bluuebunny/crossref_metadata_2025_split huggingface dataset:
In Situ Expression of Bcl‐2 in Pulmonary Artery Endothelial Cells Associates with Pulmonary Arterial Hypertension Relative to Heart Failure with Preserved Ejection Fraction
Authors: Benza Raymond L. , Williams Gretchen , Wu Changgong , Shields Kelly J. , Raina Amresh , Murali Srinivas , Passineau Michael J. 
Published: August 2016

We have previously reported that pulmonary artery endothelial cells (PAECs) can be harvested from the tips of discarded Swan‐Ganz catheters after right heart catheterization (RHC). In this study, we tested the hypothesis that the existence of an antiapoptotic phenotype in PAECs obtained during RHC is a distinctive feature of pulmonary arterial hypertension (PAH; World Health Organization group 1) and might be used to differentiate PAH from other etiologies of pulmonary hypertension. Specifically, we developed a flow cytometry‐based measure of Bcl‐2 activity, referred to as the normalized endothelial Bcl‐2 index (NEBI). We report that higher NEBI values are associated with PAH to the exclusion of heart failure with preserved ejection fraction (HFpEF) and that this simple diagnostic measurement is capable of differentiating PAH from HFpEF without presenting addition risk to the patient. If validated in a larger, multicenter study, the NEBI has the potential to assist physicians in the selection of appropriate therapeutic interventions in the common and dangerous scenario wherein patients present a clinical and hemodynamic phenotype that makes it difficult to confidently differentiate between PAH and HFpEF.
Tadalafil Therapy for Sarcoidosis‐Associated Pulmonary Hypertension
Authors: Ford H. J. , Baughman R. P. , Aris R. , Engel P. , Donohue J. F. 
Published: August 2016

Sarcoidosis‐associated pulmonary hypertension (SAPH) is estimated to occur in at least 5% or more of sarcoidosis patients, and it contributes to significant morbidity and mortality. Optimal therapy for SAPH is not well established. We performed a 24‐week open‐label trial of tadalafil for SAPH at 2 academic medical centers. Subjects were required to have confirmed sarcoidosis plus a right heart catheterization within 12 months of enrollment showing a mean pulmonary artery pressure ≥ 25 mmHg, a pulmonary artery wedge pressure ≤ 15 mmHg, and a calculated pulmonary vascular resistance ≥ 3 Wood units. Subjects received 20 mg/day of tadalafil for the first 4 weeks and then 40 mg/day for the subsequent 20 weeks. Sixteen patients were screened, 12 of whom met criteria for enrollment. At 24 weeks, there was no overall improvement in 6‐minute walk distance (6MWD). Five of the 12 subjects dropped out of the study early (2 for social reasons, 3 for medical reasons). There was no significant change in short form 36, St. George's respiratory questionnaire, or maximum Borg dyspnea scores over the 24 weeks. There were no significant adverse events or laboratory abnormalities clearly related to tadalafil in the cohort. The study did not meet the primary end point of change in 6MWD because of the small sample size. Tadalafil was generally safely administered in this cohort of SAPH patients. There was a relatively high dropout rate but no major adverse events and no clinical worsening. Larger studies are needed to explore this question further. (Trial registration: ClinicalTrials.gov identifier: NCT01324999)
Tritium production assessment for the DCLL EUROfusion DEMO
Authors: Palermo Iole , Rapisarda David , Fernández-Berceruelo Iván , Ibarra Angel 
Published: August 2016

Abstract
The viability of a fusion reactor is preeminently conditioned by the tritium self-sufficiency. An assessment of different parameters representing the tritium production, as the tritium breeding ratio (TBR), the tritium production rate (TPR) density and their poloidal and radial variations along the PbLi breeder zones has been performed for the last DCLL DEMO designs developed in the frame of the EUROfusion Programme. The final overall value of 1.104 obtained allows accomplishing the fuel self-sufficiency requirement. This TBR value includes not only the contribution of the breeding blanket (BB) modules but also of the back supporting structure (BSS). The BSS design resulted fundamental to reach the 1.1 criterion. Lastly, the influence of the integration in the reactor of the heating and current drive (H&CD) systems that will penetrate the breeder volume has been evaluated. Assuming different configurations for them, the TBR loss has been determined. All the calculations have entailed the use of the particle transport Monte Carlo code MCNP5.
Analytical collisionless damping rate of geodesic acoustic mode
Authors: Ren H. , Xu X.Q. 
Published: August 2016

