bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optical magnetic detection of single-neuron action potentials using quantum defects in diamond
Authors: Barry John F. , Turner Matthew J. , Schloss Jennifer M. , Glenn David R. , Song Yuyu , Lukin Mikhail D. , Park Hongkun , Walsworth Ronald L. 
Published: November 2016

Significance
We demonstrate noninvasive detection of action potentials with single-neuron sensitivity, including in whole organisms. Our sensor is composed of quantum defects within a diamond chip, which detect time-varying magnetic fields generated by action potentials. The sensor is biocompatible and can be brought into close proximity to the organism without adverse effect, allowing for long-term observation and superior resolution of neuron magnetic fields. Optical magnetic detection with quantum defects also provides information about action potential propagation that is not easily available with existing methods. The quantum diamond technique requires no labeling or genetic modification, allows submillisecond time resolution, does not bleach, and senses through opaque tissue. With further development, we expect micrometer-scale magnetic imaging of a variety of neuronal phenomena.
Rapid emergence and mechanisms of resistance by U87 glioblastoma cells to doxorubicin in an in vitro tumor microfluidic ecology
Authors: Han Jeonghun , Jun Yukyung , Kim So Hyun , Hoang Hong-Hoa , Jung Yeonjoo , Kim Suyeon , Kim Jaesang , Austin Robert H. , Lee Sanghyuk , Park Sungsu 
Published: November 2016

Significance
Drug resistance is among the most critical problems in cancer treatment. This proof-of-principle study demonstrates that a combination of in vitro microecology and deep sequencing could provide an extremely efficient method to elucidate the in vivo resistance mechanisms of cancer drugs and predict if drug resistance is likely to occur. Remarkably, drug resistance was seen within 7 d in our microfluidic chip, enabling characterization of molecular mechanisms within a month. This would be of great value for clinicians in selecting drugs likely to be slow in drug resistance emergence, and choose therapies for resistant tumors more effectively. In principle, our microecology technology can be used for many combinations of cancer types and drugs.
High-performance multiplexed fluorescence in situ hybridization in culture and tissue with matrix imprinting and clearing
Authors: Moffitt Jeffrey R. , Hao Junjie , Bambah-Mukku Dhananjay , Lu Tian , Dulac Catherine , Zhuang Xiaowei 
Published: November 2016

SignificanceMultiplexed single-molecule FISH allows spatially resolved gene-expression profiling in single cells. However, because of off-target binding of FISH probes and cellular autofluorescence, background can become limiting in multiplexed single-molecule FISH measurements, especially when tissue samples are imaged or when the degree of multiplexing is increased. Here we report a sample clearing approach for FISH that substantially reduced these background sources by anchoring RNAs to a polymer matrix and then removing proteins and lipids. This approach allows measurements with higher detection efficiency and sensitivity across more color channels in both cell culture and tissue with no detectable loss in RNA. We anticipate that this clearing approach will greatly facilitate applications of multiplexed FISH measurements in a wide variety of biological systems.
The content and distribution of steryl ferulates in wheat produced in Japan
Authors: Tsuzuki Wakako , Mogushi Hiroyuki , Kawahara Shuji , Kotake-Nara Eiichi , Komba Shiro , Kanai Yoshikazu , Yamada Sumiyo , Horigane Akira 
Published: November 2016

Abstract
Oryzanol contained in rice bran is a complex mixture of steryl ferulates (SFs) with many identified health benefits. Recently, SF has been shown to exist in other cereals such as wheat, rye, and corn. In this study, SFs in several wheats produced in Japan were analyzed. For instance, SF content of whole wheat grain, Yumekaori (Japan) was 15.2 ± 1.4 mg-oryzanol-equivalent/100 g grain, while that of the imported one, 1CW (Canada) was 11.4 ± 1.3 mg-oryzanol-equivalent/100 g grain. The main SF components in the examined wheats were campesteryl ferulate, campestanyl ferulate, and sitostanyl ferulate. SF distribution in whole wheat grain was investigated using 14 fractions produced by a conventional test milling machine. SF was intensively accumulated in the four bran fractions (24 − 95 mg-oryzanol-equivalent/100 g bran fraction). These results suggest that the wheat bran would be an important source of SF.
DeFCoM: analysis and modeling of transcription factor binding sites using a motif-centric genomic footprinter
Authors: Quach Bryan , Furey Terrence S 
Published: November 2016

