bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of alternative splicing events for cancer diagnosis using a multiplexing nanophotonic biosensor
Authors: Huertas César S. , Domínguez-Zotes Santos , Lechuga Laura M. 
Published: January 2017

AbstractPersonalized medicine is a promising tool not only for prevention, screening and development of more efficient treatment strategies, but also for diminishing the side effects caused by current therapies. Deciphering gene regulation pathways provides a reliable prognostic analysis to elucidate the origin of grave diseases and facilitate the selection of the most adequate treatment for each individual. Alternative splicing of mRNA precursors is one of these gene regulation pathways and enables cells to generate different protein outputs from the same gene depending on their developmental or homeostatic status. Its deregulation is strongly linked to disease onset and progression constituting a relevant and innovative class of biomarker. Herein we report a highly selective and sensitive nanophotonic biosensor based on the direct monitoring of the aberrant alternative splicing of Fas gene. Unlike conventional methods, the nanobiosensor performs a real-time detection of the specific isoforms in the fM-pM range without any cDNA synthesis or PCR amplification requirements. The nanobiosensor has been proven isoform-specific with no crosshybridization, greatly minimizing detection biases. The demonstrated high sensitivity and specificity make our nanobiosensor ideal for examining significant tumor-associated expression shifts of alternatively spliced isoforms for the early and accurate theranostics of cancer.
Carbon
dioxide versus room air insufflation during balloon-assisted enteroscopy: A
systematic review with meta-analysis
Authors: Shiani Ashok , Lipka Seth , Lai Andrew , Rodriguez Andrea , Andrade Christian , Kumar Ambuj , Brady Patrick 
Published: January 2017

Abstract
Background and study aims Carbon dioxide (CO2) insufflation has
been suggested to be an ideal alternative to room air insufflation to reduce
trapped air within the bowel lumen after balloon assisted enteroscopy (BAE). We
performed a systematic review and meta-analysis to assess the safety and
efficacy of utilizing CO2 insufflation as compared to room air during
BAE.
Patients and methods The primary outcome is mean change in visual analog
scale (VAS; 10 cm) at 1, 3, and 6 hours to assess pain. Secondary outcomes
include insertion depth (anterograde or retrograde), adverse events, total
enteroscopy rate, diagnostic yield, mean anesthetic dosage, and PaCO2
at procedure completion. We searched MEDLINE and the Cochrane Central Register
of Controlled Trials (CENTRAL) from inception until May 2015. Multiple
independent extractions were performed, the process was executed as per the
standards of the Cochrane collaboration.
Results Four randomized controlled trials (RCTs) were included in the
meta-analysis. VAS at 6 hours favored CO2 over room air (MD 0.13;
95 % CI 0.01, 0.25; p = 0.03). Anterograde insertion depth (cm) was improved in
the CO2 group (MD, 58.2; 95 % CI 17.17, 99.23; p = 0.005), with an
improvement in total enteroscopy rate in the CO2 group (RR 1.91; 95 %
CI 1.20, 3.06; p = 0.007). Mean dose of propofol (mg) favored CO2
compared to air (MD, – 70.53; 95 % CI – 115.07, – 25.98; P = 0.002).
There were no differences in adverse events in either group.
Conclusions Despite the ability of CO2 to improve insertion
depth and decrease amount of anesthesia required, further randomized control
trials are needed to determine the agent of choice for insufflation in balloon
assisted enteroscopy.
Evaluation of the severity of ulcerative colitis using endoscopic dual red imaging targeting deep vessels
Authors: Naganuma Makoto , Yahagi Naohisa , Bessho Rieko , Ohno Keiko , Arai Mari , Mutaguchi Makoto , Mizuno Shinta , Fujimoto Ai , Uraoka Toshio , Shimoda Masayuki , Hosoe Naoki , Ogata Haruhiko , Kanai Takanori 
Published: January 2017

