bluuebunny/crossref_metadata_2025_split huggingface dataset:
E2F1-miR-20a-5p/20b-5p auto-regulatory feedback loop involved in myoblast proliferation and differentiation
Authors: Luo Wen , Li Guihuan , Yi Zhenhua , Nie Qinghua , Zhang Xiquan 
Published: June 2016

AbstractmiR-17 family microRNAs (miRNAs) are crucial for embryo development, however, their role in muscle development is still unclear. miR-20a-5p and miR-20b-5p belong to the miR-17 family and are transcribed from the miR-17~92 and miR-106a~363 clusters respectively. In this study, we found that miR-20a-5p and miR-20b-5p promoted myoblast differentiation and repressed myoblast proliferation by directly binding the 3′ UTR of E2F transcription factor 1 (E2F1) mRNA. E2F1 is an important transcriptional factor for organism’s normal development. Overexpression of E2F1 in myoblasts promoted myoblast proliferation and inhibited myoblast differentiation. Conversely, E2F1 inhibition induced myoblast differentiation and repressed myoblast proliferation. Moreover, E2F1 can bind directly to promoters of the miR-17~92 and miR-106a~363 clusters and activate their transcription and E2F1 protein expression is correlated with the expression of pri-miR-17~92 and pri-miR-106a~363 during myoblast differentiation. These results suggested an auto-regulatory feedback loop between E2F1 and miR-20a-5p/20b-5p and indicated that miR-20a-5p, miR-20b-5p and E2F1 are involved in myoblast proliferation and differentiation through the auto-regulation between E2F1 and miR-20a-5p/20b-5p. These findings provide new insight into the mechanism of muscle differentiation and further shed light on the understanding of muscle development and muscle diseases.
Refraction-Assisted Solar Thermoelectric Generator based on Phase-Change Lens
Authors: Kim Myoung-Soo , Kim Min-Ki , Jo Sung-Eun , Joo Chulmin , Kim Yong-Jun 
Published: June 2016

AbstractSolar thermoelectric generators (STEGs), which are used for various applications, (particularly small size electronic devices), have optical concentration systems for high energy conversion efficiency. In this study, a refraction-assisted STEG (R-STEG) is designed based on phase-change materials. As the phase-change material (PCM) changes phase from solid to liquid, its refractive index and transmittance also change, resulting in changes in the refraction of the sunlight transmitted through it, and concentration of solar energy in the phase-change lens. This innovative design facilitates double focusing the solar energy through the optical lens and a phase-change lens. This mechanism resulted in the peak energy conversion efficiencies of the R-STEG being 60% and 86% higher than those of the typical STEG at solar intensities of 1 kW m−2 and 1.5 kW m−2, respectively. In addition, the energy stored in PCM can help to generate steady electrical energy when the solar energy was removed. This work presents significant progress regarding the optical characteristic of PCM and optical concentration systems of STEGs.
Al0.3Ga0.7N PN diode with breakdown voltage >1600 V
Authors: Allerman A.A. , Armstrong A.M. , Fischer A.J. , Dickerson J.R. , Crawford M.H. , King M.P. , Moseley M.W. , Wierer J.J. , Kaplar R.J. 
Published: June 2016

Demonstration of Al0.3Ga0.7N PN diodes grown with breakdown voltages in excess of 1600 V is reported. The total epilayer thickness is 9.1 μm and was grown by metal‐organic vapour‐phase epitaxy on 1.3‐mm‐thick sapphire in order to achieve crack‐free structures. A junction termination edge structure was employed to control the lateral electric fields. A current density of 3.5 kA/cm2 was achieved under DC forward bias and a reverse leakage current <3 nA was measured for voltages <1200 V. The differential on‐resistance of 16 mΩ cm2 is limited by the lateral conductivity of the n‐type contact layer required by the front‐surface contact geometry of the device. An effective critical electric field of 5.9 MV/cm was determined from the epilayer properties and the reverse current–voltage characteristics. To our knowledge, this is the first aluminium gallium nitride (AlGaN)‐based PN diode exhibiting a breakdown voltage in excess of 1 kV. It is noted that a Baliga figure of merit (Vbr2/Rspec,on) of 150 MW/cm2 found is the highest reported for an AlGaN PN diode and illustrates the potential of larger‐bandgap AlGaN alloys for high‐voltage devices.
Biosynthesis and antibacterial activity of gold nanoparticles coated with reductase enzymes
Authors: Hosseini Mansoure , Mashreghi Mansour , Eshghi Hossein 
Published: June 2016

