bluuebunny/crossref_metadata_2025_split huggingface dataset:
SoFIA: a data integration framework for annotating high-throughput datasets
Authors: Childs Liam Harold , Mamlouk Soulafa , Brandt Jörgen , Sers Christine , Leser Ulf 
Published: May 2016

Abstract
Motivation: Integrating heterogeneous datasets from several sources is a common bioinformatics task that often requires implementing a complex workflow intermixing database access, data filtering, format conversions, identifier mapping, among further diverse operations. Data integration is especially important when annotating next generation sequencing data, where a multitude of diverse tools and heterogeneous databases can be used to provide a large variety of annotation for genomic locations, such a single nucleotide variants or genes. Each tool and data source is potentially useful for a given project and often more than one are used in parallel for the same purpose. However, software that always produces all available data is difficult to maintain and quickly leads to an excess of data, creating an information overload rather than the desired goal-oriented and integrated result.
Results: We present SoFIA, a framework for workflow-driven data integration with a focus on genomic annotation. SoFIA conceptualizes workflow templates as comprehensive workflows that cover as many data integration operations as possible in a given domain. However, these templates are not intended to be executed as a whole; instead, when given an integration task consisting of a set of input data and a set of desired output data, SoFIA derives a minimal workflow that completes the task. These workflows are typically fast and create exactly the information a user wants without requiring them to do any implementation work. Using a comprehensive genome annotation template, we highlight the flexibility, extensibility and power of the framework using real-life case studies.
Availability and Implementation: https://github.com/childsish/sofia/releases/latest under the GNU General Public License
Contact: liam.childs@hu-berlin.de
Supplementary information: Supplementary data are available at Bioinformatics online.
In Vivo Monitoring of Sevoflurane-induced Adverse Effects in Neonatal Nonhuman Primates Using Small-animal Positron Emission Tomography
Authors: Zhang Xuan , Liu Shuliang , Newport Glenn D. , Paule Merle G. , Callicott Ralph , Thompson James , Liu Fang , Patterson Tucker A. , Berridge Marc S. , Apana Scott M. , Brown Christina C. , Maisha Mackean P. , Hanig Joseph P. , Slikker William , Wang Cheng 
Published: May 2016

AbstractAbstract
Sevoflurane exposure increased glial activation, a surrogate for neurotoxicity, as indicated by increased uptake of 18F-labeled fluoroethoxybenzyl-N-(4-phenoxypyridin-3-yl) acetamide in the frontal and temporal lobes. Acetyl-l-carnitine mitigated the adverse effects of sevoflurane. Peripheral benzodiazepine receptor can serve as biomarkers of anesthetic neurotoxicity; as such, the extent of anesthetic-induced injury can be evaluated spatially and over longer periods of time noninvasively in vivo.

Background
Animals exposed to sevoflurane during development sustain neuronal cell death in their developing brains. In vivo micro-positron emission tomography (PET)/computed tomography imaging has been utilized as a minimally invasive method to detect anesthetic-induced neuronal adverse effects in animal studies.

Methods
Neonatal rhesus monkeys (postnatal day 5 or 6, 3 to 6 per group) were exposed for 8 h to 2.5% sevoflurane with or without acetyl-l-carnitine (ALC). Control monkeys were exposed to room air with or without ALC. Physiologic status was monitored throughout exposures. Depth of anesthesia was monitored using quantitative electroencephalography. After the exposure, microPET/computed tomography scans using 18F-labeled fluoroethoxybenzyl-N-(4-phenoxypyridin-3-yl) acetamide (FEPPA) were performed repeatedly on day 1, 1 and 3 weeks, and 2 and 6 months after exposure.

Results
Critical physiologic metrics in neonatal monkeys remained within the normal range during anesthetic exposures. The uptake of [18F]-FEPPA in the frontal and temporal lobes was increased significantly 1 day or 1 week after exposure, respectively. Analyses of microPET images recorded 1 day after exposure showed that sevoflurane exposure increased [18F]-FEPPA uptake in the frontal lobe from 0.927 ± 0.04 to 1.146 ± 0.04, and in the temporal lobe from 0.859 ± 0.05 to 1.046 ± 0.04 (mean ± SE, P < 0.05). Coadministration of ALC effectively blocked the increase in FEPPA uptake. Sevoflurane-induced adverse effects were confirmed by histopathologic evidence as well.