Abstract
Collisionless damping of geodesic acoustic mode (GAM) is analytically investigated by considering the finite-orbit-width (FOW) resonance effect to the 3rd order in the gyro-kinetic equations. A concise and transparent expression for the damping rate is presented for the first time. Good agreement is found between the analytical damping rate and the previous TEMPEST simulation result (Xu 2008 et al Phys. Rev. Lett.
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215001) for systematic q scans. Our result also shows that it is of sufficient accuracy and has to take into account the FOW effect to the 3rd order.
PathScore: a web tool for identifying altered pathways in cancer data
Authors: Gaffney Stephen G. , Townsend Jeffrey P. 
Published: August 2016

Summary: PathScore quantifies the level of enrichment of somatic mutations within curated pathways, applying a novel approach that identifies pathways enriched across patients. The application provides several user-friendly, interactive graphic interfaces for data exploration, including tools for comparing pathway effect sizes, significance, gene-set overlap and enrichment differences between projects.
Availability and Implementation: Web application available at pathscore.publichealth.yale.edu. Site implemented in Python and MySQL, with all major browsers supported. Source code available at: github.com/sggaffney/pathscore with a GPLv3 license.
Contact: stephen.gaffney@yale.edu
BiDiFuse: a FIJI plugin for fusing bi-directionally recorded microscopic image volumes
Authors: Detrez Jan R. , Vanderwinden Jean-Marie , Barbier Michaël , Verschuuren Marlies , Nuydens Rony , Langlois Xavier , Timmermans Jean-Pierre , De Vos Winnok H. 
Published: August 2016

Summary: Deep tissue imaging is increasingly used for non-destructive interrogation of intact organs and small model organisms. An intuitive approach to increase the imaging depth by almost a factor of 2 is to record a sample from two sides and fuse both image stacks. However, imperfect three-dimensional alignment of both stacks presents a computational challenge. We have developed a FIJI plugin, called BiDiFuse, which merges bi-directionally recorded image stacks via 3D rigid transformations. The method is broadly applicable, considering it is compatible with all optical sectioning microscopes and it does not rely on fiducial markers for image registration.
Availability and Implementation: The method is freely available as a plugin for FIJI from https://github.com/JanDetrez/BiDiFuse/.
Contact: winnok.devos@uantwerpen.be
RNAcommender: genome-wide recommendation of RNA–protein interactions
Authors: Corrado Gianluca , Tebaldi Toma , Costa Fabrizio , Frasconi Paolo , Passerini Andrea 
Published: August 2016

Motivation: Information about RNA–protein interactions is a vital pre-requisite to tackle the dissection of RNA regulatory processes. Despite the recent advances of the experimental techniques, the currently available RNA interactome involves a small portion of the known RNA binding proteins. The importance of determining RNA–protein interactions, coupled with the scarcity of the available information, calls for in silico prediction of such interactions.
Results: We present RNAcommender, a recommender system capable of suggesting RNA targets to unexplored RNA binding proteins, by propagating the available interaction information taking into account the protein domain composition and the RNA predicted secondary structure. Our results show that RNAcommender is able to successfully suggest RNA interactors for RNA binding proteins using little or no interaction evidence. RNAcommender was tested on a large dataset of human RBP-RNA interactions, showing a good ranking performance (average AUC ROC of 0.75) and significant enrichment of correct recommendations for 75% of the tested RBPs. RNAcommender can be a valid tool to assist researchers in identifying potential interacting candidates for the majority of RBPs with uncharacterized binding preferences.
Availability and Implementation: The software is freely available at http://rnacommender.disi.unitn.it.
Contact: gianluca.corrado@unitn.it or andrea.passerini@unitn.it
Supplementary information: Supplementary data are available at Bioinformatics online.
A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes
Authors: Wheeler Nicole E. , Barquist Lars , Kingsley Robert A. , Gardner Paul P. 
Published: August 2016

