bluuebunny/crossref_metadata_2025_split huggingface dataset:
The recovery trajectory of adolescent social defeat stress-induced behavioral, 1H-MRS metabolites and myelin changes in Balb/c mice
Authors: Zhang Handi , Yan Gen , Xu Haiyun , Fang Zeman , Zhang Jinling , Zhang Jie , Wu Renhua , Kong Jiming , Huang Qingjun 
Published: June 2016

AbstractAdolescent exposure to social stress precipitates emotion-related disorders and affects the development and function of medial prefrontal cortex (mPFC). However, this adversity-induced behavioral and neurological changes remain not fully explored. Adolescent Balb/c mice were subjected to intermittent social defeat stress during postnatal days 28 to 42. Proton magnetic resonance spectroscopy (1H-MRS) measurements, behavioral tests and immunohistochemistry were performed one day or 3 weeks after the last stress episode. Defeated mice exhibited hypoactivity and social avoidance with the latter lasting into the early adulthood, while the anxiety level was unchanged. Social defeat experience lead to temporary decreases in the levels of total creatines (Cr + pCr) and Glx (Glu + Gln), but a delayed increase of N- acetylaspartate (NAA) levels. These alternations were accompanied with a persistent reduction of myelin basic protein expression although the number of mature oligodendrocyte did not change. These findings provide evidence that adolescent adverse social experience permanently impairs the emotion-related behavioral performance and induces biochemical and molecular changes in the brain which at least lasts into early adulthood, thus enhancing our understanding of the neurobiology of social defeat stress. Our finding also implicates that NAA signals on MRS may reflect myelin status.
Reviews of leeson model of oscillator phase noise
Authors: Huang Xianhe , Hu Jianguo , Bai Qingsong , Tang Yuanlin 
Published: June 2016

Through theoretical deduction, two new explanations of Leeson model are presented: the corner frequency of high Q oscillators in the phase noise curve should be the frequency at the intersection of the f 0 curve segment after adding 3 dB and the f −1 curve segment; f0/2QL of low Q oscillators in the phase noise curve should also be the frequency at the intersection of the f 0 curve segment after adding 3 dB and the f −2 curve segment. Moreover, these two new explanations were verified by the experimental data of a reported 80 MHz high Q quartz crystal oscillator and a reported low Q lithium tantalate (LiTaO3) oscillator, respectively. The results could help researchers and engineers properly estimate the key parameters of oscillator phase noise.
Developments and future opportunities for the economic and wider socio-cultural valuation of ecosystem services.
Authors: Bullock C. 
Published: June 2016

Abstract
This paper explores the limits to the economic valuation of ecosystem services. It observes that economics has an important role in the design of policy tools that can stimulate the delivery of beneficial ecosystem services, but acknowledges that the relationship between human beings and the environment is more complex than one that can be explained by a reliance on utility-based values alone. This paper reviews the nature and role of socio-cultural values and efforts by both social and natural scientists to recognize the range and diversity of values that people attach to the environment. It explores the contribution of alternative valuation approaches, specifically deliberative methods and indicates where we might choose to look for more integrated approaches while not losing sight of our dependence on fundamental ecosystem services.
Cancellation of drift kinetic effects between thermal and energetic particles on the resistive wall mode stabilization
Authors: Guo S.C. , Liu Y.Q. , Xu X.Y. , Wang Z.R. 
Published: June 2016

Abstract
Drift kinetic stabilization of the resistive wall mode (RWM) is computationally investigated using MHD-kinetic hybrid code MARS-K following the non-perturbative approach (Liu et al 2008 Phys. Plasmas
15 112503), for both reversed field pinch (RFP) and tokamak plasmas. Toroidal precessional drift resonance effects from trapped energetic ions (EIs) and various kinetic resonances between the mode and the guiding center drift motions of thermal particles are included into the self-consistent toroidal computations. The results show cancellation effects of the drift kinetic damping on the RWM between the thermal particles and EIs contributions, in both RFP and tokamak plasmas, even though each species alone can provide damping and stabilize RWM instability by respective kinetic resonances. The degree of cancellation generally depends on the EIs equilibrium distribution, the particle birth energy, as well as the toroidal flow speed of the plasma.
MIA: non-targeted mass isotopolome analysis
Authors: Weindl Daniel , Wegner Andre , Hiller Karsten 
Published: June 2016