Abstract
Background and study aims Colonoscopies can predict long-term prognoses in patients with ulcerative colitis (UC). Recently, a new imaging technology has been developed that uses 3 types of illumination with center wavelengths of 540 nm, 600 nm, and 630 nm. The use of both the 600-nm and 630-nm lights (Dual red imaging; DRI) is critical for identifying blood vessels in deeper tissue. The aim of this study was to evaluate the usefulness of DRI for assessing the severity of inflammation in patients with UC.
Patients and methods A total of 43 UC patients were retrospectively enrolled to evaluate the endoscopic severity of 112 colon segments, and Mayo endoscopic scores, DRI scores and the severity of inflammation on a visual analogue scale (VAS) were compared. The Mayo endoscopic scores, DRI scores, and histologic scores were evaluated, and the interobserver agreement on DRI scores among 5 investigators was also assessed. The usefulness of DRI scores for predicting prognoses was also assessed in patients with clinical remission.
Results The DRI scores were closely correlated with the VAS for the severity of colonic inflammation (r = 0.96) and the histologic scores (r = 0.72 – 0.8). The DRI scores had a higher rate of interobserver agreement (κ values = 0.63 – 0.88) than the Mayo endoscopic scores (κ values = 0.44 – 0.59). Inter-observer agreement between 4 non-experts was also excellent (mean κ value = 0.76, range 0.63 – 0.82). The expected time until recurrence was significantly longer in patients with lower DRI scores (P < 0.01).
Conclusion DRI can be used in patients with mild to moderate endoscopic severity because it targets the deep vascular pattern. The prognosis of UC can be predicted by assessing deep vessels using DRI.
Low Bycatch Rates Add Up to Big Numbers for a Genus of Small Fishes
Authors: Lawson Julia M. , Foster Sarah J. , Vincent Amanda C. J. 
Published: January 2017

Abstract
Nonselective fishing gears extract a great many small marine species, with limited documentation or assessment of their impacts. Among those species, seahorses (genus Hippocampus) are unusual because this genus has been the focus of scientific surveys and international trade regulation. Our review of published and unpublished data sources analyzed data on seahorse bycatch for five gear-type categories and 22 countries. The median catch per unit effort of seahorse bycatch across all five gear types was 0.96 seahorses per vessel−1 day−1. Nonetheless, fleet sizes were so large that annual catches were estimated at approximately 37 million seahorses across our sampled countries. Fisher interviews suggested that seahorse catches were declining (although information on changes in effort over time were not available). Furthermore, international export data did not capture the magnitude of seahorses in bycatch. Our work emphasizes the importance of evaluating bycatch, even for taxa where reported daily catch rates are low.
Influence of processing factors on the stability of model mayonnaise with whole egg during long-term storage
Authors: Ariizumi Masahiro , Kubo Megumi , Handa Akihiro , Hayakawa Takashi , Matsumiya Kentaro , Matsumura Yasuki 
Published: January 2017

Abstract
Mayonnaise-like oil-in-water emulsions with different stabilities—evaluated from the degree of macroscopic defects, e.g., syneresis—were prepared by different formulations and processing conditions (egg yolk weight, homogenizer speed, and vegetable oil temperature). Emulsions prepared with lower egg yolk content were destabilized for shorter periods. The long-term stability of emulsions was weakly related to initial properties, e.g., oil droplet distribution and protein coverage at the interface. Protein aggregation between oil droplets was observed and would be responsible for the instability of emulsions exhibited by the appearance defects. SDS-PAGE results for adsorbed and unadsorbed proteins at the O/W interface suggested that predominant constituents adsorbed onto the interface were egg white proteins as compared with egg yolk components when the amount of added egg yolk was low. In present condition, egg white proteins adsorbed at the O/W interface could be a bridge of neighboring oil droplets thereby causing flocculation in emulsions.
Assessment of subcutaneous adipose tissue using ultrasound in highly trained junior rowers
Authors: Kelso Anne , Trájer Emese , Machus Katja , Treff Gunnar , Müller Wolfram , Steinacker Jürgen M. 
Published: January 2017

