bluuebunny/crossref_metadata_2025_split huggingface dataset:
regNet: an R package for network-based propagation of gene expression alterations
Authors: Seifert Michael , Beyer Andreas 
Published: August 2017

Abstract

Summary
Gene expression alterations and potentially underlying gene copy number mutations can be measured routinely in the wet lab, but it is still extremely challenging to quantify impacts of altered genes on clinically relevant characteristics to predict putative driver genes. We developed the R package regNet that utilizes gene expression and copy number data to learn regulatory networks for the quantification of potential impacts of individual gene expression alterations on user-defined target genes via network propagation. We demonstrate the value of regNet by identifying putative major regulators that distinguish pilocytic from diffuse astrocytomas and by predicting putative impacts of glioblastoma-specific gene copy number alterations on cell cycle pathway genes and patient survival.

Availability and implementation
regNet is available for download at https://github.com/seifemi/regNet under GNU GPL-3.

Supplementary information
Supplementary data are available at Bioinformatics online.
A Model to Integrate Health Promotion and Wellness in Physical Therapist Practice: Development and Validation
Authors: Lein Donald H. , Clark Diane , Graham Cecilia , Perez Patricia , Morris David 
Published: August 2017

Abstract

Background
Globally, physical therapy professional organizations have called for physical therapists to perform lifestyle behavior management during customary care, or health-focused care, due to increasing morbidity and mortality related to noncommunicable diseases. Given the potential for health-focused care to improve health outcomes, physical therapists should integrate health promotion into their daily clinical practice. A clinical model that illustrates necessary steps to deliver health-focused care would be helpful to educate present and future physical therapists.

Objective
The purpose of the study was to develop and validate the Health-Focused Physical Therapy Model (HFPTM) for physical inactivity and smoking.

Methods
The authors used a mixed method approach. The preliminary model was informed by previous research and the investigators’ shared experience in health promotion and physical therapy. An interdisciplinary group of health professionals provided input into the preliminary model by way of a World Café format. Eight physical therapists with health promotion and education expertise then engaged in a Delphi process to establish content validity.

Results
World Café participants indicated that: (1) physical therapists are well positioned to engage in health promotion and wellness, and (2) the model facilitates interdisciplinary collaboration and consultation. Delphi process participants reached majority consensus in 1 round. The average model content validity index (CVI) was .915 for physical inactivity and .899 for smoking. Agreement concerning the model schematic was 88% for either behavior. Investigators made few editorial changes after the Delphi process.

Limitations
Limitations of this study include using only 2 unhealthy lifestyle behaviors for testing, and performing the testing in a nonclinical setting.

Conclusions
An interdisciplinary group of health professionals believes that physical therapists should practice health-focused care and that the HFPTM is a valid model. This model could help physical therapist educators when educating physical therapist students and clinicians to practice health-focused care.
Does E-Government Improve Government Capacity? Evidence from Tax Compliance Costs, Tax Revenue, and Public Procurement Competitiveness
Authors: Kochanova Anna , Hasnain Zahid , Larson Bradley 
Published: August 2017

Abstract
Using cross-country data on e-government systems, this paper analyzes whether e-filing of taxes and e-procurement implementation improves the capacity of governments to raise and spend fiscal resources through lowering tax compliance costs, improving tax collection and public procurement competitiveness, and reducing corruption. Adopting e-filing systems reduces tax compliance costs as measured by the time to prepare and pay taxes, the likelihood and frequency of firms being visited by a tax official, and the perception of tax administration as an obstacle to firms’ operation and growth. E-filing is also associated with a moderate increase in the income tax revenue to GDP ratio. The results for e-procurement are weaker, with the number of firms securing or attempting to secure a government contract increasing only in countries with higher levels of development and better institutions. There is no strong relationship between e-government and corruption.
The effects of obesity on pulmonary function in children
Authors: Durbin Courtney , Egan Robin , Gervasi Kristin , Nadeau Nicole , Neal Emily , Reich Suzanne , Gregory Tanya 
Published: August 2017