Abstract
Summary: MIA detects and visualizes isotopic enrichment in gas chromatography electron ionization mass spectrometry (GC–EI-MS) datasets in a non-targeted manner. It provides an easy-to-use graphical user interface that allows for visual mass isotopomer distribution analysis across multiple datasets. MIA helps to reveal changes in metabolic fluxes, visualizes metabolic proximity of isotopically enriched compounds and shows the fate of the applied stable isotope labeled tracer.
Availability and Implementation: Linux and Windows binaries, documentation, and sample data are freely available for download at http://massisotopolomeanalyzer.lu. MIA is a stand-alone application implemented in C ++  and based on Qt5, NTFD and the MetaboliteDetector framework.
Contact: karsten.hiller@uni.lu
TaggerOne: joint named entity recognition and normalization with semi-Markov Models
Authors: Leaman Robert , Lu Zhiyong 
Published: June 2016

Abstract
Motivation: Text mining is increasingly used to manage the accelerating pace of the biomedical literature. Many text mining applications depend on accurate named entity recognition (NER) and normalization (grounding). While high performing machine learning methods trainable for many entity types exist for NER, normalization methods are usually specialized to a single entity type. NER and normalization systems are also typically used in a serial pipeline, causing cascading errors and limiting the ability of the NER system to directly exploit the lexical information provided by the normalization.
Methods: We propose the first machine learning model for joint NER and normalization during both training and prediction. The model is trainable for arbitrary entity types and consists of a semi-Markov structured linear classifier, with a rich feature approach for NER and supervised semantic indexing for normalization. We also introduce TaggerOne, a Java implementation of our model as a general toolkit for joint NER and normalization. TaggerOne is not specific to any entity type, requiring only annotated training data and a corresponding lexicon, and has been optimized for high throughput.
Results: We validated TaggerOne with multiple gold-standard corpora containing both mention- and concept-level annotations. Benchmarking results show that TaggerOne achieves high performance on diseases (NCBI Disease corpus, NER f-score: 0.829, normalization f-score: 0.807) and chemicals (BioCreative 5 CDR corpus, NER f-score: 0.914, normalization f-score 0.895). These results compare favorably to the previous state of the art, notwithstanding the greater flexibility of the model. We conclude that jointly modeling NER and normalization greatly improves performance.
Availability and Implementation: The TaggerOne source code and an online demonstration are available at: http://www.ncbi.nlm.nih.gov/bionlp/taggerone
Contact: zhiyong.lu@nih.gov
Supplementary information: Supplementary data are available at Bioinformatics online.
The organization and content of informatics doctoral dissertations
Authors: Shortliffe Edward H 
Published: June 2016

Abstract
This article offers suggested guidelines for graduate students who are embarking on informatics doctoral studies and anticipating the dissertation research and its documentation. Much of the guidance is pertinent for writing dissertations in other disciplines as well. The messages are largely directed at doctoral students, but some elements are also pertinent for master’s students. All are relevant for faculty research advisors. The value of the dissertation is often underestimated. Too often it is seen as a hurdle to be overcome rather than an opportunity to gain insight into one’s own research and to learn how to communicate effectively about it. Ideas that have been ill-formed often do not gel effectively until one tries to write about them. The main lesson is that the preparation of a carefully crafted, rigorous, logically evidence-based, and influential dissertation can be remarkably rewarding, both personally and professionally.
Analysis of National Institutes of Health R01 Application Critiques, Impact, and Criteria Scores: Does the Sex of the Principal Investigator Make a Difference?
Authors: Kaatz Anna , Lee You-Geon , Potvien Aaron , Magua Wairimu , Filut Amarette , Bhattacharya Anupama , Leatherberry Renee , Zhu Xiaojin , Carnes Molly 
Published: June 2016

Purpose
Prior text analysis of R01 critiques suggested that female applicants may be disadvantaged in National Institutes of Health (NIH) peer review, particularly for renewals. NIH altered its review format in 2009. The authors examined R01 critiques and scoring in the new format for differences due to principal investigator (PI) sex.