AbstractIntroduction: There is a large variety of body fat (BF) measurements, which differ in validity and reliability. The aim of this study was to measure subcutaneous adipose tissue (SAT) using ultrasound (US) in highly trained junior rowers in a field setting, establish fat patterning profiles, and compare the profiles between male and female athletes. Skinfold thickness (SKF) measurements were also taken and compared to US measurements. Methods: Sixteen athletes participated. US measurements were taken at eight sites and reported as a sum of SAT (D): D Excl (without embedded structures) and D Incl (including embedded structures). SKF was measured at three sites and reported as a sum of adipose tissue thickness (SUMSKF). Results: Mean SAT thickness (D Incl) was 27.6 ± 12.4 mm for males and 65.5 ± 11.8 mm for females. Females had significantly more embedded structures than males (P = .016). Significant correlations were found (P < .001, r = 0.92) comparing SUMSKF to D Incl and between SKF and US measurements at the thigh site (P < .001, r = 0.86). Conclusion: US is a suitable tool to measure BF in the field testing of athletes and enables measurements of SAT with an accuracy and reliability not reached before. The sum of thicknesses (D Incl or D Excl) can be used to represent subcutaneous fat based on accurate measurements of uncompressed SAT thicknesses.
ASCIIGenome: a command line genome browser for console terminals
Authors: Beraldi Dario 
Published: January 2017

Abstract

Summary
Current genome browsers are designed to work via graphical user interfaces (GUIs), which, however intuitive, are not amenable to operate within console terminals and therefore are difficult to streamline or integrate in scripts. To circumvent these limitations, ASCIIGenome runs exclusively via command line interface to display genomic data directly in a terminal window. By following the same philosophy of UNIX tools, ASCIIGenome aims to be easily integrated with the command line, including batch processing of data, and therefore enables an effective exploration of the data.

Implementation
ASCIIGenome is written in Java. Consequently, it is a cross-platform tool and requires minimal or no installation. Some of the common genomic data types are supported and data access on remote ftp servers is possible. Speed and memory footprint are comparable to or better than those of common genome browsers.

Availability and Implementation
Software and source code (MIT License) are available at https://github.com/dariober/ASCIIGenome with detailed documentation at http://asciigenome.readthedocs.io.

Supplementary information
Supplementary data are available at Bioinformatics online.
Effects of Mindfulness-Based Stress Reduction on the Mental Health of Clinical Clerkship Students: A Cluster-Randomized Controlled Trial
Authors: van Dijk Inge , Lucassen Peter L.B.J. , Akkermans Reinier P. , van Engelen Baziel G.M. , van Weel Chris , Speckens Anne E.M. 
Published: January 2017

Purpose
To examine the effect of mindfulness-based stress reduction training (MBSR) on the mental health of medical students during clinical clerkships.

Method
Between February 2011 and May 2014, the authors conducted a cluster-randomized controlled trial of clerkships as usual (CAU) and clerkships with additional MBSR in medical students during their first year of clinical clerkships at a Dutch university medical center. MBSR consisted of eight weekly two-hour sessions, comprising didactic teaching, meditation exercises, and group dialogues. Students completed online assessments at baseline and after 3, 7, 12, 15, and 20 months. Outcome measures were psychological distress, positive mental health, life satisfaction, physician empathy, mindfulness skills, and dysfunctional cognitions as measured by validated tools.

Results
Of 232 eligible students, 167 students (72%) participated and were randomized by clerkship group into MBSR (n = 83) or CAU (n = 84). The MBSR group reported a small reduction of psychological distress (P = .03, Cohen’s d = 0.20) and dysfunctional cognitions (P = .05, Cohen’s d = 0.18) and a moderate increase of positive mental health (P = .002, Cohen’s d = 0.44), life satisfaction (P = .01, Cohen’s d = 0.51), and mindfulness skills (P = .05, Cohen’s d = 0.35) compared with CAU during the 20-month follow-up. The authors detected no significant effect on physician empathy (P = .18, Cohen’s d = 0.27).

Conclusions
MBSR appeared feasible and acceptable to medical clerkship students and resulted in a small to moderate improvement of mental health compared with CAU over the 20-month follow-up.
The Academic RVU: Ten Years Developing a Metric for and Financially Incenting Academic Productivity at Oregon Health & Science University
Authors: Ma O. John , Hedges Jerris R. , Newgard Craig D. 
Published: January 2017

Purpose
Established metrics reward academic faculty for clinical productivity. Few data have analyzed a bonus model to measure and reward academic productivity. This study’s objective was to describe development and use of a departmental academic bonus system for incenting faculty scholarly and educational productivity.