ABSTRACT
The prevalence of obesity has risen rapidly in the United States in the past 20 years. Up to 25% of US children are obese, and obesity can be directly correlated with immediate and long-term health consequences. Pediatric obesity can harm multiple body systems and is a public health issue. This article focuses on how obesity affects a child's respiratory system, including pulmonary function, exercise intolerance, gas exchange, and airway musculature.
Acceptability of an Opioid Relapse Prevention Text-message Intervention for Emergency Department Patients
Authors: Suffoletto Brian , Yanta Joseph , Kurtz Ryan , Cochran Gerald , Douaihy Antoine , Chung Tammy 
Published: August 2017

Objective:
To explore whether a text message-based relapse prevention intervention (Preventing and Interrupting Early Relapse [PIER]1) is acceptable to treatment-seeking adults with opioid use disorder (OUD) after Emergency Department (ED) discharge using mixed-methods design.

Methods:
Adults seeking care in an urban ED for OUD (n = 20; mean age 22; 55% female; 75% white race) completed a baseline survey, and were invited to enroll in PIER1, which was delivered in 7-day blocks, with the option to re-enroll at the end of each block, up to 4 blocks. PIER1 included a morning “push” message focused on positive thinking, adaptive coping feedback tailored to twice-daily assessments of craving severity and contextual correlates of craving, and end-of-day feedback on daily opioid use and goal commitment. Participants were asked to complete a follow-up phone interview after the first 7 days of PIER1. Transcripts were thematically coded.

Results:
Seventeen out of 20 participants enrolled in PIER1. In the first 7 days, response rates to text-message assessments averaged 30%. Ten out of 17 participants re-enrolled after 7 days. Main themes from follow-up interviews (n = 9) included ease of use, social connection, and self-empowerment. Participants desired more personalized support and the ability to communicate through text messaging with another person about their struggles. Event-level data suggest that higher craving severity increased risk of opioid lapses.

Conclusions:
In this mixed-methods intervention development study, we found conflicting evidence supporting an automated text-message intervention providing relapse prevention support for treatment-seeking individuals with OUD discharged from the ED. Qualitative feedback suggests that PIER1 could be useful and acceptability enhanced through personalized human support.
Prescriptions Written for Opioid Pain Medication in the Veterans Health Administration Between 2000 and 2016
Authors: Grasso Michael A. , Grasso Clare T. , Jerrard David A. 
Published: August 2017

Objectives:
The purpose of this study was to identify national opioid pain medication (OPM) prescribing trends within the Veterans Health Administration (VA), and assess the impact of educational campaigns introduced in 2010 and 2013.

Methods:
We created a national cohort that documents more than 21 million patient records and 97 million outpatient OPM prescriptions covering a 17-year period. We examined OPM prescriptions in emergency departments, outpatient clinics, and inpatient settings.

Results:
The cohort accounted for 2.5 billion outpatient clinic visits, 18.9 million emergency department visits, and 12.4 million hospital admissions. The number of OPM prescriptions peaked in 2011, when they were provided during 5% of all outpatient visits and 15% of all emergency department visits. The morphine milligram equivalents (MMEs) peaked in 2014 at almost 17 billion in outpatient clinics and at 137 million in emergency departments. In 2016, OPM prescriptions were down 37% in outpatient clinics and 23% in emergency departments, and MMEs were down 30% in both settings. Prescriptions for hydrocodone and tramadol increased markedly between 2011 and 2015. OPM doses in inpatient settings continued to rise until 2015.