Potential of luminescent bacteria in production of metal nanoparticles (NPs) has not been well evaluated up until now. These bacteria contain lux operon which is included of reductase enzymes, by increasing bacterial cell density, the expression of aldehyde synthetic enzymes elevate and enhance the yields of NPs synthesis. Therefore, extracellular synthesis of gold NPs (AuNPs) using natural occurring luminescent bacteria, VLA, VLB, VLC and genetically engineered luminescent bacteria, Pseudomonas putida KT2440 and Pseudomonas fluorescence OS8 have been successfully conducted. NPs were characterised and their antibacterial activity evaluated using microtitre plates at different concentrations against some hospital pathogenic bacteria. Biosynthetic AuNPs produced had maximum absorption at the ranges of 500–550 nanometre wavelengths. Transmission electron microscopy images showed particle sizes between 10 and 50 nanometres and confirmed the success of purification process. The NPs were spherical and the FTIR analysis showed the existence of biomolecules on surface of purified NPs that could be most probably related to reductase enzymes that are stabilised on NPs surfaces. Further investigation on antibacterial properties of these novel NPs which coated by reductase enzymes showed that any increase or decrease in antibacterial activity is dependent on NPs concentration.
Football and netball in women’s struggle against HIV/AIDS in Africa
Authors: DeLancey Mark W. 
Published: June 2016

The HIV/AIDS problem has improved in recent years. The number of newly infected persons is declining year after year (2.1 million new cases in 2013). However, the news is still grim and especially so for young women. Why does HIV seem to discriminate against women, especially younger women? Women are physiologically more susceptible than men, but among the most significant causes are gender inequity and related poverty and human rights issues.
A number of strategies and tactics are used in the struggle with HIV/AIDS. Some are old ideas, found successful in campaigns against other diseases. Others are of more recent origin. Among the latter has been the use of sport. In this essay, we discuss some of the ways in which sport is used to assist women in the struggle against HIV/AIDS.
A survey of problems associated with the spread and the prevention of HIV/AIDS is indicative of the difficulties faced. Of the many strategies and tactics, is there a role for sport? Sport has been able to assist with some of the associated problems. Although in some instances a sport activity is aimed at a single issue, more often the purposes are multiple. Often, events and programmes are not specifically aimed at a female audience, though frequently separate activities are used for each gender.
Co-current toroidal rotation-driven and turbulent stresses with resonant magnetic perturbations in the edge plasmas of the J-TEXT tokamak
Authors: Zhao K.J. , Shi Yuejiang , Liu H. , Diamond P.H. , Li F.M. , Cheng J. , Chen Z.P. , Nie L. , Ding Y.H. , Wu Y.F. , Chen Z.Y. , Rao B. , Cheng Z.F. , Gao L. , Zhang X.Q. , Yang Z.J. , Wang N.C. , Wang L. , Jin W. , Xu J.Q. , Yan L.W. , Dong J.Q. , Zhuang G. 
Published: June 2016

Abstract
The acceleration of the co-current toroidal rotations around resonant surfaces by resonant magnetic perturbations (RMPs) through turbulence is presented. These experiments were performed using a Langmuir probe array in the edge plasmas of the J-TEXT tokamak. This study aims at understanding the RMP effects on edge toroidal rotations and exploring its control method. With RMPs, the flat electron temperature T
e profile, due to magnetic islands, appears around resonant surfaces (Zhao et al 2015 Nucl. Fusion
55 073022). When the resonant surface is closer to the last closed flux surface, the flat T
e profile vanishes with RMPs. In both cases, the toroidal rotations significantly increase in the direction of the plasma current around the resonant surfaces with RMPs. The characteristics of turbulence are significantly affected by RMPs around the resonant surfaces. The turbulence intensity profile changes and the poloidal wave vector k

θ
increases with RMPs. The power fraction of the turbulence components in the ion diamagnetic drift direction increases with RMPs. The measurements of turbulent Reynolds stresses are consistent with the toroidal flows that can be driven by turbulence. The estimations of the energy transfer between the turbulence and toroidal flows suggest that turbulence energy transfers into toroidal flows. The result has the implication of the intrinsic rotation being driven by RMPs via turbulence.
pong: fast analysis and visualization of latent clusters in population genetic data
Authors: Behr Aaron A. , Liu Katherine Z. , Liu-Fang Gracie , Nakka Priyanka , Ramachandran Sohini 
Published: June 2016