Conclusions
Sevoflurane-induced general anesthesia during development increases glial activation, which may serve as a surrogate for neurotoxicity in the nonhuman primate brain. ALC is a potential protective agent against some of the adverse effects associated with such exposures.
Preliminary Results of Magnetically Controlled Growing Rods for Early Onset Scoliosis
Authors: Ridderbusch Karsten , Rupprecht Martin , Kunkel Philip , Hagemann Christian , Stücker Ralf 
Published: May 2016

Background:
Growth-sparing techniques for the treatment of early onset scoliosis (EOS) have developed significantly over the last years. Traditional growing rods (GRs) require repeated surgical lengthening under anesthesia. Since June 2011 we have been using the magnetically controlled growing rods (MCGR) to treat patients with progressive EOS.

Methods:
Thirty-five patients with EOS of different etiologies underwent treatment with MCGR. We record about our preliminary results of 24 patients who fulfilled the inclusion criteria of a minimum follow-up (FU) of 12 month and >3 lengthenings. The mean age at surgery was 8.9±2.5 years. Correction of the primary curve after the index surgery and after lengthenings was measured on standing radiographs using the Cobb technique. T1-T12 and T1-S1 spinal length were also measured. Intraoperative and postoperative complications were recorded.

Results:
The mean FU was 21.1±7.3 months. All patients had a minimum of 3 outpatient lengthenings [mean, 4.6±1.5 (range, 3 to 8)]. The mean primary curve was 63±15 degrees (range, 40 to 96 degrees) and improved to 29±11 degrees (range, 11 to 53 degrees; P<0.001) after MCGR. The mean major curve after most recent lengthening was 26 degrees (range, 8 to 60 degrees; P<0.07). The T1-T12 as well as the T1-S1 length increased significantly (P<0.001). The mean preoperative thoracic kyphosis decreased from 43±24 degrees (range, −32 to 86 degrees) to 27±12 degrees (range, 9 to 50 degrees; P<0.001) after surgery, respectively, and measured 32±12 degrees (range, 12 to 64 degrees; P<0.05) at last FU. In 1 patient a loss of distraction occurred making rod exchange necessary. Three patients developed a proximal junctional kyphosis and in another patient a screw pull out occurred that required revision surgery.

Conclusions:
Our results demonstrate that MCGR is a safe and effective nonfusion technique in the treatment of progressive EOS avoiding repeated surgical lengthening procedures. It provides adequate distraction similar to standard GR. The magnetically induced transcutaneous lengthening allows noninvasive distraction achieving spinal growth comparable to conventional GR techniques.

Level of Evidence:
Level IV—retrospective nonrandomized objective study.
Combined Exercise and Inspiratory Muscle Training in Patients With Heart Failure
Authors: Neto Mansueto Gomes , Martinez Bruno Prata , Conceição Cristiano Sena , Silva Paulo Eugênio , Carvalho Vitor Oliveira 
Published: May 2016

PURPOSE:
Studies have reported the benefits of exercise and inspiratory muscle training (IMT) in patients with heart failure (HF); however, there is no meta-analysis on the effects of the combination of exercise and IMT in patients with HF. The objective of this study was to determine whether combined exercise/IMT was more effective than conventional exercise on exercise capacity, respiratory muscle strength, and quality of life in patients with HF.

METHODS:
This is a systematic review and meta-analysis. We searched MEDLINE, LILACS, CINAHL, EMBASE, PEDro, and the Cochrane Central Register of Controlled Trials (from the earliest date available to April 2015) for randomized controlled trials, examining effects of combined exercise/IMT versus conventional exercise on exercise capacity, respiratory muscle strength, and quality of life measurements in patients with HF. Two reviewers selected studies independently. Weighted mean differences and 95% CIs were calculated.

RESULTS:
Three studies met the study criteria. Combined exercise/IMT resulted in improvement in maximal inspiratory pressure weighted mean differences (20.89 cm H2O; 95% CI, 14.0-27.78) and Minnesota Living with Heart Failure Questionnaire weighted mean differences (4.43; 95% CI, 0.72-8.14). Nonsignificant difference was observed in peak

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2 for participants in the combined exercise/IMT group compared with the conventional exercise group. No serious adverse events were reported.