Motivation: Next generation sequencing technologies have provided us with a wealth of information on genetic variation, but predicting the functional significance of this variation is a difficult task. While many comparative genomics studies have focused on gene flux and large scale changes, relatively little attention has been paid to quantifying the effects of single nucleotide polymorphisms and indels on protein function, particularly in bacterial genomics.
Results: We present a hidden Markov model based approach we call delta-bitscore (DBS) for identifying orthologous proteins that have diverged at the amino acid sequence level in a way that is likely to impact biological function. We benchmark this approach with several widely used datasets and apply it to a proof-of-concept study of orthologous proteomes in an investigation of host adaptation in Salmonella enterica. We highlight the value of the method in identifying functional divergence of genes, and suggest that this tool may be a better approach than the commonly used dN/dS metric for identifying functionally significant genetic changes occurring in recently diverged organisms.
Availability and Implementation: A program implementing DBS for pairwise genome comparisons is freely available at: https://github.com/UCanCompBio/deltaBS.
Contact: nicole.wheeler@pg.canterbury.ac.nz or lars.barquist@uni-wuerzburg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Transfusion-free treatment strategies for acute anemia in critical care
Authors: Morgan Caitlin A. , Byul (Sarah) Sae , Forest Christopher P. 
Published: August 2016

ABSTRACT
Acute anemia is a frequently encountered diagnosis in critically ill patients, and can be a challenge if blood products are not readily available or if patients refuse these products on the basis of their religious beliefs. This article discusses the goals of anemia management and summarizes several alternatives to blood transfusions that can be used to prevent and treat acute anemia.
Diagnostic utility of challenge procedures for physical urticaria/angioedema syndromes: a systematic review
Authors: Cuervo-Pardo Lyda , Gonzalez-Estrada Alexei , Lang David M. 
Published: August 2016

Purpose of review
Physical urticaria/angioedema syndromes (PUAs) are commonly encountered. They are identified by a history of physical factors provoking cutaneous symptoms, and confirmed by provocation testing. Recent guidelines have recommended use of challenge procedures for diagnosis; however, their positive/negative likelihood ratios have not been established.

Recent findings
We conducted a systematic review to determine the diagnostic utility of recommended office procedures for three common PUAs: dermatographia (DERMATO), cholinergic urticaria (CHOL), and delayed pressure urticaria/angioedema (DPUA). In this study, we were unable to identify studies of sufficient methodologic quality to calculate positive/negative likelihood ratios for recommended diagnostic challenges for PUAs.

Summary
The study highlights the need for well designed studies to aid the clinician in interpretation of diagnostic challenges for patients with DERMATO, CHOL, and DPUA. There are limited high-quality data available to support the diagnostic utility of office challenges for PUAs. There is a low sensitivity associated with methacholine intradermal challenge for confirming a diagnosis of CHOL.
The rich and the poor: environmental biodiversity protecting from allergy
Authors: Ruokolainen Lasse , Fyhrquist Nanna , Haahtela Tari 
Published: August 2016

Purpose of review
It has been proposed that biodiversity loss leads to reduced interaction between environmental and human microbiotas. This, in turn, may lead to immune dysfunction and impaired tolerance mechanisms in humans. That is, contact with environmental biodiversity is expected to protect from allergies. However, direct evidence linking contact with biodiversity and risk of allergy has been lacking. In this review, we consider the latest research on the biodiversity hypothesis of allergy.

Recent findings
It is becoming clear that what you eat, drink, inhale, and touch all contribute to the grand scheme of host–microbial crosstalk that is needed for a balanced, healthy immune system to develop and maintain a healthy recognition between harmful and harmless invasions. Microbes can either communicate directly with host immune cells or affect the host via metabolism that can even lead to epigenetic modifications. Our living environment plays a key role in this process. Although especially, early exposure to diverse, beneficial microbiota from the environment is repeatedly found crucial, studies on immigrants demonstrate that condition in later life can also be decisive.