Abstract

Motivation
Identifying the locations of transcription factor binding sites is critical for understanding how gene transcription is regulated across different cell types and conditions. Chromatin accessibility experiments such as DNaseI sequencing (DNase-seq) and Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) produce genome-wide data that include distinct ‘footprint’ patterns at binding sites. Nearly all existing computational methods to detect footprints from these data assume that footprint signals are highly homogeneous across footprint sites. Additionally, a comprehensive and systematic comparison of footprinting methods for specifically identifying which motif sites for a specific factor are bound has not been performed.

Results
Using DNase-seq data from the ENCODE project, we show that a large degree of previously uncharacterized site-to-site variability exists in footprint signal across motif sites for a transcription factor. To model this heterogeneity in the data, we introduce a novel, supervised learning footprinter called Detecting Footprints Containing Motifs (DeFCoM). We compare DeFCoM to nine existing methods using evaluation sets from four human cell-lines and eighteen transcription factors and show that DeFCoM outperforms current methods in determining bound and unbound motif sites. We also analyze the impact of several biological and technical factors on the quality of footprint predictions to highlight important considerations when conducting footprint analyses and assessing the performance of footprint prediction methods. Finally, we show that DeFCoM can detect footprints using ATAC-seq data with similar accuracy as when using DNase-seq data.

Availability and Implementation
Python code available at https://bitbucket.org/bryancquach/defcom

Supplementary information
Supplementary data are available at Bioinformatics online.
Improved VCF normalization for accurate VCF comparison
Authors: Bayat Arash , Gaëta Bruno , Ignjatovic Aleksandar , Parameswaran Sri 
Published: November 2016

Abstract

Motivation
The Variant Call Format (VCF) is widely used to store data about genetic variation. Variant calling workflows detect potential variants in large numbers of short sequence reads generated by DNA sequencing and report them in VCF format. To evaluate the accuracy of variant callers, it is critical to correctly compare their output against a reference VCF file containing a gold standard set of variants. However, comparing VCF files is a complicated task as an individual genomic variant can be represented in several different ways and is therefore not necessarily reported in a unique way by different software.

Results
We introduce a VCF normalization method called Best Alignment Normalisation (BAN) that results in more accurate VCF file comparison. BAN applies all the variations in a VCF file to the reference genome to create a sample genome, and then recalls the variants by aligning this sample genome back with the reference genome. Since the purpose of BAN is to get an accurate result at the time of VCF comparison, we define a better normalization method as the one resulting in less disagreement between the outputs of different VCF comparators.

Availability and Implementation
The BAN Linux bash script along with required software are publicly available on https://sites.google.com/site/banadf16

Supplementary information
Supplementary data are available at Bioinformatics online.
Peidong Yang: cultivating ground-breaking research in China
Authors: Wang Ling , Poo Mu-ming 
Published: November 2016

Abstract
Opened in September 2013, ShanghaiTech University is a small-scale research university jointly established by Shanghai Municipal Government and the Chinese Academy of Sciences. As the founding dean of the newly launched School of Physical Science and Technology (SPST) of ShanghaiTech, Peidong Yang has been busy in drawing up the roadmap, initiating new programs and recruiting faculty members over the past two years. His mission at SPST is to make breakthroughs in interdisciplinary areas and promote cutting-edge original research, which he refers to as research ‘from 0 to 1’. In a recent interview with NSR, Yang pointed out that many research programs in China are incremental or just simple optimization of ground-breaking work by others, leading to duplication and fragmentation of research programs. And lack of differentiation and signature contribution is a major problem for the science community in China. He hopes to wriggle out of this situation through training the young generation to be independent and innovative.
Linear Folliculotropic CD30-Positive Lymphomatoid Drug Reaction
Authors: Chen Yi-Chin , Wu Yu-Hung 
Published: November 2016