CONCLUSIONS:
Combined exercise/IMT may improve maximal inspiratory pressure and quality of life in patients with HF and should be considered for inclusion in cardiac rehabilitation programs.
Utility of Screening for Obstructive Sleep Apnea in Cardiac Rehabilitation
Authors: Marzolini Susan , Sarin Michael , Reitav Jaan , Mendelson Monique , Oh Paul 
Published: May 2016

PURPOSE:
Obstructive sleep apnea (OSA) is prevalent in patients with cardiovascular disease and is often undiagnosed. The purpose of this study was to determine the utility of communicating OSA risk with the patients in a diabetes and cardiac rehabilitation program (CRP) and primary care physicians.

METHODS:
Following an OSA education session, 295 patients in diabetes and CRPs were screened for OSA and daytime sleepiness by STOP-BANG and Epworth Sleepiness Scale questionnaires. Letters were sent to patients at high risk or noncompliant with continuous positive airway pressure (CPAP) treatment and their physicians. Follow-up questionnaires were sent to patients 6 months later.

RESULTS:
Of the 295 patients screened, 16.6% (n = 49) had an OSA diagnosis and had been prescribed CPAP. A smaller proportion patients in the diabetes program than in the CRP had discontinued CPAP (22.2% vs 45.2%; P = .03) with discomfort being the greatest barrier. Three of the 7 patients (42.9%) who had contact with their physician resumed CPAP. Of the remaining 246 patients who scored high on ≥1 questionnaire (77.6%; n = 191) and returned the 6-month questionnaire (53.9%; n = 103), communication of risk assessment resulted in 49.5% (n = 51) of patients consulting with their physician. Of those, half were referred for polysomnography. All were diagnosed with OSA.

CONCLUSION:
More than three quarters of patients in diabetes and CRPs scored high on ≥1 questionnaire suggesting signs/symptoms of OSA. However, only 16.6% were prescribed CPAP and compliance to treatment was poor (63.3%). Education and communication of OSA risk with patients and physicians resulted in a de novo diagnosis in at least 1 of 10 patients screened and 16.7% restarted CPAP.
Insulin Resistance and Diabetes Mellitus in Contemporary Cardiac Rehabilitation
Authors: Khadanga Sherrie , Savage Patrick D. , Ades Philip A. 
Published: May 2016

PURPOSE:
The goal of this study was to determine the prevalence of insulin resistance (IR) and type 2 diabetes mellitus (T2DM) in contemporary cardiac rehabilitation (CR) and to compare clinical responses in CR between these subsets of patients with coronary heart disease (CHD).

METHODS:
The study cohort included 818 patients enrolled in CR and separated into 3 groups: (1) individuals with normal hemoglobin A1c (HbA1c) (NoIR: HbA1c < 5.7%); (2) individuals with IR (IR: HbA1c ≥ 5.7 to <6.5%); (3) and individuals with T2DM (HbA1c ≥ 6.5%).

RESULTS:
The combined prevalence of IR (44%) and T2DM (23%) was 67%, which paralleled the prevalence of metabolic syndrome (MetSyn), present in 65% of patients. Women had a higher prevalence of IR and MetSyn than men (73% vs 64%, 72% vs. 63%, respectively) and a greater percentage with an elevated waist circumference (71% vs 60%) (all P < .05). All 3 groups experienced decreases in body weight (NoIR = −2.3 ± 4.0, IR = −1.7 ± 4.0, T2DM = −1.0 ± 4.2 kg) and increases in maximal metabolic equivalents (METs) at exercise testing (NoIR = +2.2 ± 2.5 vs IR = +2.1 ± 2.8 vs T2DM = +1.3 ± 2.3) (all P < .05). Individuals with NoIR achieved greater improvements in weight, body mass index, and METs than patients with T2DM (all P < .05). Selected individuals who participated in a 4-session behavioral weight-loss program lost more than twice the weight as nonparticipants.

CONCLUSIONS:
The combined prevalence of IR and T2DM in patients with CHD enrolled in CR was remarkably high (67%). To reverse the deleterious consequences of IR and T2DM, targeted interventions involving exercise and weight loss need to be a central focus of CR programming.
Severity of Depressive Symptoms Pre- and Postcardiac Rehabilitation
Authors: Ghisi Gabriela Lima de Melo , Santos Claudia Victoria Anchique , Benaim Briseida , Lopez-Jimenez Francisco , Herdy Artur Haddad , Inojosa Jose Medina , Terzic Carmen M. , Janovik Lisiane , Rojas Maria Fernanda , Grace Sherry L. 
Published: May 2016

PURPOSE:
Depression is 3 times more prevalent in the cardiac than the general population in high-income countries and is particularly high in middle-income countries. Comorbid depression is associated with twice the mortality after a cardiovascular event. The objectives of this study were to describe and compare depressive symptoms pre- and postcardiac rehabilitation (CR) among patients in high-income countries and middle-income countries in the Americas.

