bluuebunny/crossref_metadata_2025_split huggingface dataset:
Longitudinal Findings on Changes in and the Link Between HIV-Related Communication, Risky Sexual Behavior, and Relationship Status in Men Who Have Sex With Men Living With HIV
Authors: Serovich Julianne M. , Laschober Tanja C. , Brown Monique J. , Kimberly Judy A. 
Published: July 2017

Background
Reducing the risk of HIV transmission among men who have sex with men (MSM) is a national health priority. This study longitudinally examined changes in and the link between HIV-related communication, unprotected anal intercourse (UAI), and relationship status among MSM.

Methods
Data were obtained from 337 MSM living with HIV who participated in a randomized controlled study. Approximately equal percentages of men were randomized to either the disclosure intervention group or the attention control case management group. Repeated measures were collected at 5 time points for 12 months and included health-protective sexual communication (HPSC), HIV disclosure, insertive and receptive UAI, and relationship status. Data were analyzed using mixed-effects models.

Results
Independent of the treatment condition, HPSC and HIV disclosure increased over time; insertive UAI showed a curvilinear pattern but no significant decrease over time. Relationship status was related to HIV-related communication and UAI. Greater HPSC was related to less insertive and receptive UAI; disclosure was positively related to insertive UAI.

Conclusions
Based on the findings, prevention programs should continue to focus on improving HIV-related communication among MSM and consider relationship status in prevention messages. Intervention studies are needed to continue to identify and test factors that help reduce risky sexual behaviors.
Aberrometry Repeatability and Agreement with Autorefraction
Authors: Nguyen Mylan T. , Berntsen David A. 
Published: July 2017

SIGNIFICANCE
Commercially available aberrometers are essential to clinical studies evaluating refractive error and image quality. The Discovery System (Innovative Visual Systems, Elmhurst, IL) is a promising clinical instrument that allows investigators to export aberration data for research and analysis purposes. An assessment of the Discovery System’s performance is essential to the interpretation of the data obtained.

PURPOSE
The aims of this study were to determine the between-visit repeatability of refractive error and higher-order aberration measurements with the Discovery System and to examine between-instrument agreement of refractive error measurements with the Discovery System and Grand Seiko WAM-5500 open-field autorefractor (Grand Seiko Co., Hiroshima, Japan).

METHODS
Cycloplegic refractive error values from the Discovery System (over a 3-mm pupil) and the Grand Seiko autorefractor were converted to power vectors (M, J
0, and J
45), and averaged. Zernike coefficients were also calculated by the Discovery System over a 6-mm pupil through the sixth radial order. Between-visit repeatability and agreement were evaluated using Bland-Altman difference-versus-mean plots. A t-test compared each mean difference (bias) to zero, and the 95% limits of agreement were calculated.

RESULTS
Twenty-five young adults with a mean (±SD) cycloplegic spherical-equivalent refractive error of −2.91 ± 1.85 diopters (D) (range, −6.96 to +0.74 D) were enrolled. There were no significant between-visit differences with the Discovery System for M, J
0, J
45, third- through sixth-order root mean square (RMS), higher-order RMS, or spherical aberration (all P > .30), and the repeatability for defocus and higher-order RMS were ±0.31 D and ±0.095 μm, respectively, for a 6-mm pupil. At a 3-mm pupil, the Discovery System, on average, measured slightly more positive values than the Grand Seiko for M (0.28 D), J
0 (0.11 D), and J
45 (0.12 D; all P < .005).

CONCLUSIONS
The Discovery System was very repeatable and would be an appropriate instrument to measure cycloplegic refractive error and higher-order aberration changes in adults. Small differences in refractive error were found between the Discovery System and Grand Seiko.
Atrial Natriuretic Peptide: A Potential Early Therapy for the Prevention of Multiple Organ Dysfunction Syndrome Following Severe Trauma
Authors: Zhang Rong-Wei , Liu Li-Li , Zeng Lan-Lan , Li Rui-Jie , Shen Ye-Hua , Zhang Bin , Liu Zi-Zhuo , Chen Meng-Fei , Jiang Sheng-Mao , Jiang Li-Bing , Zhao Xiao-Gang , Jiang Shou-Yin 
Published: July 2017