Method
This cross-sectional study analyzed a departmental bonus system among emergency medicine academic faculty at Oregon Health & Science University, including growth from 2005 to 2015. All faculty members with a primary appointment were eligible for participation. Each activity was awarded points based on a predetermined education or scholarly point scale. Faculty members accumulated points based on their activity (numerator), and the cumulative points of all faculty were the denominator. Variables were individual faculty member (deidentified), academic year, bonus system points, bonus amounts awarded, and measures of academic productivity. Data were analyzed using descriptive statistics, including measures of variance.

Results
The total annual financial bonus pool ranged from $211,622 to $274,706. The median annual per faculty academic bonus remained fairly constant over time ($3,980 in 2005–2006 vs. $4,293 in 2014–2015), with most change at the upper quartile of academic bonus (max bonus $16,920 in 2005–2006 vs. $39,207 in 2014–2015). Bonuses rose linearly among faculty in the bottom three quartiles of academic productivity, but increased exponentially in the 75th to 100th percentile.

Conclusions
Faculty academic productivity can be measured and financially rewarded according to an objective academic bonus system. The “academic point” used to measure productivity functions as an “academic relative value unit.”
Engaging Learners in Health System Quality Improvement Efforts
Authors: Johl Karnjit , Grigsby R. Kevin 
Published: January 2017

In 1999, an Institute of Medicine report spurred health care organizations to implement systems-based quality improve ment efforts and tackle patient safety. Simultaneously, the Accreditation Council for Graduate Medical Education asked residency programs to address Practice-Based Learning and Systems-Based Practice competencies. Medical educators now advocate incorporation of these competencies in undergraduate medical education.
The authors examine the success of these efforts both from the health care delivery and systems perspective as well as from the perspective of educators as they aspire to engage medical students and residents in these domains. The authors argue that the missing element that prevents health care systems from the full realization of the promise of quality improvement is bidirectional alignment. Included are examples from the literature to demonstrate how medical educators are moving toward alignment of learners with health system quality improvement and safety needs. Finally, the authors explore business and information technology governance literature in support of the hypothesis that bidirectional alignment should be the next step in moving from reactive to proactive systems of care.
Types of internal facilitation activities in hospitals implementing evidence-based interventions
Authors: Baloh Jure , Zhu Xi , Ward Marcia M. 
Published: January 2017

Background:
Implementation models, frameworks, and theories recognize the importance of activities that facilitate implementation success. However, little is known about internal facilitation activities that hospital personnel engage in during implementation efforts.

Purpose:
The aim of the study was to examine internal facilitation activities at 10 critical access hospitals in rural Iowa during their implementation of TeamSTEPPS, a patient safety intervention, and to identify characteristics that distinguish different types of facilitation activities.

Methods:
We followed 10 critical access hospitals for 2 years after the onset of implementation, conducting quarterly interviews with key informants. On the basis of the transcripts from the first two quarters, a coding template was developed using inductive analyses. The template was then applied deductively to code all interview transcripts. Using comparative analysis, we examined the characteristics that distinguish between the facilitation types.

Results:
We identified four types of facilitation activities—Leadership, Buy-in, Customization, and Accountability. Individuals and teams engaged in different types of facilitation activities, both in a planned and an ad hoc manner. These activities targeted at both people and practices and exhibited varying temporal patterns (start and peak time).

Conclusion:
There are four types of facilitation activities that hospitals engage in while implementing evidence-based practices, offering a parsimonious way to characterize facilitation activities. New theoretical and empirical research opportunities are discussed.

Practice Implications:
Understanding the types of facilitation activities and their distinguishing characteristics can assist managers in planning and executing implementations of evidence-based interventions.
POSTTRAUMATIC ENDOPHTHALMITIS
Authors: Li Xintong , Zarbin Marco A. , Langer Paul D. , Bhagat Neelakshi 
Published: January 2017

Purpose:
To describe the demographics, characteristics, management, and visual outcomes of eyes diagnosed with endophthalmitis after open globe injury.

Methods:
Retrospective cohort analysis of all patients diagnosed with endophthalmitis after open globe injury from 1997 to 2015 at University Hospital, Newark, NJ.