Abstract:
We report a unique case of probable drug-induced CD30-positive lymphomatoid reaction. A 58-year-old woman presented with bilateral facial eruptions of 3 weeks duration composed of erythematosus papules in a linear distribution. The pathological features demonstrated a dense dermal and follicular infiltrate of many medium- to large-sized atypical CD30-positive lymphoid cells. The rash resolved rapidly after discontinuation of her medication 1 week later and did not recur. This case highlights the importance of clinicopathological correlation.
Bullous Pyoderma Gangrenosum With Subungual Involvement Associated With Ulcerative Colitis
Authors: Aktaş Karabay Ezgi , Aksu Cerman Aslı , Kıvanc Altunay İlknur , Yalçın Özben 
Published: November 2016

Abstract:
Pyoderma gangrenosum (PG) is a rare inflammatory and ulcerative skin disease of unknown etiology characterized by neutrophilic infiltration of the dermis, mainly affecting the lower extremities. Bullous PG is a rare variant of this disease, usually associated with hematologic disorders. Here, we report a case of pathergy-positive bullous PG with subungual involvement associated with ulcerative colitis.
Transaortic Edge-To-Edge Repair for Functional Mitral Regurgitation during Aortic Valve Replacement: A 13-Year Experience
Authors: Mihos Christos G. , Larrauri-Reyes Maiteder , Hung Judy , Santana Orlando 
Published: November 2016

Objective The study evaluated the feasibility of a transaortic edge-to-edge mitral valve repair (Alfieri stitch) for moderate or greater (≥2+) functional mitral regurgitation (MR) in high-risk patients undergoing aortic valve replacement. Methods We retrospectively evaluated 40 consecutive patients who underwent aortic valve replacement combined with a transaortic edge-to-edge mitral valve repair for 2+ or greater functional MR, between February 2002 and April 2015. The MR was graded semiquantitatively as 0 (trace/none), mild moderate (2+), or moderate to severe (3–4+). Results Thirty-two patients had aortic stenosis, and eight had aortic regurgitation. The mean ± standard deviation (SD) age was 77.5 ± 5 years, 34 (85%) were male, and the mean ± SD EuroSCORE II was 14.3% ± 12.9. At a median follow-up of 1 month (interquartile range, 0.75–10), there were significant improvements in preoperative versus postoperative median MR grade (3+ vs 1+, P < 0.001), mean left ventricular ejection fraction (34% vs 41%, P = 0.018), left ventricular end-diastolic diameter (54 vs 49 mm, P = 0.005), and pulmonary artery systolic pressure (49 vs 35 mm Hg, P < 0.001). Persistent 3 to 4+ MR occurred in two patients (5%). In 12 patients with at least 6-month follow-up (mean ± SD, 18 ± 11 months), a sustained improvement in all echocardiographic parameters was observed, with persistent 3 to 4+ MR occurring in one patient (8.3%). Actuarial survival at 1, 3, and 4.5 years was 82% ± 6, 71% ± 8, and 65% ± 10, respectively. Conclusions A transaortic edge-to-edge repair for 2+ or greater functional MR can be safely performed during aortic valve replacement and is associated with improvements in MR grade, left ventricular remodeling, and pulmonary hemodynamics.
The Angiovac Device: Understanding the Failures on the Road to Success
Authors: Worku Berhane , Salemi Arash , D'Ayala Marcus D. , Tranbaugh Robert F. , Girardi Leonard N. , Gulkarov Iosif M. 
Published: November 2016