ABSTRACT
Trauma remains a tremendous medical burden partly because of increased expenditure for the management of multiple organ dysfunction syndrome (MODS) developed during hospital stay. The intestinal barrier injury continues to be a second insult resulting in MODS which currently lacks efficient strategies for prevention. Recent studies have uncovered multi-organ protective benefits of atrial natriuretic peptide (ANP) in cardiovascular disease. However, the role of ANP in the prevention of MODS following severe trauma has not been understood. In our laboratory study, 1-h infusion of exogenous ANP during hemorrhagic shock following severe trauma induced high-level expression of endogenous serum ANP after 24 h, this effect was related to the improved level of functional biomarkers in multiple organs. Such phenomenon has not been found in other laboratories. A thorough literature review consequently was performed to uncover the potential mechanisms, to appraise therapy safety, and to propose uncertainties. In severe trauma, short-term exogenous ANP therapy during hemorrhagic shock may promote sustained endogenous expression of ANP from intestinal epithelium through activating a positive feedback loop mechanism involving phospholipase C-γ1 and reactive oxygen species crosstalk. This feedback loop may prevent MODS through multiple signaling pathways. Administration of ANP during hemorrhagic shock is thought to be safe. Further studies are required to confirm our proposed mechanisms and to investigate the dose, duration, and timing of ANP therapy in severe trauma.
Clinical Outcomes of Esophagojejunostomy in Totally Laparoscopic Total Gastrectomy: A Multicenter Study
Authors: Sugiyama Masahiko , Oki Eiji , Ogaki Kippei , Morita Masaru , Sakaguchi Yoshihisa , Koga Satoshi , Saeki Hiroshi , Maehara Yoshihiko 
Published: July 2017

Purpose:
To examine the short-term outcomes of intracorporeal anastomosis during totally laparoscopic total gastrectomy retrospectively at multiple institutions.

Patients and Methods:
We collected data of the patients who had undergone totally laparoscopic total gastrectomy at 4 institutions. All patients received an intracorporeal esophagojejunostomy.

Results:
Of the 215 patients evaluated, 147 underwent functional end-to-end anastomosis (FEEA) as the intracorporeal esophagojejunostomy (FEEA group), and 68 patients received a circular stapler anastomosis (Circular group). The rate of tumor invasion to the esophagus was significantly higher in the Circular group than in the FEEA group (33% vs. 6%, respectively; P<0.0001). Univariate and multivariate analyses revealed that the circular stapler anastomosis and high preoperative BMI were statistically significant risk factors for postoperative leakage. However, the rates of complications and mortality were not significantly different between groups.

Consideration:
Our results showed that each type of esophagojejunostomy is safe and feasible for patients with gastric cancer with acceptable morbidity and mortality.
Assessment of Weight Loss With the Intragastric Balloon in Patients With Different Degrees of Obesity
Authors: Nunes Gabriel C. , Pajecki Denis , de Melo Maria E. , Mancini Marcio C. , de Cleva Roberto , Santo Marco A. 
Published: July 2017

Introduction:
The intragastric balloon (IGB) is an endoscopic device for the treatment of obesity. Best results are observed in patients who follow a dietary program but few studies have assessed the results of this treatment in patients with different degrees of obesity.

Aim:
The aim of this study is to compare the efficacy of IGB in patients with different degrees of obesity.

Method:
A total of 2002 patients with IGB were retrospectively evaluated and were divided into groups according to initial body mass index (BMI) range, as follows: group 1, 27 to 29.9 kg/m2; group 2, 30 to 34.9 kg/m2; group 3, 35 to 39.9 kg/m2; group 4, 40 to 44.9 kg/m2; group 5, ≥45 kg/m2. Weight was assessed in 3 different times: before (T0), 1 month (T1), 6 months (T2), and 6 months after removal of the IGB (T3).

Results:
A total of 946 patients lost follow-up. Overall, 40 (3.78%) removed the device before programmed by intolerance, and 1016 patients completed the 6-month treatment. The mean weight loss was 18.9%, excess weight loss 60.1% and an BMI reduction of 6.76 points. 6 months after removal of the balloon 842 patients had continued follow-up (82.8%). At this time, weight loss was 19.84%, excess weight loss was 59.49%, and BMI reduction of 7.06 points. In all groups there was statistical difference between the times T0 and T1 and between T1 and T2 (P<0.001). There was no statistical difference between T2 and T3, in any group.

Conclusion:
IGB provided sustained weight loss in patients who remained in dietary follow-up for 1 year.
Laparoscopic Pancreaticoduodenectomy: A Single Team Preliminary Experience
Authors: Duan Xiaohui , Jiang Bo , Zhou Lixue , Yang Jianhui , Tian Bingzhang , Wen Huiming , Mao Xianhai 
Published: July 2017

Objective:
The present study aimed to describe the authors’ experience and the perioperative outcome for laparoscopic pancreaticoduodenectomy (LPD).