Abstract
Motivation: A series of methods in population genetics use multilocus genotype data to assign individuals membership in latent clusters. These methods belong to a broad class of mixed-membership models, such as latent Dirichlet allocation used to analyze text corpora. Inference from mixed-membership models can produce different output matrices when repeatedly applied to the same inputs, and the number of latent clusters is a parameter that is often varied in the analysis pipeline. For these reasons, quantifying, visualizing, and annotating the output from mixed-membership models are bottlenecks for investigators across multiple disciplines from ecology to text data mining.
Results: We introduce pong, a network-graphical approach for analyzing and visualizing membership in latent clusters with a native interactive D3.js visualization. pong leverages efficient algorithms for solving the Assignment Problem to dramatically reduce runtime while increasing accuracy compared with other methods that process output from mixed-membership models. We apply pong to 225 705 unlinked genome-wide single-nucleotide variants from 2426 unrelated individuals in the 1000 Genomes Project, and identify previously overlooked aspects of global human population structure. We show that pong outpaces current solutions by more than an order of magnitude in runtime while providing a customizable and interactive visualization of population structure that is more accurate than those produced by current tools.
Availability and Implementation: pong is freely available and can be installed using the Python package management system pip. pong’s source code is available at https://github.com/abehr/pong.
Contact: aaron_behr@alumni.brown.edu or sramachandran@brown.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
compendiumdb: an R package for retrieval and storage of functional genomics data
Authors: Nandal Umesh K. , van Kampen Antoine H. C. , Moerland Perry D. 
Published: June 2016

Abstract
Summary: Currently, the Gene Expression Omnibus (GEO) contains public data of over 1 million samples from more than 40 000 microarray-based functional genomics experiments. This provides a rich source of information for novel biological discoveries. However, unlocking this potential often requires retrieving and storing a large number of expression profiles from a wide range of different studies and platforms. The compendiumdb R package provides an environment for downloading functional genomics data from GEO, parsing the information into a local or remote database and interacting with the database using dedicated R functions, thus enabling seamless integration with other tools available in R/Bioconductor.
Availability and Implementation: The compendiumdb package is written in R, MySQL and Perl. Source code and binaries are available from CRAN (http://cran.r-project.org/web/packages/compendiumdb/) for all major platforms (Linux, MS Windows and OS X) under the GPLv3 license.
Contact: p.d.moerland@amc.uva.nl
Supplementary information: Supplementary data are available at Bioinformatics online.
KCMBT: a k-mer Counter based on Multiple Burst Trees
Authors: Mamun Abdullah-Al , Pal Soumitra , Rajasekaran Sanguthevar 
Published: June 2016

Abstract
Motivation: A massive number of bioinformatics applications require counting of k-length substrings in genetically important long strings. A k-mer counter generates the frequencies of each k-length substring in genome sequences. Genome assembly, repeat detection, multiple sequence alignment, error detection and many other related applications use a k-mer counter as a building block. Very fast and efficient algorithms are necessary to count k-mers in large data sets to be useful in such applications.
Results: We propose a novel trie-based algorithm for this k-mer counting problem. We compare our devised algorithm k-mer Counter based on Multiple Burst Trees (KCMBT) with available all well-known algorithms. Our experimental results show that KCMBT is around 30% faster than the previous best-performing algorithm KMC2 for human genome dataset. As another example, our algorithm is around six times faster than Jellyfish2. Overall, KCMBT is 20–30% faster than KMC2 on five benchmark data sets when both the algorithms were run using multiple threads.
Availability and Implementation: KCMBT is freely available on GitHub: (https://github.com/abdullah009/kcmbt_mt).
Contact: rajasek@engr.uconn.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Understanding the mechanisms in accelerated drug reactions
Authors: Torres María J. , Salas Maria , Ariza Adriana , Fernández Tahia D. 
Published: June 2016

Purpose of review
The purpose is to understand the underlying mechanisms of accelerated allergic reactions to drugs, defined here as reactions occurring between 1 and 24 h after drug intake.

