pulmonary Embolism, and Myocardial Infarction
Authors: Shiu Brian , Le Elizabeth , Jazini Ehsan , Weir Tristan B. , Costales Timothy , Caffes Nicholas , Paryavi Ebrahim , O’Hara Nathan , Gelb Daniel E. , Koh Eugene Y. , Ludwig Steven C. 
Published: December 2017

Study Design.
A retrospective review (2001–2014) was conducted using prospectively collected data at a level I trauma center.

Objective.
We sought to determine the incidence and characteristics of complications occurring secondary to therapeutic anticoagulation in adult spine trauma patients.

Summary of Background Data.
Numerous studies have assessed prophylactic anticoagulation after spine surgery, but none has investigated the risks of therapeutic doses of anticoagulation for treatment of postoperative thromboembolic events.

Methods.
Patients were included if they sustained a postoperative thromboembolic event (deep venous thrombosis, pulmonary embolism, or myocardial infarction). Patients were excluded if anticoagulation was subtherapeutic. Of 1712 patients, 62 who received therapeutic anticoagulation and 174 propensity-matched control patients who did not receive therapeutic anticoagulation were included in the study.

Results.
Initial anticoagulation was obtained by heparin infusion (51%), low-molecular-weight heparin (LMWH, 46%), and warfarin (3%). Complications requiring unplanned reoperation occurred in 18% of anticoagulated patients and 10% of nonanticoagulated patients (P = 0.17). The reoperation rate after heparin infusion was 31% and after LMWH was 6.5% (P = 0.02). Epidural hematoma occurred in 3% and 1% of anticoagulated and nonanticoagulated patients, respectively. Multivariate logistic regression analysis of the two groups showed a trend toward increased risk of reoperation in the anticoagulation group. Analysis of the heparin infusion subgroup separate from the LMWH subgroup compared with the control group showed an increased risk of reoperation for any complication (odds ratio, 3.57; P = 0.01) and for bleeding complications (odds ratio, 43.1; P = 0.01).

Conclusion.
This is the first study to quantify complications secondary to postoperative therapeutic anticoagulation in spine patients. Postoperative spine trauma patients who underwent therapeutic anticoagulation experienced an unplanned reoperation rate of 18%, including a 3% incidence of spinal epidural hematoma. Therapeutic anticoagulation using heparin infusion seems to drive the overall rate of reoperation (31%) compared with LMWH.

Level of Evidence: 3
The New York Sepsis Severity Score: Development of a Risk-Adjusted Severity Model for Sepsis
Authors: Phillips Gary S. , Osborn Tiffany M. , Terry Kathleen M. , Gesten Foster , Levy Mitchell M. , Lemeshow Stanley 
Published: December 2017

Objectives:
In accordance with Rory’s Regulations, hospitals across New York State developed and implemented protocols for sepsis recognition and treatment to reduce variations in evidence informed care and preventable mortality. The New York Department of Health sought to develop a risk assessment model for accurate and standardized hospital mortality comparisons of adult septic patients across institutions using case-mix adjustment.

Design:
Retrospective evaluation of prospectively collected data.

Patients:
Data from 43,204 severe sepsis and septic shock patients from 179 hospitals across New York State were evaluated.

Settings:
Prospective data were submitted to a database from January 1, 2015, to December 31, 2015.

Interventions:
None.

Measurement and Main Results:
Maximum likelihood logistic regression was used to estimate model coefficients used in the New York State risk model. The mortality probability was estimated using a logistic regression model. Variables to be included in the model were determined as part of the model-building process. Interactions between variables were included if they made clinical sense and if their p values were less than 0.05. Model development used a random sample of 90% of available patients and was validated using the remaining 10%. Hosmer-Lemeshow goodness of fit p values were considerably greater than 0.05, suggesting good calibration. Areas under the receiver operator curve in the developmental and validation subsets were 0.770 (95% CI, 0.765–0.775) and 0.773 (95% CI, 0.758–0.787), respectively, indicating good discrimination. Development and validation datasets had similar distributions of estimated mortality probabilities. Mortality increased with rising age, comorbidities, and lactate.