Materials and Methods:
Perioperative clinical data of 57 consecutive pancreaticoduodenectomy (PD) procedures performed from January 2014 to May 2016 in the Department of Hepatobiliary Surgery, Hunan Provincial People’s Hospital were retrospectively analyzed.

Results:
The median of operative time was 315 minutes (range, 220 to 575 min) and the median of intraoperative estimated blood loss was 200 mL (range, 100 to 550 mL). Conversion to open PD was required in 3 patients (5.3%) as a result of difficult dissection. Hand-assisted LPD was used in 2 patients (3.5%). Mean length of hospital stay was 14.8 days (8 to 29 d). Cumulative surgery-related morbidity was 28.1%, included bleeding (n=4), pancreatic ﬁstula (n=3), biliary ﬁstula (n=1), delayed gastric emptying (n=1), intra-abdominal infection (n=3), pulmonary infection (n=3), and ileus (n=1). Postoperative severe complications (Clavien≥III) were detected in 4 patients (7.0%) including 1 intra-abdominal infection, 2 postoperative bleeding event, and 1 afferent delayed gastric emptying. Three patients required reoperation. There was no 30-day or in-hospital mortality. Pathologic diagnoses were pancreatic ductal adenocarcinoma (n=5), ampullary adenocarcinoma (n=10), duodenal adenocarcinoma (n=24), distal common bile duct cancer (n=13), atypical hyperplasia of bile duct (n=2), and chronic pancreatitis (n=3). No patient had margin positive resection; the number of harvested lymph nodes were (16.7±4.2), the number of positive lymph nodes were (1.3±1.1).

Conclusions:
LPD, although complicated and difficult, serve as a safe and effective method for experienced surgeons.
But will they evenwearit? Exploring the tolerability of social communication coaching smartglasses in children and adults with autism
Authors: Keshav Neha U. , Salisbury Joseph P. , Vahabzadeh Arshya , Sahin Ned T. 
Published: July 2017

AbstractIntroductionAugmented reality smartglasses are an emerging technology that are under investigation as a social communication aid for children and adults with autism spectrum disorder (ASD), and as a research tool to aid with digital phenotyping. Tolerability of this wearable technology in people with ASD is an important area for research, especially as these individuals may experience sensory, cognitive, and attentional challenges.AimsThe aim of this study was to assess the tolerability and usability of a novel smartglasses system that has been designed as a social communication aid for children and adults with autism (theBrain Power Autism System;BPAS). BPAS runs on Google Glass Explorer Edition and other smartglasses, utilizes both augmented reality and affective artificial intelligence, and helps users learn key social and emotional skills.MethodTwenty-one children and adults with ASD across a spectrum of severity used BPAS for a coaching session. The user’s tolerability to the smartglasses was determined through caregiver report, and user being able to wear the smartglasses for one-minute (initial tolerability threshold), and for the entire duration of the coaching session (whole session tolerability threshold).ResultsNineteen out of 21 users (90.5%) demonstrated tolerability on all three measures. Caregivers reported 21 out of 21 users (100%) as tolerating the experience, while study staff found only 19 out of 21 users managed to demonstrate initial tolerability (90.5%). Of the 19 users who demonstrated initial tolerability, all 19 were able to use the smartglasses for the entire session (whole session tolerability threshold) (n= 19 of 19, 100%). Caregiver’s reported that 19 out of 21 users (90.5%) successfully used BPAS, and users surpassed their caregiver’s expectations in 15 of 21 cases (71.4%). Users who could communicate reported BPAS as being comfortable (94.4%).DiscussionThis preliminary report suggests that BPAS is well tolerated and usable to a diverse age- and severity-range of people with ASD. This is encouraging as these devices are being developed as assistive technologies for people with ASD. Further research should focus on improving smartglasses design and exploring their efficacy in helping with social communication in children and adults with ASD.
Engrailed homeoprotein blocks degeneration in adult dopaminergic neurons through LINE-1 repression
Authors: Blaudin de Thé François-Xavier , Rekaik Hocine , Peze-Heidsieck Eugenie , Massiani-Beaudoin Olivia , Joshi Rajiv L. , Fuchs Julia , Prochiantz Alain 
Published: July 2017