Conclusions:
We used a large national cohort to study trends in OPM prescriptions within the VA. Educational efforts to reduce the number of OPM prescriptions coincided with these reductions, but were initially associated with an increase in OPM dosage, an increase in the use of tramadol and hydrocodone, and an increase in the use of OPMs in inpatient settings.
Cracking the case: should orthopaedic case carts be subjected to more stringent regulations?
Authors: Darnley James , Denham Zachary , Phieffer Laura S. , Scharschmidt Thomas J. , Mayerson Joel L. , Glassman Andrew H. , Moffatt-Bruce Susan D. , Quatman Carmen E. 
Published: August 2017

Background:
Long periods of time with opened, uncovered sterile case carts and high rates of operating room (OR) traffic are correlated with contamination risk. We studied the length of time the case cart was open before incision and compared room traffic frequency before and after surgical incision.

Methods:
Thirty-three orthopaedic implant cases were observed at three hospitals over an 8-week period. Observation began at the opening of the implant case cart and concluded when the final dressing was placed. The length of time the sterile case cart was open before the patient was in the room and before an incision was made was recorded. Traffic was counted any time a surgical door opened and stratified on a per-hour basis. The traffic rate was counted before and after incision.

Results:
The average length that the case cart was open prior to the patient being in the room was 43.2 (±29.7) mins, (range, 0-153). On average the case cart was open 91.5 (±31.2) mins, (range, 45-189) prior to the incision. The room traffic was significantly greater during preincision period (45.0±12.8), than during postincision period (26.6±12.8) (P<0.0001). The average number of people in the operating room was 6.9 (±2.7).

Conclusions:
Room traffic during orthopaedic implant cases is high, with more than one door opening every 2 min. The highest frequencies of traffic occurred before incision but after case carts were opened. Case carts usually were opened more than 1 hr before incision for orthopaedic implant cases.
Colonoscopy in Patients With Postmyocardial Infarction Gastrointestinal Bleeding
Authors: Modi Rohan M. , Li Feng , Mumtaz Khalid , Hinton Alice , Lilly Scott M. , Hussan Hisham , Levine Edward , Zhang Cheng , Conwell Darwin L. , Krishna Somashekar G. , Stanich Peter P. 
Published: August 2017

Goals:The goal of this study was to evaluate outcomes of colonoscopy in the setting of post myocardial infarction (MI) gastrointestinal bleeding (GIB) in a large population-based data set.Background:The literature to substantiate the proposed safety of colonoscopy following an acute MI is limited.Study:The Nationwide Inpatient Sample (2007 to 2013) was utilized to identify all adult patients (age, 18 y or above) hospitalized with a primary diagnosis of ST-elevation MI and receiving left heart catheterization (STEMI-C). The outcomes of patients with concomitant diagnosis of GIB receiving endoscopic intervention with esophagogastroduodenoscopy (EGD) or colonoscopy postcatheterization were compared with those who did not. Primary outcomes including mortality, length of stay, and hospital costs were evaluated with univariate and multivariate analysis.Results:There were 131,752 patients with post-STEMI-C GIB (5.35% of all STEMI-C patients) and same admission colonoscopy was performed in 1599 patients (1.21%). Although the prevalence of post-STEMI-C GIB increased from 4.27% in 2007 to 5.87% in 2013 (P<0.001), patients receiving colonoscopy decreased from 1.42% to 1.09% (P<0.001) over the course of the study period. Multivariate analysis revealed that patients receiving no endoscopic intervention [odds ratio, 3.61; 95% confidence interval: 1.57, 8.31] or EGD alone (OR, 2.70; 95% confidence interval: 1.12, 6.49) have higher mortality compared with those receiving colonoscopy.Conclusions:Same admission colonoscopy performed for post-STEMI-C GIB was associated with lower mortality. However, despite increased incidence of GIB in these patients during the study period, a lower percentage of patients received colonoscopy. These results suggest that colonoscopy is safe but underutilized in this setting.
Six Weeks Versus 3 Months of Anticoagulant Treatment for Pediatric Central Venous Catheter-related Venous Thromboembolism
Authors: Smith Rowenne , Jones Sophie , Newall Fiona 
Published: August 2017

Objective:
Central venous catheters (CVCs) are the single most important predisposing factor for the development of pediatric venous thromboembolism (VTE). Treatment recommendations suggest anticoagulation for the duration of 6 weeks to 3 months. This project investigated clinical outcomes associated with 6 weeks compared with 3 months of enoxaparin therapy following diagnosis of a CVC-related VTE.

