bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards region-specific propagation of protein functions
Authors: Koo Da Chen Emily , Bonneau Richard 
Published: October 2018

AbstractMotivationDue to the nature of experimental annotation, most protein function prediction methods operate at the protein-level, where functions are assigned to full-length proteins based on overall similarities. However, most proteins function by interacting with other proteins or molecules, and many functional associations should be limited to specific regions rather than the entire protein length. Most domain-centric function prediction methods depend on accurate domain family assignments to infer relationships between domains and functions, with regions that are unassigned to a known domain-family left out of functional evaluation. Given the abundance of residue-level annotations currently available, we present a function prediction methodology that automatically infers function labels of specific protein regions using protein-level annotations and multiple types of region-specific features.ResultsWe apply this method to local features obtained from InterPro, UniProtKB and amino acid sequences and show that this method improves both the accuracy and region-specificity of protein function transfer and prediction. We compare region-level predictive performance of our method against that of a whole-protein baseline method using proteins with structurally verified binding sites and also compare protein-level temporal holdout predictive performances to expand the variety and specificity of GO terms we could evaluate. Our results can also serve as a starting point to categorize GO terms into region-specific and whole-protein terms and select prediction methods for different classes of GO terms.Availability and implementationThe code and features are freely available at: https://github.com/ek1203/rsfp.Supplementary informationSupplementary data are available at Bioinformatics online.
Impact of Next-generation Sequencing Defined Human Immunodeficiency Virus Pretreatment Drug Resistance on Virological Outcomes in the ANRS 12249 Treatment-as-Prevention Trial
Authors: Derache Anne , Iwuji Collins C , Baisley Kathy , Danaviah Siva , Marcelin Anne-Geneviève , Calvez Vincent , de Oliveira Tulio , Dabis François , Porter Kholoud , Pillay Deenan 
Published: October 2018

Abstract

Background
Previous studies in human immunodeficiency virus (HIV)-positive individuals on thymidine analogue backbone antiretroviral therapy (ART) with either nevirapine or efavirenz have suggested poorer virological outcomes in the presence of pretreatment drug resistance (PDR). We assessed the impact of PDR on virological suppression (VS; <50 copies/mL) in individuals prescribed primarily tenofovir/emtricitabine/efavirenz in rural KwaZulu-Natal within a treatment-as-prevention trial.

Methods
Among 1557 HIV-positive individuals who reported no prior ART at study entry and provided plasma samples, 1328 individuals with entry viral load (VL) >1000 copies/mL had next-generation sequencing (NGS) of the HIV pol gene with MiSeq technology. Results were obtained for 1148 individuals, and the presence of PDR was assessed at 5% and 20% detection thresholds. Virological outcome was assessed using Cox regression in 837 of 920 ART initiators with at least 1 follow-up VL after ART initiation.

Results
PDR prevalence was 9.5% (109/1148) and 12.8% (147/1148) at 20% and 5% thresholds, respectively. After a median of 1.36 years (interquartile range, 0.91–2.13), mostly on fixed-dose combination tenofovir/emtricitabine/efavirenz, presence of both nonnucleoside reverse transcriptase inhibitor (NNRTI)/nucleoside reverse transcriptase inhibitor PDR vs no PDR was associated with longer time to VS (adjusted hazard ratio [aHR], 0.32; 95% confidence interval [CI], 0.12–0.86), while there was no difference between those with only NNRTI PDR vs no PDR (aHR, 1.05; 95% CI, 0.82–1.34) at the 5% threshold. Similar differences were observed for mutations detected at the 20% threshold, although without statistical significance.

Conclusions
NGS uncovered a high prevalence of PDR among participants enrolled in trial clinics in rural KwaZulu-Natal. Dual-class PDR to a mainly tenofovir/emtricitabine/efavirenz regimen was associated with poorer VS. However, there was no impact of NNRTI PDR alone.

Clinical Trials Tegistration
NCT01509508; South African National Clinical Trials Register: DOH-27-0512-3974.
Patients at low surgical risk as defined by the Society of Thoracic Surgeons Score undergoing isolated interventional or surgical aortic valve implantation: in-hospital data and 1-year results from the German Aortic Valve Registry (GARY)
Authors: Bekeredjian Raffi , Szabo Gabor , Balaban Ümniye , Bleiziffer Sabine , Bauer Timm , Ensminger Stephan , Frerker Christian , Herrmann Eva , Beyersdorf Friedhelm , Hamm Christian , Beckmann Andreas , Möllmann Helge , Karck Matthias , Katus Hugo A , Walther Thomas 
Published: October 2018

Abstract

Aims
Transcatheter aortic valve implantation (TAVI) has become the standard treatment for patients with severe aortic valve stenosis at high surgical risk and may be considered for patients with intermediate risk. During the last few years, an increasing number of patients with low surgical risk have been treated with TAVI. In this study, low-risk patients undergoing isolated TAVI or surgical aortic valve replacement (SAVR) were analysed using data from the German Aortic Valve Registry (GARY).