Conclusions:
The New York Sepsis Severity Score accurately estimated the probability of hospital mortality in severe sepsis and septic shock patients. It performed well with respect to calibration and discrimination. This sepsis-specific model provides an accurate, comprehensive method for standardized mortality comparison of adult patients with severe sepsis and septic shock.
Numeracy and Interpretation of Prognostic Estimates in Intracerebral Hemorrhage Among Surrogate Decision Makers in the Neurologic ICU
Authors: Leiter Nikita , Motta Melissa , Reed Robert M. , Adeyeye Temitope , Wiegand Debra L. , Shah Nirav G. , Verceles Avelino C. , Netzer Giora 
Published: December 2017

Objective:
Clinicians caring for patients with intracerebral hemorrhage must often discuss prognosis and goals of care with their patients’ surrogate decision makers, and may make numeric estimates of likelihood of survival and functional independence, informed by validated prediction models. Surrogates’ prognostic estimates are often discordant with physicians’, suggesting that physicians’ numeric statements may not be accurately interpreted. We sought to assess the relationship between numeracy and interpretation of prognostic estimates in intracerebral hemorrhage among surrogate decision makers. We also assessed surrogates’ application of prognostic estimates to decisions regarding goals of care.

Design:
Single-center, survey-based, cross-sectional study.

Setting:
Twenty-two–bed neurologic ICU at an urban, academic hospital.

Subjects:
Surrogate decision makers for patients admitted to the neurologic ICU.

Interventions:
Participants completed a survey containing five clinical vignettes describing patients with nontraumatic intracerebral hemorrhage. For each patient, numerical estimates of survival and functional independence were explicitly provided, based on the validated outcome risk stratification scale (intracerebral hemorrhage score) and the Prediction of Functional Outcome in Patients with Primary Intracerebral Hemorrhage score.

Measurements and Main Results:
Participants were asked to make their own prognostic estimates, as well as to describe their preferred goals of care for each hypothetical patient. Respondent demographics were collected, and numeracy was assessed using a modified Lipkus 11-item scale. Poor numeracy was common (42 of 96 total subjects) in this relatively highly educated population. Most prognostic estimates (55%) made by surrogates were discordant with the provided estimates. High numeracy correlated with better concordance (odds ratio, 23.9 [5.57–97.64]; p < 0.001), independent of several factors, including level of education and religion. Numeracy also affected goals-of-care decisions made by surrogates.

Conclusions:
Poor numeracy is common among surrogate decision makers in an intensive care setting and poses a barrier to communication between surrogates and clinicians regarding prognosis and goals of care.
Assessment of Ileostomy Output Using Telemedicine: A Feasibility Trial
Authors: Bednarski Brian K. , Slack Rebecca S. , Katz Matthew , You Y. Nancy , Papadopolous John , Rodriguez-Bigas Miguel A. , Skibber John M. , Matin Surena F. , Chang George J. 
Published: December 2017

BACKGROUND:
Ileostomies are a routine part of the care of patients with rectal cancer, but are associated with significant risk for dehydration, readmission, and acute kidney injury. Telemedicine has proven beneficial in decreasing readmission in chronic medical illnesses, but its utility in patients with an ileostomy is not well studied.

OBJECTIVE:
The purpose of this study was to evaluate the feasibility of televideoconferencing in the assessment of ileostomy output.

DESIGN:
An institutional review board-approved, prospective clinical trial was conducted at a single institution from November 2014 through December 2015.

SETTINGS:
The study was conducted in a single, large academic medical center.

PATIENTS:
Patients >18 years of age undergoing surgery with plans for ileostomy were eligible.

INTERVENTIONS:
Televideoconference assessments of ileostomy output and the need for medical intervention were conducted during the postoperative stay and compared with in-person assessment.

MAIN OUTCOME MEASURES:
The primary end point of the trial was the feasibility of using teleconferencing to assess the need for medical intervention, defined as 90% agreement between telemedicine and in-person assessments. Secondary end points included patient/provider satisfaction, and correlative studies examined dehydration events and readmission.

RESULTS:
Twenty-seven patients underwent 44 teleconferencing assessments of ileostomy output. Compared with in-person treatment decisions, there was a 95% match (95% CI, 85%–99%). The readmission rate for the study participants was 31%, and 18% experienced dehydration events. Both patients and faculty responded favorably to surveys regarding the use of telemedicine in the perioperative period.

LIMITATIONS:
The study is limited by its in-hospital use of technology and small sample size.