Method
The authors analyzed 739 critiques—268 from 88 unfunded and 471 from 153 funded applications for grants awarded to 125 PIs (76 males, 49 females) at the University of Wisconsin–Madison between 2010 and 2014. The authors used seven word categories for text analysis: ability, achievement, agentic, negative evaluation, positive evaluation, research, and standout adjectives. The authors used regression models to compare priority and criteria scores, and results from text analysis for differences due to PI sex and whether the application was for a new (Type 1) or renewal (Type 2) R01.

Results
Approach scores predicted priority scores for all PIs’ applications (P < .001), but scores and critiques differed significantly for male and female PIs’ Type 2 applications. Reviewers assigned significantly worse priority, approach, and significance scores to female than male PIs’ Type 2 applications, despite using standout adjectives (e.g., “outstanding,” “excellent”) and making references to ability in more critiques (P < .05 for all comparisons).

Conclusions
The authors’ analyses suggest that subtle gender bias may continue to operate in the post-2009 NIH review format in ways that could lead reviewers to implicitly hold male and female applicants to different standards of evaluation, particularly for R01 renewals.
The microbiota in pediatric rheumatic disease: epiphenomenon or therapeutic target?
Authors: Stoll Matthew L. , Cron Randy Q. 
Published: June 2016

Purpose of review
There has been increasing interest in the contents and function of the microbiota, as it relates to pediatric inflammatory diseases. Here, we discuss the factors underlying the development of the microbiota, its role in juvenile idiopathic arthritis (JIA) and prospects for therapeutic interventions in the microbiota.

Recent findings
The human microbiota undergoes a succession of changes, until it reaches a mature form. A variety of early-life exposures, including mode of delivery and form of feeding, can affect the contents of the microbiota and possibly impact upon long-term risk of developing autoimmune diseases. The microbiota is altered in children with JIA, including elevated Bacteroides genus in JIA as a whole and decreased Faecalibacterium prausnitzii in pediatric spondyloarthritis. Although there are limited data so far indicating that microbiota-based therapies can result in therapeutic improvement of arthritis, most of the data are on adults and thus may not be applicable to children.

Summary
Perturbations of the microbiota during childhood may result in the development of a microbiota associated with increased risk of pediatric rheumatic illness. Whether the microbiota can be targeted is a focus of ongoing research.
Blood Transfusion Incidence, Risk Factors, and Associated Complications in Surgical Treatment of Hip Dysplasia
Authors: Sherrod Brandon A. , Baker Dustin K. , Gilbert Shawn R. 
Published: June 2016

Background:Perioperative bleeding requiring blood transfusion is a known complication of hip dysplasia (HD) surgery. Here we examine rates of, risk factors for, and postoperative complications associated with transfusion during HD surgery.Methods:The National Surgical Quality Improvement Program (NSQIP) Pediatric database was queried for patients treated by an orthopaedist from 2012 to 2013. HD cases were categorized by Current Procedural Terminology codes into femoral osteotomies, acetabular osteotomies, combined femoral/acetabular osteotomies, and open reductions. Patients were grouped by comorbidities: neuromuscular (NM) disease (eg, cerebral palsy) group, non-NM with other comorbidity (Other) group, and no known comorbidity (NL) group. Patients were stratified by weight-normalized transfusion volume. Multivariate regression analysis of transfusion association with procedures, demographics, comorbidities, preoperative laboratory values, and 30-day complications was performed.Results:A total of 1184 HD cases were included. Transfusion rates for the NL, Other, and NM groups, respectively, were 44/451 (9.8%), 61/216 (28.2%), and 161/517 (31.1%). Transfusion volumes (mean±SD) for the NL, Other, and NM groups, respectively, were 8.4±5.4, 13.9±8.8, and 15.5±10.0 mL/kg (P<0.001). Combined osteotomies had the highest transfusion rates in the NM and Other groups (35.7% and 45.8%, respectively), whereas acetabular osteotomies had the highest rate in the NL group (15.8%). Open reductions had the lowest transfusion rate (all groups). Longer operations were independently associated with transfusion (all groups, per hour increase, OR>1.5,P<0.001). Independent patient risk factors included preoperative hematocrit <31% (NM group, OR=18.42,P=0.013), female sex (NL group, OR=3.55,P=0.008), developmental delay (NM group, OR=2.37,P=0.004), pulmonary comorbidity (NM group, OR=1.73,P=0.032), and older age (NL group, per year increase: OR=1.29,P<0.001). In all groups, transfusion was associated with longer hospitalization (P<0.001). We observed a volume-dependent increase in overall complication rate within the Other group for transfusion volumes >15 mL/kg (25.0% vs. 5.4% for <15 mL/kg,P=0.048).Conclusions:We identified several risk factors for transfusion in HD surgery. The incidence of transfusion in HD surgery and its association with adverse outcomes warrants development of appropriate patient management guidelines.Level of Evidence:Level III—prognostic.
Robot-Assisted Abdominoperineal Resection: Clinical, Pathologic, and Oncologic Outcomes
Authors: Eftaiha Saleh M. , Pai Ajit , Sulo Suela , Park John J. , Prasad Leela M. , Marecik Slawomir J. 
Published: June 2016