Recent findings
Recent publications have shown that accelerated reactions are T cell-mediated, although an IgE mechanism cannot be ruled out in some cases.

Summary
Classification of allergic reactions to drugs is complex. Based on the time interval between drug administration and appearance of the clinical reaction, as well as the type of clinical symptoms, they can be classified as: immediate, typically appearing from less than 1 to 6 h after the last drug administration and nonimmediate, occurring at any time from 1 h after drug administration. Therefore, overlap exists in what the Levine classification defined as accelerated reactions, where clinical symptoms are mainly urticaria and less often exanthema and serum sickness-like reactions. The immunological mechanisms involved suggest that they are T cell-mediated reactions with a Th1 pattern, comprising increased production of IFNγ, TNFα, the chemokine CXCL9 and its corresponding receptor CXCR3. In most cases an IgE-mediated response is ruled out because of negative immediate skin test results, no detection of serum-specific IgE antibodies or tryptase, and no skin-secreted tryptase. However, an IgE-mediated response can be demonstrated in exceptional situations. Finally, serum sickness-like reactions have been reported as an immune complex-mediated accelerated reaction. However, the exact mechanism has not been confirmed.
Longitudinal Analysis of Gender Differences in Academic Productivity Among Medical Faculty Across 24 Medical Schools in the United States
Authors: Raj Anita , Carr Phyllis L. , Kaplan Samantha E. , Terrin Norma , Breeze Janis L. , Freund Karen M. 
Published: June 2016

Purpose
To examine gender differences in academic productivity, as indicated by publications and federal grant funding acquisition, among a longitudinal cohort of medical faculty from 24 U.S. medical schools, 1995 to 2012–2013.

Method
Data for this research were taken from the National Faculty Survey involving a survey with medical faculty recruited from medical schools in 1995, and followed up in 2012–2013. Data included surveys and publication and grant funding databases. Outcomes were number of publications, h-index, and principal investigator on a federal grant in the prior two years. Gender differences were assessed using negative binomial regression models for publication and h-index outcomes, and logistic regression for the grant funding outcome; analyses adjusted for race/ethnicity, rank, specialty area, and years since first academic appointment.

Results
Data were available for 1,244 of the 1,275 (98%) subjects eligible for the follow-up study. Men were significantly more likely than women to be married/partnered, have children, and hold the rank of professor (P < .0001). Adjusted regression models documented that women had a lower rate of publication (relative number = 0.71; 95% CI = 0.63, 0.81; P < .0001) and h-index (relative number = 0.81; 95% CI = 0.73, 0.90; P < .0001) relative to men, but there was no gender difference in grant funding.

Conclusions
Women faculty acquired federal funding at similar rates as male faculty, yet lagged behind in terms of publications and their impact. Medical academia must consider how to help address ongoing gender disparities in publication records.
Comparing Trainee and Staff Perceptions of Patient Safety Culture
Authors: Bump Gregory M. , Coots Nordisha , Liberi Cindy A. , Minnier Tamra E. , Phrampus Paul E. , Gosman Gabriella , Metro David G. , McCausland Julie B. , Buchert Andrew 
Published: June 2016

Purpose
The Accreditation Council for Graduate Medical Education implemented the Clinical Learning Environment Review (CLER) program to evaluate and improve the learning environment in teaching hospitals. Hospitals receive a report after a CLER visit with observations about patient safety, among other domains, the accuracy of which is unknown. Thus, the authors set out to identify complementary measures of trainees’ patient safety experience.

Method
In 2014, they administered the Hospital Survey on Patient Safety Culture to residents and fellows and general staff at 10 hospitals in an integrated health system. The survey measured perceptions of patient safety in 12 domains and incorporated two outcome measures (number of medical errors reported and overall patient safety). Domain scores were calculated and compared between trainees and staff.

Results
Of 1,426 trainees, 926 responded (65% response rate). Of 18,815 staff, 12,015 responded (64% response rate). Trainees and staff scored five domains similarly—communication openness, facility management support for patient safety, organizational learning/continuous improvement, teamwork across units, and handoffs/transitions of care. Trainees scored four domains higher than staff—nonpunitive response to error, staffing, supervisor/manager expectations and actions promoting patient safety, and teamwork within units. Trainees scored three domains lower than staff—feedback and communication about error, frequency of event reporting, and overall perceptions of patient safety.