Methods and results
All patients with a Society of Thoracic Surgeons Score of &lt;4% undergoing TAVI or SAVR in 2014 and 2015 were evaluated. A total of 20 549 low surgical risk patients remained for further analysis, comprising 14 487 surgical patients and 6062 TAVI patients. Since TAVI patients were significantly older and had significantly more co-morbidities, a weighted propensity score model was used to compare SAVR and TAVI patients for in-hospital, 30-day, and 1-year mortality. Transcatheter aortic valve implantation patients showed a significantly higher in-hospital and 30-day survival than SAVR patients (in hospital survival TAVI vs. SAVR: 98.5% vs. 97.3%; P = 0.003; 30-day survival TAVI vs. SAVR: 98.1% vs. 97.1%; P = 0.014). At 1 year, survival rates did not differ significantly (survival TAVI vs. SAVR: 90.0% vs. 91.2%; P = 0.158).

Conclusion
In this first GARY analysis of low-risk patients, weighted comparison showed similar 1-year survival for TAVI and SAVR and higher in-hospital survival for TAVI patients.
Education Differentially Buffers Cognitive Performance in Black and White Older Adults
Authors: Jean Kharine R , Lindbergh Cutter A , Mewborn Catherine M , Robinson Talia L , Gogniat Marissa A , Miller L Stephen 
Published: October 2018

Abstract

Objectives
Given that black American older adults are more likely to have lower educational attainment and perform worse on cognitive tests than white Americans, we examined whether increased education would confer greater cognitive advantage to black Americans on measures of global and specific domains of cognitive function.

Methods
The sample included 522 community-dwelling older adults from a larger study. An analysis of covariance was conducted with race and education as between-participant factors and global cognition as the dependent variable. A multivariate analysis of covariance was conducted with five cognitive domains (immediate memory, visuospatial/constructional ability, language, attention, and delayed memory) as the dependent variables.

Results
Significant main effects indicated that black Americans, F(1,516) = 29.18, p < .001, and individuals with less education, F(1,516) = 44.93, p < .001, evidenced lower cognitive functioning, controlling for age and overall health status, and the interaction term reached statistical significance, F(1,516) = 7.95, p = .005. The impact of education on global cognitive function for black participants was more than twice as large (Cohen’s d = 1.30) than for white participants (Cohen’s d = .52). There was a significant race × education interaction for the cognitive domain of attention (p < .001) and a composite measure of non-memory domains (i.e., language, visuospatial/constructional, and attention; p < .001).

Discussion
Our findings suggest that educational attainment is particularly important for black Americans with respect to global cognitive function, attention, and non-memory domains.
Mesopelagic fish avoidance from the vessel dynamic positioning system
Authors: Peña Marian 
Published: October 2018

Abstract
The study of marine organism behaviour and vertical distribution requires the use of techniques that do not disturb their natural state. This study analyses the mesopelagic fishes behaviour influenced by the presence of a research vessel. Acoustic data recorded on board the RV “Ángeles Alvariño” during the RAPROCAN 2017 survey showed a clear pattern of mesopelagic fishes migrating deeper in the water column at night when the DP system was connected. Details on how the scatterers changed their trajectory when migrating to the surface at night and the progressive increase in avoidance depth when dawn approached is shown. An experiment was carried out to discern fish reaction to vessel lights and to the DP system. While a dispersed diving was detected when the lights were switched on, a more acute reaction to the DP system was registered with not only vertical displacement, but also an increment in scattering produced by an aggregating behaviour. Both vessel DP-noise and light modify the mesopelagic fish behaviour, which needs to be accounted for when studying mesopelagic layers close to the surface. Surveys aiming at estimating abundance and biomass from these species are encouraged to do so at day time.
On the Probability That a Stationary Gaussian Process With Spectral Gap Remains Non-negative on a Long Interval
Authors: Feldheim Naomi , Feldheim Ohad , Jaye Benjamin , Nazarov Fedor , Nitzan Shahaf 
Published: October 2018