BACKGROUND:
The extralevator approach to abdominoperineal resection is associated with a decreased incidence of rectal perforation and circumferential resection margin positivity translating to lower recurrence rates. The abdominoperineal resection, as such, is an operation associated with poorer outcomes in comparison with low anterior resections, and any improvements in short-term outcomes are likely to be related to surgical technique. Robot assistance in extralevator abdominoperineal resection has shown improvement in these pathologic outcomes. Because these are surrogate markers for local recurrence and disease-free survival, long-term survival data are needed to assess the efficacy of this robot-assisted technique, exclusively in a dedicated abdominoperineal resection cohort.

OBJECTIVE:
We assessed the perioperative, pathologic, and oncologic outcomes of the robot-assisted extralevator abdominoperineal resection for rectal cancer.

DESIGN:
This study was a review of a prospective database of patients over a 5-year period.

SETTING:
Procedures were performed in the colorectal division of a tertiary hospital from April 2007 to July 2012.

PATIENTS:
Patients with rectal cancer were operated on robotically. Indications for abdominoperineal resection were low rectal cancers invading the sphincter complex or location in the anal canal precluding anastomosis.

INTERVENTIONS:
All patients received a robot-assisted extralevator abdominoperineal resection.

MAIN OUTCOME MEASURES:
Operative and perioperative measures, pathologic outcomes, and disease-free survival and overall survival were documented and assessed.

RESULTS:
Twenty-two patients (15 men) with a mean age of 65.5 years and mean BMI of 28.6 kg/m2 underwent robotic abdominoperineal resection. Circumferential resection margin was positive in 13.6%. There was 1 tumor/rectal perforation. At a mean follow-up of 33.9 months, overall survival was 81.8% with a disease-free survival of 72.7%. Local recurrence was 4.5%.

LIMITATIONS:
This was a single-institution study with no comparative open or laparoscopic group.

CONCLUSION:
Robot-assisted abdominoperineal resection is safe, feasible, and oncologically sound with short-term and long-term outcomes comparable to open and laparoscopic surgery.
Current trends in minilaparoscopy
Authors: Small Layne Alyssa , Pinkard Lauren , Shepherd Jessica 
Published: June 2016

Purpose of review
The purpose of this review is to understand the current use of minilaparoscopy in the field and how minilaparoscopy compares with traditional laparoscopy in terms of operative times, complications, pain, and cosmesis.

Recent findings
Although there are few randomized controlled trials comparing minilaparoscopy with traditional laparoscopy in gynecologic procedures, the results suggest that minilaparoscopy can be performed safely with improved cosmetic outcomes and similar complication rates and operating times. Postoperative pain may be decreased with minimizing incisions sizes. Recently, case reports and case series have been published demonstrating the use of minilaparoscopy across many subtypes of gynecologic surgery.

Summary
Traditional laparoscopic surgery has become common practice in gynecology as it has been found to be a well tolerated procedure with improved outcomes and decreased morbidity when compared with laparotomy. Although minilaparoscopy has been used for over 2 decades, its role in gynecology is continuing to evolve. Minilaparoscopy is a growing surgical option in gynecology as we try to minimize the impact of surgery. Results of minilaparoscopy in gynecology mirror those found in urology and general surgery. Although research is limited, minilaparoscopy has proven to be a well tolerated alternative for gynecology.
Techniques in minimally invasive surgery for advanced endometriosis
Authors: King Cara R. , Lum Deirdre 
Published: June 2016

Purpose of review
Surgery can be an important treatment option for women with symptomatic endometriosis. This review summarizes the recommended preoperative work up and techniques in minimally invasive surgery for treatment of deeply infiltrating endometriosis (DIE) involving the obliterated posterior cul-de-sac, bowel, urinary tract, and extrapelvic locations.