Conclusions
Generally, trainees had comparable to more favorable perceptions of patient safety culture compared with staff. They did identify opportunities for improvement though. Hospitals can use perceptions of patient safety culture to complement CLER visit reports to improve patient safety.
Neonates and Infants Discharged Home Dependent on Medical Technology
Authors: Toly Valerie Boebel , Musil Carol M. , Bieda Amy , Barnett Kimberly , Dowling Donna A. , Sattar Abdus 
Published: June 2016

Background:
Preterm neonates and neonates with complex conditions admitted to a neonatal intensive care unit (NICU) may require medical technology (eg, supplemental oxygen, feeding tubes) for their continued survival at hospital discharge. Medical technology introduces another layer of complexity for parents, including specialized education about neonatal assessment and operation of technology. The transition home presents a challenge for parents and has been linked with greater healthcare utilization.

Purpose:
To determine incidence, characteristics, and healthcare utilization outcomes (emergency room visits, rehospitalizations) of technology-dependent neonates and infants following initial discharge from the hospital.

Methods:
This descriptive, correlational study used retrospective medical record review to examine technology-dependent neonates (N = 71) upon discharge home. Study variables included demographic characteristics, hospital length of stay, and type of medical technology used. Analysis of neonates (n = 22) with 1-year postdischarge data was conducted to identify relationships with healthcare utilization. Descriptive and regression analyses were performed.

Findings:
Approximately 40% of the technology-dependent neonates were between 23 and 26 weeks' gestation, with birth weight of less than 1000 g. Technologies used most frequently were supplemental oxygen (66%) and feeding tubes (46.5%). The mean total hospital length of stay for technology-dependent versus nontechnology-dependent neonates was 108.6 and 25.7 days, respectively. Technology-dependent neonates who were female, with a gastrostomy tube, or with longer initial hospital length of stay were at greater risk for rehospitalization.

Implications for Practice:
Assessment and support of families, particularly mothers of technology-dependent neonates following initial hospital discharge, are vital.

Implications for Research:
Longitudinal studies to determine factors affecting long-term outcomes of technology-dependent infants are needed.
Compliance With a Comprehensive Antibiotic Protocol Improves Infection Incidence in Pediatric Spine Surgery
Authors: Vandenberg Curt , Niswander Cameron , Carry Patrick , Bloch Nikki , Pan Zhaoxing , Erickson Mark , Garg Sumeet 
Published: June 2016

Background:
A multidisciplinary task force, designated Target Zero, has developed protocols for prevention of surgical site infection (SSI) for spine surgery at our institution. The purpose of this study was to evaluate how compliance with an antibiotic bundle impacts infection incidences in pediatric spine surgery.

Methods:
After institutional review board approval, a consecutive series of 511 patients (517 procedures) who underwent primary spine procedures from 2008 to 2012 were retrospectively reviewed to identify patients who developed SSI. Patients were followed for a minimum of 90 days postoperatively. Compliance data were collected prospectively in 511 consecutive patients and a total of 517 procedures. Three criteria were required for antibiotic bundle compliance: appropriate antibiotics completely administered within 1 hour before incision, antibiotics appropriately redosed intraoperatively for blood loss and time, and antibiotics discontinued within 24 hours postoperatively. A multivariable logistic regression analysis was used to test the association between compliance and the development of an infection.

Results:
Overall antibiotic bundle compliance rate was 85%. After adjusting for risk category, estimated blood loss, and study year, the likelihood of an infection was increased in the noncompliant group compared with the compliant group (adjusted odds ratio: 3.0, 95% CI, 0.96-9.47, P=0.0587). When expressed as the number needed to treat, strict adherence to antibiotic bundle compliance prevented 1 SSI within 90 days of surgery for every 26 patients treated with the antibiotic bundle. Reasons for noncompliance included failure to infuse preoperative antibiotics 1 hour before incision (10.3%), failure to redose antibiotics intraoperatively based on time or blood loss (5.5%), and failure to discontinue antibiotics within 24 hours postoperatively (1.9%).

Conclusions:
Compliance with a comprehensive antibiotic protocol can lead to meaningful reductions in SSI incidences in pediatric spine surgery. Institutions should focus on improving compliance with prophylactic antibiotic protocols to decrease SSI in pediatric spine surgery.

Level of Evidence:
Level III—retrospective cohort study.