Conclusion
We are still lacking a more detailed understanding of the interaction between natural, environmental biodiversity, and health, which calls for new innovative and more long-term investigations. The outcomes should be utilized in policy and urban planning efforts, promoting human interaction with natural biodiversity, and supporting a healthy lifestyle.
Connecting Education to Quality: Engaging Medical Students in the Development of Evidence-Based Clinical Decision Support Tools
Authors: Crabtree Elizabeth A. , Brennan Emily , Davis Amanda , Squires Jerry E. 
Published: August 2016

Problem
Evidence-based practice (EBP) skills are crucial for delivering high-quality patient care. It is essential that medical students learn EBP concepts through a practical, in-depth research project. To date, literature on preparing students in this manner is limited.

Approach
In academic year 2014–2015, the Medical University of South Carolina’s (MUSC’s) Center for Evidence-Based Practice (now known as the Value Institute) partnered with College of Medicine faculty to revitalize the undergraduate medical student EBP curriculum. Without adding to the number of the lecture hours, the curriculum was restructured to be more process driven, project based, and clinically relevant. The resulting yearlong EBP course partnered small teams of medical students with interprofessional clinical teams to engage the students in developing evidence-based clinical decision support tools.

Outcomes
The content developed during the EBP projects is currently being used to develop evidence-based clinical practice guidelines and accompanying order sets.

Next Steps
It is likely that this model will serve as a new framework for guideline development and will greatly expand the breadth of evidence-based content currently produced and available for clinicians at the MUSC. It would be feasible to offer a similar course within the MUSC to other disciplines and colleges, or at other institutions, if there were support from administration, interest on the part of clinicians and medical faculty, and individuals with the required expertise available to develop the curriculum and facilitate the course. It is worth considering how to improve the course and evaluating opportunities to implement it within other settings.
Brief Opioid Overdose Knowledge (BOOK): A Questionnaire to Assess Overdose Knowledge in Individuals Who Use Illicit or Prescribed Opioids
Authors: Dunn Kelly E. , Barrett Frederick S. , Yepez-Laubach Claudia , Meyer Andrew C. , Hruska Bryce J. , Sigmon Stacey C. , Fingerhood Michael , Bigelow George E. 
Published: August 2016

Background:
Opioid overdose is a public health crisis. This study describes efforts to develop and validate the Brief Opioid Overdose Knowledge (BOOK) questionnaire to assess patient knowledge gaps related to opioid overdose risks.

Methods:
Two samples of illicit opioid users and a third sample of patients receiving an opioid for the treatment of chronic pain (total N = 848) completed self-report items pertaining to opioid overdose risks.

Results:
A 3-factor scale was established, representing Opioid Knowledge (4 items), Opioid Overdose Knowledge (4 items), and Opioid Overdose Response Knowledge (4 items). The scale had strong internal and face validity. Patients with chronic pain performed worse than illicit drug users in almost all items assessed, highlighting the need to increase knowledge of opioid overdose risk to this population.

Conclusions:
This study sought to develop a brief, internally valid method for quickly assessing deficits in opioid overdose risk areas within users of illicit and prescribed opioids, to provide an efficient metric for assessing and comparing educational interventions, facilitate conversations between physicians and patients about overdose risks, and help formally identify knowledge deficits in other patient populations.
Bupropion “Abuse” Reported to US Poison Centers
Authors: Stassinos Gina L , Klein-Schwartz Wendy 
Published: August 2016

Objectives:
Bupropion use to obtain nonmedical psychoactive effects has been reported. The objective was to determine the prevalence, characteristics, clinical effects, and outcomes of bupropion “abuse.”

Methods:
A 14-year retrospective review was conducted of single substance bupropion cases with “intentional abuse” as the coded reason for exposure in individuals 13 and older reported to the National Poison Data System. Data were evaluated for prevalence, demographics, clinical effect, route, final management site, and coded outcome.