CONCLUSIONS:
Televideoconference evaluation is a feasible, reliable means of assessing ileostomy output with high patient and physician acceptance. Our pilot study provides rationale for further study in the postdischarge setting for patients with ileostomies. The incorporation of televideoconference assessment within a teledischarge program may enable early intervention to improve patient outcomes. See Video Abstract at http://links.lww.com/DCR/A455.
Menopause improves the predictive value of common cardiovascular risk scores in women with premature coronary artery disease
Authors: Kryczka Karolina Ewa , Kruk Mariusz , Piotrowski Walerian , Księżycka Ewa , Pracoń Radosław , Witkowski Adam , Demkow Marcin , Lubiszewska Barbara 
Published: December 2017

Abstract

Objective:
Menopause, particularly its early stage (≤3 years from onset), may be an important risk factor for premature coronary artery disease. The objective of the study was to assess whether the addition of the presence of menopause in women with premature coronary artery disease could improve the predictive value of the Atherosclerotic Cardiovascular Disease risk estimator and the Systematic COronary Risk Evaluation model.

Methods:
The case-control study included 307 women with coronary artery disease aged 55 or less, and 347 age-matched controls without coronary artery disease. Diagnostic accuracy parameters were evaluated for traditional risk models versus those enriched with menopausal status. Early and late postmenopausal periods were defined as ≤3 and >3 years from the onset of menopause, respectively.

Results:
Only the addition of the presence of the early postmenopausal stage to the 10-year Atherosclerotic Cardiovascular Disease risk classes resulted in significantly increased c-statistics from 0.66 (95% confidence interval [CI] 0.62-0.7) to 0.705 (95%CI 0.66-0.75) (P = 0.0003) and an increase of accuracy from 61.3% to 63.8% (P = 0.0025).
Adding the presence of early postmenopause to the Systematic COronary Risk Evaluation risk classes also resulted in significantly increased c-statistics from 0.59 (95% CI 0.55-0.63) to 0.641 (95%CI 0.6-0.68) (P = 0.0024) and an increase of accuracy from 64.1% versus 57.5% (P = 0.001).

Conclusion:
Adding the early menopausal period may significantly improve the predictive value of the 10-year Atherosclerotic Cardiovascular Disease risk score and the Systematic COronary Risk Evaluation model in women with premature coronary artery disease.
Vasomotor symptom characteristics: are they risk factors for incident diabetes?
Authors: Gray Kristen E. , Katon Jodie G. , LeBlanc Erin S. , Woods Nancy F. , Bastian Lori A. , Reiber Gayle E. , Weitlauf Julie C. , Nelson Karin M. , LaCroix Andrea Z. 
Published: December 2017

Abstract

Objective:
Vasomotor symptoms (VMS), encompassing hot flashes and night sweats, may be associated with diabetes, but evidence is limited. We sought to estimate these associations.

Methods:
Among 150,007 postmenopausal Women's Health Initiative participants from 1993 to 2014, we prospectively examined associations of incident diabetes with VMS characteristics at enrollment: any VMS, severity (mild/ moderate/severe), type (hot flashes/night sweats), timing (early [premenopausal or perimenopausal]/late [postmenopausal]), and duration. Cox proportional-hazards models estimated hazard ratios (HRs) and 95% confidence intervals (CIs).

Results:
Mean duration of follow-up was 13.1 years. VMS prevalence was 33%. Reporting any VMS was associated with 18% increased diabetes risk (95% CI 1.14, 1.22), which increased with severity (mild: HR 1.13, 95% CI 1.08, 1.17; moderate: HR 1.29, 95% CI 1.22, 1.36; severe: HR 1.48, 95% CI 1.34, 1.62) and duration (4% per 5 years, 95% CI 1.03, 1.05), independent of obesity. Diabetes risk was more pronounced for women reporting any night sweats (night sweats only: HR 1.20, 95% CI 1.13, 1.26; night sweats and hot flashes: HR 1.22, 95% CI 1.17, 1.27) than only hot flashes (HR 1.08, 95% CI 1.02, 1.15) and was restricted to late VMS (late: HR 1.12, 95% CI 1.07, 1.18; early and late: HR 1.16, 95% CI 1.11, 1.22; early: HR 0.99, 95% CI 0.95, 1.04).

Conclusions:
VMS are associated with elevated diabetes risk, particularly for women reporting night sweats and postmenopausal symptoms. The menopause transition may be an optimal window for clinicians to discuss long-term cardiovascular/metabolic risk with patients and leverage the bother of existing symptoms for behavior change to improve VMS and reduce diabetes risk.