AbstractLINE-1 mobile genetic elements have shaped the mammalian genome during evolution. A minority of them have escaped fossilization which, when activated, can threaten genome integrity. We report that LINE-1 are expressed in substantia nigra ventral midbrain dopaminergic neurons, a class of neurons that degenerate in Parkinson disease. InEngrailed-1heterozygotes, these neurons show a progressive degeneration that starts at 6 weeks of age, coinciding with an increase in LINE-1 expression. Similarly, DNA damage and cell death, induced by an acute oxidative stress applied to embryonic midbrain neurons in culture or to adult midbrain dopaminergic neuronsin vivo, are accompanied by enhanced LINE-1 expression. Reduction of LINE-1 activity through (i) direct transcriptional repression by Engrailed, (ii) a siRNA directed against LINE-1, (iii) the nucleoside-analogue reverse transcriptase inhibitor stavudine and (iv) viral Piwil1 expression, protects against oxidative stressin vitroandin vivo. We thus propose that LINE-1 overexpression triggers oxidative stress-induced DNA strand breaks and that an Engrailed adult function is to protect mesencephalic dopaminergic neurons through the repression of LINE-1 expression.
The largest SWI/SNF polyglutamine domain is a pH sensor
Authors: Gutiérrez J. Ignacio , Brittingham Greg , Wang Xuya , Fenyö David , Holt Liam J. 
Published: July 2017

AbstractPolyglutamines are known to form aggregates in pathogenic contexts, such as in Huntington’s disease, however little is known about their role in normal biological processes. We found that a polyglutamine domain in the SNF5 subunit of the yeast SWI/SNF complex, histidines within this sequence, and transient intracellular acidification are required for efficient transcriptional regulation during carbon starvation. We hypothesized that a pH-driven oligomerization of the SNF5 polyglutamine region is required for transcriptional reprogramming. In support of this idea, we found that a synthetic spidroin domain from spider silk, which is soluble at pH 7 but oligomerizes at pH ~ 6.3, could partially complement the function of the SNF5 polyglutamine. These results suggest that the SNF5 polyglutamine domain acts as a pH-driven transcriptional regulator.
A model-based clustering method to detect infectious disease transmission outbreaks from sequence variation
Authors: McCloskey Rosemary M , Poon Art FY 
Published: July 2017

AbstractClustering infections by genetic similarity is a popular technique for identifying potential outbreaks of infectious disease, in part because sequences are now routinely collected for clinical management of many infections. A diverse number of nonparametric clustering methods have been developed for this purpose. These methods are generally intuitive, rapid to compute, and readily scale with large data sets. However, we have found that nonparametric clustering methods can be biased towards identifying clusters of diagnosis — where individuals are sampled sooner post-infection — rather than the clusters of rapid transmission that are meant to be potential foci for public health efforts. We develop a fundamentally new approach to genetic clustering based on fitting a Markov-modulated Poisson process (MMPP), which represents the evolution of transmission rates along the tree relating different infections. We evaluated this model-based method alongside five nonparametric clustering methods using both simulated and actual HIV sequence data sets. For simulated clusters of rapid transmission, the MMPP clustering method obtained higher mean sensitivity (85%) and specificity (91%) than the nonparametric methods. When we applied these clustering methods to published HIV-1 sequences from a study cohort of men who have sex with men in Seattle, USA, we found that the MMPP method categorized about half (46%) as many individuals to clusters compared to the other methods, and that the MMPP clusters were more consistent with transmission outbreaks. This new approach to genetic clustering has significant implications for the application of pathogen sequence analysis to public health, where it is critical to robustly and accurately identify clusters for the most cost-effective deployment of resources.
Serial dependence transfers between perceptual objects
Authors: Huffman Greg , Pratt Jay , Honey Christopher J. 
Published: July 2017

AbstractJudgments of the present visual world are affected by what came before. When judgments of visual properties such as orientation are biased in the direction of preceding stimuli, this is called visual serial dependence. Visual serial dependence is thought to arise from mechanisms that support perceptual continuity: because physical properties of an object usually vary smoothly in time, perception might be accurately stabilized by smoothing the perceived features in time. However, mechanisms that support perceptual continuity should be object-specific, because the orientation of one object is more related to its own past than to the past of a distinct object. Thus, we tested the perceptual continuity explanation by comparing the magnitude of serial dependence between objects and within objects. Across three experiments, we manipulated objecthood by varying the color, the location, and both the color and the location of Gabor patches. We observed a serial dependence effect in every experiment but did not observe an effect of objecthood in any experiment. We further observed serial dependence even when the orientations of two successive stimuli were nearly orthogonal. These data are inconsistent with explanations of serial dependence based on visual continuity. We hypothesize that serial dependence arises from a combination of perceptual features and internal response variables, which interact within a common task or decisional context.
Analysis of Ultrafast Transient Absorption Spectroscopy Data using Integrative Data Analysis Platform: 1. Data Processing, Fitting, and Model Selection
Authors: Kovrigin Evgenii L. 
Published: July 2017