Results:
Twenty-six eyes were identified (all male patients; mean age: 37 ± 15 years). Cultures were positive in 16 eyes (62%), with Staphylococcus species (7 eyes, 44%) being the most common organism. Twelve eyes (46%) presented with open globe injury and concurrent endophthalmitis; 14 eyes (54%) developed endophthalmitis a mean of 14 days after open globe repair (OGR; 1 outlier of 98 days excluded). All eyes were managed with systemic and intravitreal antibiotics. The presence of intraocular foreign body (P < 0.05) and delayed primary OGR (P < 0.03) were significantly more common with concurrent versus post-OGR endophthalmitis. Four (29%) eyes in the post-OGR endophthalmitis group had corneal wound leak after OGR. Four (15%) eyes with no light perception vision were enucleated. Ten (40%) of 25 eyes with documented best-corrected visual acuity had final best-corrected visual acuity ≥20/200; final best-corrected visual acuity ranged from no light perception to 20/20.

Conclusion:
The presence of intraocular foreign body and delayed presentation were significantly more common with concurrent endophthalmitis. Twenty-nine percent of eyes that presented with endophthalmitis after OGR had a wound leak. Final best-corrected visual acuity ≥20/200 was achieved in 40% of cases.
Pseudobulbar Affect: What Nurses, Stroke Survivors, and Caregivers Need to Know
Authors: Schneider Melissa A. , Schneider Matthew D. 
Published: January 2017

ABSTRACT
Pseudobulbar affect (PBA) is a neurologic condition that can happen after a patient has had some kind of neurological insult. In this syndrome, involuntary, uncontrollable, and inappropriate emotional outbursts unrelated or out of proportion to the situation are common symptoms. This can be very frustrating and scary. Because stroke survivors and their caregivers are overloaded with information during the transition from hospital to home, information about PBA is not usually discussed. In a survey by the National Stroke Association, 53% of stroke survivors reported that they had some of the symptoms of this disorder. Even if they discussed these symptoms with their health care providers, less than half were given a diagnosis, and less than a quarter received any kind of treatment. The purpose of this article is to give nurses more information about PBA so they can share this with patients and families/significant others and encourage them to seek help if they experience these symptoms once discharged. It is hoped that increased knowledge about this condition will lead to better diagnosis and treatment and increased quality of life for stroke survivors.
Usefulness of the Glasgow–Blatchford score to predict 1-week mortality in patients with esophageal variceal bleeding
Authors: Iino Chikara , Shimoyama Tadashi , Igarashi Takasato , Aihara Tomoyuki , Ishii Kentaro , Sakamoto Jyuichi , Tono Hiroshi , Fukuda Shinsaku 
Published: January 2017

Objectives
Esophageal variceal bleeding is one of the most severe complications of liver cirrhosis, with high mortality. However, there is no established scoring system for short-term mortality in patients with esophageal variceal bleeding. The aim of this study was to evaluate the usefulness of the Glasgow–Blatchford score (GBS), the Model for End-Stage Liver Disease (MELD) score, and the Child–Pugh score for predicting short-term and hospital mortality in patients with esophageal variceal bleeding.

Methods
A total of 47 patients with esophageal variceal bleeding were studied between September 2009 and March 2015. The GBS, the MELD score, and the Child–Pugh score were assessed for their ability to predict 1- and 6-week mortality rates using a receiver operating characteristic curve.

Results
The 1- and 6-week mortality rates were 17.0 and 31.9%, respectively. The median GBS, MELD, and Child–Pugh scores were 13 (range: 4–19), 10 (range: 0–34), and 9 (range: 5–13), respectively. The GBS was superior to both the MELD and the Child–Pugh scores for prediction of 1-week mortality [area under the curve=0.82 (95% confidence interval: 0.66–0.98) vs. 0.71 (0.47–0.96) and 0.72 (0.53–0.91)]. The MELD score was superior to both the Child–Pugh score and the GBS for prediction of 6-week mortality [area under the curve=0.83 (95% confidence interval: 0.69–0.97) vs. 0.69 (0.52–0.85) and 0.67 (0.50–0.83)].

Conclusion
For 1-week mortality, the GBS was superior to the Child–Pugh and the MELD scores in patients with esophageal variceal bleeding. However, for 6-week mortality, the MELD score was superior in patients with esophageal variceal bleeding.