METHODS:
The study design was prospective and observational. A convenience sample of CR participants completed the Patient Health Questionnaire-9 (PHQ-9) at CR intake and again at program discharge. Clinical data were extracted from medical charts.

RESULTS:
There were 779 participants: 45 Brazilian (5.8% of sample), 214 Canadian (27.5%), 126 Colombian (16.2%), 309 American (39.7%), and 85 Venezuelan (10.9%). Pre-CR depressive symptoms significantly differed between countries (P < .05), with Colombian participants reporting higher scores than Canadians and Venezuelans. Total PHQ-9 scores significantly decreased during CR in Colombia (mean change =−2.33; P < .001), the United States (mean change =−1.12; P < .001), and Venezuela (mean change =−2.14; P < .001), but not in Brazil (where less psychosocial intervention was offered) or Canada (where pre-CR scores were low). Among the 102 (13.1%) participants with scores in the elevated range pre-CR, the mean change in PHQ-9 scores was −6.57 ± 1.09 and 40 (39.2%) participants no longer had elevated symptoms postprogram.

CONCLUSIONS:
Depressive symptoms are variable among patients with CR in South and North American countries. CR programs incorporating psychosocial components can reduce these symptoms.
Short- and Long-Term Prognostic Utility of the HEART Score in Patients Evaluated in the Emergency Department for Possible Acute Coronary Syndrome
Authors: Jain Tarun , Nowak Richard , Hudson Michael , Frisoli Tiberio , Jacobsen Gordon , McCord James 
Published: May 2016

Introduction:
The HEART score is a risk-stratification tool that was developed and validated for patients evaluated for possible acute coronary syndrome (ACS) in the emergency department (ED). We sought to determine the short-term and long-term prognostic utility of the HEART score.

Methods:
A retrospective single-center analysis of 947 patients evaluated for possible ACS in the ED in 1999 was conducted. Patients were followed for major adverse cardiac events (MACEs) at 30 days: death, acute myocardial infarction, or revascularization procedure. All-cause mortality was assessed at 5 years. The HEART score was compared with the Thrombolysis in Myocardial Infarction (TIMI) score.

Results:
At 30 days, 14% (135/947) of patients had an MACE: 48 deaths (5%), 84 acute myocardial infarctions (9%), and 48 (5%) revascularization procedures. The MACE rate in patients with HEART score ≤3 was 0.6% (1/175) involving a revascularization procedure, 9.5% (53/557) in patients with HEART score between 4 and 6, and 38% (81/215) with HEART score ≥7. The C-statistic for the HEART score was 0.82 and 0.68 for the TIMI score for predicting 30-day MACE (P < 0.05). Patients with HEART score ≤3 had lower 5-year mortality rate compared with those with TIMI score of 0 (10.6% vs. 20.5%, P = 0.02).

Conclusions:
The HEART score is a valuable risk-stratification tool in predicting not only short-term MACE but also long-term mortality in patients evaluated for possible ACS in the ED. The HEART score had a superior prognostic value compared with the TIMI score.
Chest Pain Risk Stratification
Authors: Stopyra Jason P. , Miller Chadwick D. , Hiestand Brian C. , Lefebvre Cedric W. , Nicks Bret A. , Cline David M. , Askew Kim L. , Riley Robert F. , Russell Gregory B. , Burke Greg L. , Herrington David , Hoekstra James W. , Mahler Simon A. 
Published: May 2016

Background:
The 2-hour accelerated diagnostic protocol (ADAPT) and the history electrocardiogram age risk factors troponin (HEART) Pathway are decision aids designed to identify Emergency Department (ED) patients with chest pain who are safe for early discharge. Both have demonstrated high sensitivity (>99%) for major adverse cardiac events (MACE) at 30 days and early discharge rates ≥20%. The objective of this study is to compare the sensitivity and early discharge rates of the ADAPT and HEART Pathway decision aids in a cohort of ED patients with acute chest pain.