Methods:
This retrospective cohort study enrolled patients aged 18 years and below treated with enoxaparin with/without unfractionated heparin for a radiologically confirmed CVC-related VTE. Patients were identified using the pharmacy database, radiologic imaging, and medical records. Patients were divided into 2 groups based on the duration of anticoagulation (6+1 or 12±2 wk) and data were analyzed using descriptive statistics.

Results:
Seventy-four patients were included. Higher rates of complete thrombosis resolution were observed in children treated for 6 weeks at treatment cessation (39.4%) and long-term follow-up (61.5%), compared with 3 months (11.8% and 9.0%, respectively).

Conclusions:
Six weeks of treatment for CVC-related VTE may provide noninferior clinical outcomes compared with 3 months of anticoagulation. An international randomized-controlled trial (Kids-DOTT) is underway to explore the optimal duration of anticoagulation for acute-provoked VTE in children. This manuscript highlights that data from such studies is urgently needed.
Childhood Blastic Plasmacytoid Dendritic Cell Neoplasm Mimicking Acute Rheumatic Fever: Report of an Unusual Clinical Presentation and Review of Literature
Authors: Rajkumari Banashree Devi , Munikoty Vinay , Sreedharanunni Sreejesh , Jain Richa , Sachdeva Man Updesh Singh , Varma Neelam 
Published: August 2017

Background:
Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is very rarely diagnosed in children with less than 50 cases in the literature.

Observation:
We report a case of childhood BPDCN who mimicked acute rheumatic fever at presentation. Majority of the reported childhood BPDCN received acute lymphoblastic leukemia–like chemotherapy with/without stem cell therapy, whereas those who received acute myeloid leukemia–like therapy predominantly succumbed to disease or sepsis. Overall 68% of the patients were alive and achieved complete remission with an overall prognosis slightly better in children compared with adults.

Conclusions:
The case is reported due to its unique unusual clinical presentation and its rarity in pediatric population.
Seizures Induced by Exiting Water
Authors: Appavu Brian , Fox Jordana , Little Robert , Kerrigan John F. , Obeid Makram 
Published: August 2017

Introduction:
Reflex epilepsies represent a form of epilepsy in which unique modes of seizure precipitation are characterized by endogenous or exogenous stimuli. Hot water epilepsy represents a subtype of reflex epilepsy in which seizure precipitation arises from the act of immersing the head with hot water. Bathing epilepsy represents another subtype of reflex epilepsy in which seizure precipitation arises from the immersion with water at lukewarm temperatures.

Case Series:
We report on 2 boys with a unique form of bathing epilepsy characterized by the act of exiting out of water. The first patient had a family history significant for a brother with frontal lobe epilepsy. He underwent an evaluation in the epilepsy monitoring unit in which a reflex seizure was recorded while exiting the shower. This seizure was characterized by an ictal onset in the left frontal lobe and subsequent secondary generalization. The second patient initially had nonreflex seizures arising from the left temporal lobe and went on to develop reflex seizures upon exiting water. For both patients, the precipitation of seizures was independent of water or environmental temperature, exposure of specific body parts, or duration of water immersion. Both children experienced a sensation of coldness, followed by convulsive or atonic activity.

Conclusions:
Our cases represent a unique form of bathing epilepsy in which seizure precipitation is dependent upon exiting water.
Development and Psychometric Evaluation of the Speaking Up About Patient Safety Questionnaire
Authors: Richard Aline , Pfeiffer Yvonne , Schwappach David D.L. 
Published: August 2017

Objective
Speaking up about safety concerns by staff is important to prevent medical errors. Knowledge about healthcare workers’ speaking up behaviors and perceived speaking up climate is useful for healthcare organizations (HCOs) to identify areas for improvement. The aim of this study was to develop a short questionnaire allowing HCOs to assess different aspects of speaking up among healthcare staff.