Recent findings
Surgical management of DIE can pose a challenge to the gynecologic surgeon given that an extensive dissection is usually necessary. Given the high risk of recurrence, it is vital that an adequate excision is performed. With improved imaging modalities, preoperative counseling and surgical planning can be optimized. It is essential to execute meticulous surgical technique and include a multidisciplinary surgical team when indicated for optimal results.

Summary
Advanced laparoscopic skills are often necessary to completely excise DIE. A thorough preoperative work up is essential to provide correct patient counseling and incorporation of the preferred surgical team to decrease complications and optimize surgical outcomes. Surgical management of endometriosis is aimed at ameliorating symptoms and preventing recurrence.
Comparison of Rotational Thromboelastography Findings in Pseudoexfoliation Syndrome Patients and Healthy Controls
Authors: Goren Sahin Deniz , Sahin Afsun , Akay Olga M. 
Published: June 2016

Purpose:
Rotational thromboelastography (ROTEM) is a useful test for studying the characteristics of fibrin clot formation. As patients with pseudoexfoliation (PEX) have an increased risk for thrombotic events, clot-forming dysfunction may play a role. The aim of this study is to compare ROTEM findings in PEX syndrome patients with age-matched and sex-matched healthy controls.

Patients and Methods:
A total of 21 patients with PEX syndrome and 22 age-matched and sex-matched healthy controls were included. All study participants underwent detailed ophthalmologic and systemic medical examination, including blood pressure measurement, hemoglobin-hematocrit levels, platelet count, coagulation parameters including prothrombin time, activated partial thromboplastin time, fibrinogen levels, and D-dimer levels. Peripheral blood samples were collected and analyzed with ROTEM Coagulation Analyzer.

Results:
The mean age of patients with PEX and controls was 66.5±8.3 and 65.9±9.5 years, respectively (P=0.7). The 2 groups did not differ with respect to age, sex, hemoglobin, hematocrit, platelet numbers, prothrombin time, activated partial thromboplastin time, fibrinogen levels, D-dimer levels, and glucose levels. When extrinsic thromboelastometry results were analyzed, PEX patients showed a significantly decreased clotting time when compared with healthy controls (79.8 vs. 98.0 s; P=0.01), indicating faster clot formation. Other ROTEM parameters did now show any difference between the 2 groups.

Conclusions:
PEX patients showed faster clotting time when compared with healthy controls. This fibrin clot formation dysfunction may lead to vascular thrombotic events in these patients. Further studies are needed to elucidate the exact underlying mechanism of thrombosis seen in PEX patients.
Testing a Model to Reveal the Predictive Mechanism of Care-Seeking Decisions Among Patients With Acute Myocardial Infarction
Authors: Li Polly W.C. , Yu Doris S.F. 
Published: June 2016

Background:
Extensive research has been conducted to examine the factors affecting care-seeking decisions in patients with acute myocardial infarction (AMI). Such a decision-making process is multifactorial, and its underlying mechanism is yet to be determined.

Objectives:
Our aim was to test a theoretically integrated model to identify the mechanisms underlying patients’ care-seeking decisions in the context of AMI.

Methods:
On the basis of both empirical and theoretical evidence, we proposed that patients’ care-seeking decisions are driven by 2 sequential perceptual-cognitive processes concerned with illness labeling and interpretation, as well as the contextual influences of perceived barriers to care seeking and cues from others. A sample of 301 patients was recruited to test this model using structural equation modeling.

Results:
The model testing revealed good fit with the data (χ
2 = 38.48, df = 30, P = .72; root-mean-square error of approximation = 0.03, normed fit index = 0.96, nonnormed fit index = 0.98, and comparative fit index = 0.99) and explained 46% of the variance in AMI care-seeking delay. Successful action relied on whether patients could correctly attribute the symptom experience to AMI, were aware of their own susceptibility to the condition, and had a good understanding of how the disease manifested itself. Lowering perceived barriers and positive cues from others in advising care seeking played favorable roles to promote care-seeking behaviors.

Conclusions:
This integrative theoretical model is shown to be valid in explaining care-seeking delay among AMI patients and can guide the development of interventions to promote appropriate care-seeking behaviors among high-risk individuals.