AbstractLet $f$ be a zero mean continuous stationary Gaussian process on $\mathbb{R}$ whose spectral measure vanishes in a $\delta $-neighborhood of the origin. Then, the probability that $f$ stays non-negative on an interval of length $L$ is at most $e^{-c\delta ^2 L^2}$ with some absolute $c&gt;0$ and the result is sharp without additional assumptions.
The effects of diesel price on regional trade in the USA
Authors: Szewerniak Wojciech W , Xu Yilan , Dall’erba Sandy 
Published: October 2018

Abstract
The abundant trade literature offers little insight on how diesel prices affect intranational trade. We fill this gap by calibrating a structural gravity model to recent U.S. interstate trade data. We discover that, for any distance, the elasticity of trade to diesel prices is much greater for low-valued commodities than for high-valued commodities. The general equilibrium result shows that a nationwide diesel price increase leads to heterogeneous decreases in trade across distances from the exporting state because of adjustments in multilateral costs and trade portfolio. Moreover, it increases the share of high-valued commodities in interstate trade.
Effect of Spinal Cord Stimulation on Early Disability Pension in 198 Failed Back Surgery Syndrome Patients: Case-Control Study
Authors: Kaijankoski Hanna , Nissen Mette , Ikäheimo Tiina-Mari , von Und Zu Fraunberg Mikael , Airaksinen Olavi , Huttunen Jukka 
Published: October 2018

ABSTRACT

BACKGROUND
Spinal cord stimulation (SCS) has proven to be a cost-effective treatment for failed back surgery syndrome (FBSS). However, the effect on patients’ working capability remains unclear.

OBJECTIVE
To evaluate the impact of SCS on working capability and to identify the factors behind permanent disability in FBSS patients.

METHODS
The study group consisted of 198 working-age patients with SCS trialed or implanted for FBSS in a single center between 1996 and 2014. For each patient, 3 living controls, matched by age, gender, and birthplace, were otherwise randomly selected by the Population Register Center. The data on working ability were obtained from the Social Insurance Institution. Patients were divided into 3 groups: SCS trial only, SCS implanted permanently, and SCS implanted but later explanted.

RESULTS
A rehabilitation subsidy was given to 68 patients and 8 controls for a mean of 5.2 (95% confidence interval [CI] 2.4-8.2) and 0.2 (95% CI 0.05-0.6) days per month (P < .05). At the end of follow-up, 16 (37%), 13 (33%), 25 (22%), and 27 (5%) subjects were on disability pension (DP) in the SCS trial, SCS explanted, SCS permanent, and control groups. Patients in the SCS trial-only group were significantly more often on DP than were patients with permanent SCS (odds ratio 2.6; 95% CI 1.2-5.9; P = .02)

CONCLUSION
Permanent SCS usage was associated with reduced sick leave and DP. Prospective study will be required to assess possible predictive value.
A review of ENSO theories
Authors: Wang Chunzai 
Published: October 2018

Abstract
The El Niño and the Southern Oscillation (ENSO) occurrence can be usually explained by two views of (i) a self-sustained oscillatory mode and (ii) a stable mode interacting with high-frequency forcing such as westerly wind bursts and Madden-Julian Oscillation events. The positive ocean–atmosphere feedback in the tropical Pacific hypothesized by Bjerknes leads the ENSO event to a mature phase. After ENSO event matures, negative feedbacks are needed to cease the ENSO anomaly growth. Four negative feedbacks have been proposed: (i) reflected Kelvin waves at the ocean western boundary, (ii) a discharge process due to Sverdrup transport, (iii) western-Pacific wind-forced Kelvin waves and (iv) anomalous zonal advections and wave reflection at the ocean eastern boundary. These four ENSO mechanisms are respectively called the delayed oscillator, the recharge–discharge oscillator, the western-Pacific oscillator and the advective–reflective oscillator. The unified oscillator is developed by including all ENSO mechanisms, i.e. all four ENSO oscillators are special cases of the unified oscillator. The tropical Pacific Ocean and atmosphere interaction can also induce coupled slow westward- and eastward-propagating modes. An advantage of the coupled slow modes is that they can be used to explain the propagating property of interannual anomalies, whereas the oscillatory modes produce a standing oscillation. The research community has recently paid attention to different types of ENSO events by focusing on the central-Pacific El Niño. All of the ENSO mechanisms may work for the central-Pacific El Niño events, with an addition that the central-Pacific El Niño may be related to forcing or processes in the extra-tropical Pacific.
Results of Early Virologic Monitoring May Facilitate Differentiated Care Monitoring Strategies for Clients on ART, Rakai, Uganda
Authors: Ssempijja Victor , Chang Larry W , Nakigozi Gertrude , Ndyanabo Anthony , Quinn Thomas C , Cobelens Frank , Wawer Maria , Gray Ronald , Serwadda David , Reynolds Steven J 
Published: October 2018

Abstract

Background
Viral load (VL) monitoring is standard of care in HIV-infected persons initiated on antiretroviral therapy (ART). We evaluated the predictive value of VL measurements at 6 and 12 months after initiation of firstline ART to estimate the future risk of virologic failure (VF).