Methods:
A secondary analysis of participants enrolled and randomized to the HEART Pathway arm of the HEART pathway randomized controlled trial was conducted. Each patient was prospectively classified as low risk (suitable for early discharge) or high risk by ADAPT and the HEART Pathway. Sensitivity for MACE at 30 days and the number of patients identified as low-risk were calculated for each decision aid. Decision aid performance was compared using McNemar’s test.

Results:
MACE occurred in 8 of 141 (5.7%); there were no deaths, 7 patients had myocardial infarction, and 1 patient had coronary revascularization without myocardial infarction. ADAPT and the HEART pathway identified all patients with MACE as high risk; sensitivity for MACE of 100% [95% confidence interval (CI): 63–100%]. ADAPT identified 34 of 141 patients (24%; 95% CI: 17–32%) as low-risk, whereas the Heart pathway identified 66 of 141 patients (47%, 95% CI: 38–55%) as low risk (P < 0.001).

Conclusions:
Within a cohort of ED patients with acute chest pain, ADAPT and the HEART pathway had high sensitivity for MACE. The HEART pathway outperformed ADAPT by correctly identifying more patients as low risk and safe for early discharge.
Nationwide 30-Day Readmissions After Elective Orthopedic Surgery: Reasons and Implications
Authors: Minhas Shobhit V. , Kester Benjamin S. , Lovecchio Francis C. , Bosco Joseph A. 
Published: May 2016

Introduction:
Reducing readmissions after orthopedic surgery is important for decreasing hospital costs and patient morbidity. Our goals were to establish national rates and reasons for 30-day readmissions after common elective orthopedic procedures.

Methods:
Patients undergoing total knee arthroplasty, total hip arthroplasty, posterior lumbar fusion, anterior cervical discectomy and fusion, or total shoulder arthroplasty were identified from the American College of Surgeons National Surgical Quality Improvement Program database. Thirty-day readmission rates, timing, and reasons were recorded for each procedure. Multivariate analysis was used to identify risk factors of readmissions.

Results:
A total of 3.8% of patients had an all-cause readmission, 3.6% had an unplanned readmission, and 2.4% had an unplanned readmission related to surgery (URRS). The most common reason was surgical site complication followed by venous thromboembolism and bleeding. Only 3.2% of all patients with a URRS were readmitted because of a predischarge complication. Independent predictors of URRS were current smoking, any inpatient complication, and non–home discharge.

Conclusions:
Unplanned readmissions were a proxy for new postdischarge complications rather than a re-exacerbation of previous inpatient events. Emphasis should be on more effective prevention strategies for surgical site infections, continuing to prevent inpatient complications and focusing on home discharge.
Age-related Morbidity and Mortality After Transjugular Intrahepatic Portosystemic Shunts
Authors: Suraweera Duminda , Jimenez Melissa , Viramontes Matthew , Jamal Naadir , Grotts Jonathan , Elashoff David , Lee Edward W. , Saab Sammy 
Published: May 2016

Aim:
To compare age-related morbidity and mortality after transjugular intrahepatic portosystemic shunts (TIPS).

Methods:
We performed a retrospective chart review of patients who underwent TIPS at the University of California Los Angeles Medical Center between 2008 to 2014. Elderly patients (65 y and older) were matched with nonelderly patients (controls, below 65 y) by model for end-stage liver disease (MELD) score (±3), indication for TIPS (refractory ascites vs. variceal bleeding), serum sodium level (±5), in a ratio of 1:1. Endpoints measures were hospital stay post-TIPS, rifaximin, or lactulose use, TIPS failure at 30 days, readmission at 90 days, MELD at 90 days, and mortality at 90 days.

Results:
A total of 30 patient matches were included in this study: 30 control and 30 elderly patients. The median [interquartile (IQR)] MELD scores for controls and elderly were 11 (9, 13.8) for the controls and 11.5 (9, 14.8) for elderly patients (P=0.139). There were no significant differences in serum sodium and indication for TIPS. Thirty and 90-day follow-up laboratory test results were also similar between elderly and control patients. Event-free survival at 90 days was similar between controls and elderly patients [odds ratio (OR), 0.86; 95% confidence interval (CI), 0.3-2.5; P>0.05]. There was a trend toward greater hospitalization (OR, 1.76; 95% CI, 0.52-5.95; P=0.546) and mortality (OR, 3.3; 95% CI, 0.3-14.01; P=0.182).

Conclusions:
The results of this study suggest event-free survival is similar between nonelderly and elderly patients. Although statistically significant, there is a tendency toward greater mortality and hospitalization in the elderly.