Results:
There were 975 bupropion abuse cases, which accounted for 3.3% of single substance bupropion cases reported to US poison centers. The prevalence of abuse increased by 75%, from 2000 to 2012, declining slightly in 2013. The majority of cases were 13 to 29 years old (67.4%). The most frequent clinical effects were tachycardia (57.0%), seizures (33.5%), agitation/irritable (20.2%), hallucinations/delusions (14.0%), and tremor (13.1%). Most exposures were ingestions (745) followed by insufflation (166), parenteral (17), and other/unknown (17); 30 cases involved 2 routes. Seizure frequency was not significantly different between routes (P = 0.783) or exposure chronicity (P = 0.264). Final management sites were predominantly emergency department (36.9%) and admission to critical care unit (27.3%) or noncritical care unit (20.1%). Outcomes were major (11.4%), moderate (48.2%), minor (24.5%), and no effect (15.5%). There were 4 deaths.

Conclusions:
Most bupropion abuse occurs in adolescents and young adults. Tachycardia and seizures are common indicating the potential for serious effects. Seizures occur regardless of route. Providers should be aware of risk of bupropion abuse.
Sex Differences in the Association Between Internalizing Symptoms and Craving in Methamphetamine Users
Authors: Hartwell Emily E. , Moallem Nathasha R. , Courtney Kelly E. , Glasner-Edwards Suzette , Ray Lara A. 
Published: August 2016

Objectives:
Methamphetamine (MA) users often have substantial psychiatric comorbidities, with nearly a third reporting lifetime mood disorders and over a quarter reporting lifetime anxiety disorders. Female MA users are more likely to endorse depression and anxiety symptoms compared with men. Craving has been related to mood/anxiety symptoms in MA users. To extend the literature on sex differences in MA use disorder, the present study examines the role of sex as a moderator of the relationship between mood/anxiety symptoms and MA craving.

Methods:
Participants (N = 203) were nontreatment-seeking, current MA users, recruited from the Los Angeles community for enrollment in a larger pharmacotherapy trial. At the assessment visit, participants completed multiple measures including the Methamphetamine Urge Questionnaire, the Beck Depression Inventory, and the Beck Anxiety Inventory.

Results:
The relationship between depression symptomatology and MA craving was moderated by sex (F = 6.18, P = 0.01), such that the relationship was positive and significant for men (P < 0.001), but was not significant for women. Similarly, sex significantly moderated the relationship between anxiety and MA craving (F = 5.99, P = 0.02), such that the relationship was also positive and significant in men, but not in women (P < 0.001).

Conclusions:
These results suggest that men may be more sensitive to the effects of internalizing symptoms on MA craving than women. Given craving's propensity to predict relapse, these initial findings indicate the necessity of treating comorbid psychiatric problems in male MA users, which may in turn assist in the attenuation of craving.
Acceptance and Commitment Therapy (ACT) for Chronic Pain
Authors: Hughes Laura S. , Clark Jodi , Colclough Janette A. , Dale Elizabeth , McMillan Dean 
Published: August 2016

Objectives:
Chronic pain places a burden on individuals and the economy. Although there is evidence for the effectiveness of cognitive-behavior therapy, it is recognized that the effects are limited. Acceptance and Commitment Therapy (ACT), which aims to increase valued action in the presence of pain, has been suggested as an alternative approach. The objective of this review was to determine the clinical effectiveness of ACT for chronic pain in adults when compared with control conditions and other active treatments.

Methods:
The searches of this systematic review were conducted in the Cochrane library, MEDLINE, EMBASE, CINAHL Plus (EBSCO), and PsycINFO. Grey literature, reference list, and reverse citation searches were also completed.

Results:
Eleven trials were included. ACT was favored over controls (no alternative intervention or treatment as usual). Significant, medium to large effect sizes were found for measures of pain acceptance and psychological flexibility, which are typically considered processes of ACT. Significant small to medium effect sizes were found for measures of functioning, anxiety, and depression. Measures of pain intensity and quality of life were not significantly different than zero. Generally effect sizes were smaller at follow-up.

Discussion:
ACT was more clinically effective than controls on a number of outcomes. It is possible that methodological limitations, some of which are common to psychological trials, may have led to overestimated effects. Only a few studies compared ACT to active treatments and while the evidence is promising for ACT in the treatment of chronic pain, further methodologically robust trials are required.