Methods
Healthcare workers (n = 523) from 2 Swiss hospitals completed a questionnaire covering various aspects of speak up–related behaviors and climate. Psychometric testing included descriptive statistics, correlations, reliabilities (Cronbach α), principal component analysis, and t tests for assessing differences in hierarchical groups.

Results
Principal component analysis confirmed the structure of 3 speaking up behavior-related scales, that is, frequency of perceived concerns (concern scale, α = 0.73), withholding voice (silence scale, α = 0.76), and speaking up (speak up scale, α = 0.85). Concerning speak up climate, principal component analysis revealed 3 scales (psychological safety, α = 0.84; encouraging environment, α = 0.74; resignation, α = 0.73). The final survey instrument also included items covering speaking up barriers and a vignette to assess simulated behavior. A higher hierarchical level was mostly associated with a more positive speak up–related behavior and climate.

Conclusions
Patient safety concerns, speaking up, and withholding voice were frequently reported. With this questionnaire, we present a tool to systematically assess and evaluate important aspects of speaking up in HCOs. This allows for identifying areas for improvement, and because it is a short survey, to monitor changes in speaking up—for example, before and after an improvement project.
The Theory is Out There: The Use of ALPHA-2 Agonists in Treatment of Septic Shock
Authors: Ferreira Jason 
Published: August 2017

ABSTRACT
The sympathetic nervous system plays an important role in the initial response to sepsis. This response enables the host to respond to invading pathogens; however, prolonged activation can become pathological. The potential for unregulated sympathetic tone to become detrimental in the septic patient has fueled interest in the role and impact of sympathetic manipulation, including the selective inhibition of sympathetic tone to return and augment vascular reactivity. While conventional understanding of alpha 2 agonists activity is depletion of sympathetic outflow, novel evidence suggests mitigation rather than depletion. The mechanism by which these agents exert these properties remains controversial and appears to be condition-specific. The hypothesis by which alpha agonists affect the pathology of sepsis is multifactorial, but includes influence on inflammatory regulation, coagulopathy, dynamic flow, as well as vascular responsiveness and integrity. Theory and basic science evidence supports the use of α agonists in the septic population. The clinical evidence shedding light on this topic is limited and confounded by intention or trial design. Future evidence should focus on adjuvant therapy in patients progressing to or at high risk of shock development.
Neutrophil Activation During Septic Shock
Authors: Stiel Laure , Meziani Ferhat , Helms Julie 
Published: August 2017

ABSTRACT
In addition to their well-known role as the cellular mediators of immunity, key other roles have been identified for neutrophils during septic shock. Importantly, neutrophils indeed play a critical role in the recently described immunothrombosis concept and in septic shock-induced coagulopathy. Septic shock is one of the most severe forms of infection, characterized by an inadequate host response to the pathogenic organism. This host response involves numerous defense mechanisms with an intense cellular activation, including neutrophil activation. Neutrophils are key cells of innate immunity through complex interactions with vascular cells and their activation may participate in systemic tissue damages. Their activation also leads to the emission of neutrophil extracellular traps, which take part in both pathogen circumscription and phagocytosis, but also in coagulation activation. Neutrophils thus stand at the interface between hemostasis and immunity, called immunothrombosis.
The present review will develop a cellular approach of septic shock pathophysiology focusing on neutrophils as key players of septic shock-induced vascular cell dysfunction and of the host response, associating immunity and hemostasis. We will therefore first develop the role of neutrophils in the interplay between innate and adaptive immunity, and will then highlight recent advances in our understanding of immunothrombosis septic shock-induced coagulopathy.