ABSTRACTThis manuscript describes a workflow for analysis of transient absorption (TA) spectroscopy data using Integrative Data Analysis Platforms (IDAP) software package. Time-dependent spectral series are analyzed through evaluation of the isosbestic point and kinetics of excited state and ground-state bleach decays. Model fitting and selection based on Akaike’s Information Criterion is discussed. As a practical example, we analyze excitation decays of a common protein label, Alexa Fluor 647.
ssbio: A Python Framework for Structural Systems Biology
Authors: Mih Nathan , Brunk Elizabeth , Chen Ke , Catoiu Edward , Sastry Anand , Kavvas Erol , Monk Jonathan M. , Zhang Zhen , Palsson Bernhard O. 
Published: July 2017

AbstractSummaryWorking with protein structures at the genome-scale has been challenging in a variety of ways. Here, we presentssbio, a Python package that provides a framework to easily work with structural information in the context of genome-scale network reconstructions, which can contain thousands of individual proteins. Thessbiopackage provides an automated pipeline to construct high quality genome-scale models with protein structures (GEM-PROs), wrappers to popular third-party programs to compute associated protein properties, and methods to visualize and annotate structures directly in Jupyter notebooks, thus lowering the barrier of linking 3D structural data with established systems workflows.Availability and Implementationssbiois implemented in Python and available to download under the MIT license athttp://github.com/SBRG/ssbio. Documentation and Jupyter notebook tutorials are available athttp://ssbio.readthedocs.io/en/latest/. Interactive notebooks can be launched using Binder athttps://mybinder.org/v2/gh/SBRG/ssbio/master?filepath=Binder.ipynb.Contactnmih@ucsd.eduSupplementary InformationSupplementary data are available atBioinformaticsonline.
Pseudopaline, a staphylopine-like metallophore involved in zinc and nickel uptake inPseudomonas aeruginosa
Authors: Lhospice Sébastien , Gomez Nicolas Oswaldo , Ouerdane Laurent , Brutesco Catherine , Ghssein Ghassan , Hajjar Christine , Liratni Ahmed , Wang Shuanglong , Richaud Pierre , Bleves Sophie , Ball Geneviève , Borezée-Durant Elise , Lobinski Ryszard , Pignol David , Arnoux Pascal , Voulhoux Romé 
Published: July 2017

ABSTRACTMetal uptake is vital for all living organisms. In metal scarce conditions, a common bacterial strategy consists in the biosynthesis of metallophores, their export in the extracellular medium and the recovery of a metal-metallophore complex through dedicated membrane transporters. Staphylopine is a recently described metallophore distantly related to plant nicotianamine that contributes to the broad-spectrum metal uptake capabilities ofStaphylococcus aureus. Here, we characterize a four genes operon (PA4837–PA4834) inPseudomonas aeruginosainvolved in the biosynthesis and trafficking of a staphylopine-like metallophore named pseudopaline. Pseudopaline differs from staphylopine with regard to the stereochemistry of its histidine moiety associated to an alpha ketoglutarate moiety instead of pyruvate.In vivo, the pseudopaline operon is regulated by zinc through the Zur repressor. The metal-uptake property of the pseudopaline system appears different from that of staphylopine with a predominant effect on nickel uptake, and on zinc uptake in metal scarce conditions mimicking a chelating environment, thus reconciling the regulation of thecntoperon by zinc with its function as a zinc importer under metal scarce conditions.AUTHOR SUMMARYZinc is an essential micronutrients for bacteria, particularly important at the host-pathogen interface where the host tends to sequester metals in a so called nutritional immunity framework, and the pathogenic bacterium increases its metal uptake efforts in order to keep up with its metal requirements. Here we reveal a novel metallophore, named pseudopaline, which is synthesized and exported byPseudomonas aeruginosaand serves for the uptake of nickel in metal poor media, and for the uptake of zinc in metal scarce conditions that mimic the chelating environment that presumably prevails within a host.