Objective Current percutaneous thromboembolectomy techniques may obviate surgical intervention in high-risk patients with iliocaval thrombus or thrombus of the right side of the heart, but typically require thrombus fragmentation and thrombolysis with associated bleeding and thromboembolic complications. The AngioVac (Angiodynamics, Latham, NY USA) device uses a percutaneous venovenous bypass circuit to aspirate intact thrombus. A review of the literature was performed with regard to the AngioVac device to determine the factors correlating with successful thrombus extraction. Methods A literature search was performed with regard to use of the AngioVac device using the PubMed database. A meta-analysis was not performed given the small size and lack of statistical analysis of the individual reports included. Results Twenty-three reports describing 57 procedures in 56 patients were analyzed. Indications for thrombectomy included iliocaval thrombus in 53% (30), thrombus of the right side of the heart, in 49% (28), pulmonary embolus in 14% (8), and upper extremity venous/Glenn shunt thrombosis in 7% (4). The complete success rate, defined as removal of all thrombus, was 75% (43), with an 11% (6) partial success rate. In 14% (8) of cases, minimal or no thrombus was retrieved. When analyzed by indication, iliocaval thrombus and thrombus of the right side of the heart demonstrated 87% (26) and 82% (23) complete success rates, respectively. Pulmonary embolus demonstrated a significantly lower success rate at 12.5% [1; (P < .001)]. Complications occurred in 12% (7), including six hematomas and one retroperitoneal bleed. Conclusions The AngioVac device offers an excellent alternative to surgical thrombectomy for patients presenting with iliocaval or intracardiac thrombus, with success rates of more than 80%, although it seems that pulmonary emboli are less amenable. Appropriate patient selection can lead to improved outcomes. Larger numbers are needed to make more definite conclusions.
Myocardial Protection and Financial Considerations of Custodiol Cardioplegia in Minimally Invasive and Open Valve Surgery
Authors: Hummel Brian W. , Buss Randall W. , DiGiorgi Paul L. , Laviano Brittany N. , Yaeger Nalani A. , Lucas M. Lee , Comas George M. 
Published: November 2016

Objective Single-dose antegrade crystalloid cardioplegia with Custodiol-HTK (histidine-tryptophan-ketoglutarate) has been used for many years. Its safety and efficacy were established in experimental and clinical studies. It is beneficial in complex valve surgery because it provides a long period of myocardial protection with a single dose. Thus, valve procedures (minimally invasive or open) can be performed with limited interruption. The aim of this study is to compare the use of Custodiol-HTK cardioplegia with traditional blood cardioplegia in patients undergoing minimally invasive and open valve surgery. Methods A single-institution, retrospective case-control review was performed on patients who underwent valve surgery in Lee Memorial Health System at either HealthPark Medical Center or Gulf Coast Medical Center from July 1, 2011, through March 7, 2015. A total of 181 valve cases (aortic or mitral) performed using Custodiol-HTK cardioplegia were compared with 181 cases performed with traditional blood cardioplegia. Each group had an equal distribution of minimally invasive and open valve cases. Right chest thoracotomy or partial sternotomy was performed on minimally invasive valve cases. Demographics, perioperative data, clinical outcomes, and financial data were collected and analyzed. Results Patient outcomes were superior in the Custodiol-HTK cardioplegia group for blood transfusion, stroke, and hospital readmission within 30 days (P < 0.05). No statistical differences were observed in the other outcomes categories. Hospital charges were reduced on average by $3013 per patient when using Custodiol-HTK cardioplegia. Conclusions Use of Custodiol-HTK cardioplegia is safe and cost-effective when compared with traditional repetitive blood cardioplegia in patients undergoing minimally invasive and open valve surgery.
Online Ratings of ASOPRS Surgeons: What Do Your Patients Really Think of You?
Authors: Vu Alexander F. , Espinoza Gabriela M. , Perry Julian D. , Chundury Rao V. 
Published: November 2016

Purpose:
To characterize patient evaluations of American Society of Ophthalmic Plastic and Reconstructive Surgery (ASOPRS) surgeons on a popular online physician rating website in an effort to determine which factors play a role in determining the likelihood of a patient recommending an ASOPRS surgeon to family and friends.

Methods:
After obtaining approval and access from Healthgrades.com, the website database was searched for 612 U.S.-based ASOPRS members using their name as published on http://www.asoprs.org/ as of May 2015. For each surgeon, the total number of ratings and average ratings were recorded under each category. The evaluator recommendation, defined as the response to the questions of “likelihood of recommending Dr. X to family and friends,” constituted the main outcome measure. Variables from each surgeon were compared using unpaired t tests, with statistical significance set at p < 0.05. Correlations were analyzed using Spearman correlation (r
s), with coefficients of greater than or equal to 0.40 or less than or equal to −0.40 considered significant.

Results:
Five-hundred nineteen members (85%) had at least 1 rating while 222 members (36%) had 10 or more ratings. The mean number of ratings for all rated members was 11.4 (range, 1–77; standard deviation [SD] = 11.1) and mean evaluator recommendation score was 4.16 (range, 1–5; SD = 0.79). There was a strong negative correlation between total wait time and evaluator recommendation score (r
s = −0.409, p < 0.001). The average number of ratings and rating scores for all categories were not significantly different when comparing male with female members. University-employed members had significantly fewer ratings (8.46; range, 1–52; SD = 9.3) compared with other members (11.9; range, 1–77; SD = 11.3) (p < 0.016). There were no differences in any other rating score when comparing those university-employed members with other members.

Conclusion:
Online patient-reported evaluations of ASOPRS surgeons appear high in many categories. Long wait times correlate strongly with lower recommendation scores. Further study is required to determine how online patient reviews correlate to objective outcome measures, and how these reviews affect surgeon selection by patients.
Prospective interventional study of tenofovir in pregnancy to prevent vertical transmission of hepatitis B in highly viremic women
Authors: Sellier Pierre O. , Maylin Sarah , Berçot Béatrice , Chopin Dorothée , Lopes Amanda , Simoneau Guy , Evans John , Delcey Véronique , Bénifla Jean-Louis , Simon François , Bergmann Jean-François 
Published: November 2016

Background
The risk of vertical transmission of hepatitis B virus (HBV) increases as maternal HBV DNA increase, despite serovaccination to newborns.

Methods
From 1 July 2012 to 1 January 2016, all pregnant women in Lariboisiere Hospital, Paris, France, with HBV DNA of 5 log10 IU/ml and above were administered tenofovir from week 28 of pregnancy until delivery. HBV DNA was measured at months 1, 2 of tenofovir and at delivery. The newborns were serovaccinated, tested for hepatitis B surface antigen, hepatitis B core antibody (HBcAb)±HBV DNA, and hepatitis B surface antibody (HBsAb) when aged 9 months, and then 24 months. This study was registered in
http://www.ClinicalTrials.gov
(NCT02039362).

Results
Thirty-one women gave birth to 37 newborns. Maternal HBV DNA at baseline was 8.23 log10 IU/ml and above in 12 pregnancies. The mean (median) HBV DNA were 4.4±1.2 (4.8), 3.3±1.7 (3.8), and 2.1±1.9 (2.0) log10 IU/ml at months 1, 2 of tenofovir and at delivery, respectively. Twenty-seven newborns were followed up: none of the 19 children aged 9 months or older was positive for hepatitis B surface antigen when aged 9 months; 14 children tested positive for HBcAb (probably transferred maternal antibodies, not found when aged 24 months) and for HBsAb without HBV DNA. Four of the 19 children showed HBsAb without HBcAb, the last being doubtful for HBcAb and HBsAb without HBV DNA. Eight newborns aged less than 9 months were not tested.

Conclusion
Tenofovir from week 28 of pregnancy to highly viremic HBV women plus serovaccination to newborns could prevent chronic and past infection.
Mental health promotion for junior physicians working in emergency medicine: evaluation of a pilot study
Authors: Mache Stefanie , Bernburg Monika , Baresi Lisa , Groneberg David 
Published: November 2016

Objectives
Work-related stress is highly prevalent among physicians working in emergency medicine. Mental health promotion interventions offer the chance to strengthen physicians’ health, work ability, and performance. The aim of this study was to implement and evaluate a mental health promotion program for junior physicians working in emergency medicine.

Methods
In total, 70 junior physicians working in emergency medicine were randomized to either the mental health promotion program (n=35) or a waitlist control arm (n=35). The training involved 90-min sessions over a time period of 3 months. The primary outcome was perceived stress. The secondary outcomes included emotional exhaustion, emotion regulation, work engagement, and job satisfaction. Self-report assessments for both groups were scheduled at baseline, after the training, after 12 weeks, and 6 months.

Results
The intervention group showed a highly significant reduction in perceived stress and emotional exhaustion from baseline to all follow-up time points, with no similar effects found in the comparison group. The benefit of the mental health promotion program was also evident in terms of improved emotion regulation skills, job satisfaction, and work engagement. Participating physicians evaluated the training with high scores for design, content, received outcome, and overall satisfaction.

Conclusion
The results suggest that this health promotion program is a promising intervention to strengthen mental health and reduce perceived work stress. It is suitable for implementation as a group training program for junior physicians working in emergency medicine. Comparable interventions should be pursued further as a valuable supportive offer by hospital management.