Methods
HIV-infected persons with VL measurements at 6 and 12 months post-ART initiation and at least 2 additional VL measurements thereafter were assessed for risk of future VF, defined per World Health Organization guidelines. VL at 6 or 12 months post-ART was categorized into &lt;400, 400–1000, 1001–2000, and &gt;2000 copies/mL. Cox proportional hazard models were used to compare VF incidence associated with 6-month, 12-month, and a composite of 6- and 12-month VL prediction indicators.

Results
Overall, 1863 HIV-infected adults had a 6- and 12-month VL measurement, and 1588 had at least 2 additional VLs thereafter for predicting future VF. The majority (67%) were female (median age: females 33 years and males 37 years). At 12 months post-ART, 90% had VL&lt;400 copies/mL (cumulative incidence of VF at 1.5%), 3% had 400–1000 copies/mL (VF 12%), 2% had 1001–2000 copies/mL (VF 22%), and 5% had &gt;2000 copies/mL (VF 71%). The predictive value of the 12-month VL measurement was comparable to the composite of both the 6- and 12-month VL measurements and better than the 6-month VL measurement.

Conclusions
At 12 months after ART initiation, 90% of patients were virally suppressed with a low likelihood of future VF. VL measurement at 12 months post–ART initiation predicts risk of VF and could inform differentiated virologic monitoring strategies.
Facilitators and Barriers to Implementation of a Peer Support Intervention for Patients with Chronic Pain: A Qualitative Study
Authors: Shue Sarah A , McGuire Alan B , Matthias Marianne S 
Published: October 2018

Abstract

Objective
Pain self-management information and support, delivered by peers, are a potentially useful approach to help patients who are struggling to manage their chronic pain. Before implementation into clinical settings, it is important to understand factors that may influence the success of implementation. The purpose of this study was to explore facilitators and barriers to implementation of peer support for chronic pain.

Design
Semistructured interviews were conducted with clinicians who provide care to patients with chronic pain, regarding their perceptions of the proposed peer support intervention.

Setting
A single US Veterans Affairs Medical Center.

Subjects
Using maximum variation sampling, 15 providers were interviewed (11 women, four men). Clinicians’ disciplines included primary care, physical therapy, nursing, clinical psychology, social work, and pharmacy.

Results
Findings indicated that clinicians 1) had an overall positive perception of the intervention; 2) had specific intervention outcomes they wanted for patients; 3) anticipated that the intervention could positively influence their role; 4) anticipated barriers to intervention participation and maintenance; and 5) had concerns regarding peer coach selection. Findings are discussed in the context of the Consolidated Framework for Implementation Research.

Conclusions
Understanding clinician perceptions of a peer support intervention is critical for successful implementation. The feedback collected in this study will facilitate implementation of the intervention on a broader scale, allowing more patients to benefit.
Associations Among Sleep Latency, Subjective Pain, and Thermal Pain Sensitivity in Gynecologic Cancer
Authors: Kirsch Janae L , Robinson Michael E , McCrae Christina S , Kacel Elizabeth L , Wong Shan S , Patidar Seema , Sannes Timothy S , Garey Stephanie , Castagno Jacqueline C , Pereira Deidre B 
Published: October 2018

Abstract

Objective
Pain is common among women with gynecologic cancer and contributes to depressed mood, sleep disturbances, and likelihood of future chronic pain. Little is known about how psychosocial factors are associated with central sensitization of pain in gynecologic cancer. This study examined relations among depressive symptoms, sleep, subjective pain, and aftersensation pain (a proxy for central sensitization of pain) in gynecologic cancer.

Methods
Participants were 42 women (mean age [SD] = 59.60 [10.11] years) enrolled in a randomized clinical trial examining psychological intervention effects on sleep, pain, mood, and stress hormones/cytokines in gynecologic cancer. Six to eight weeks after surgery, participants completed an assessment of depressive symptoms, sleep, and subjective pain and a temporal summation of pain protocol via quantitative sensory testing (QST).

Results
Controlling for recent chemotherapy, history of chronic pain, and analgesic medication use, regression analyses revealed that longer sleep onset latency (SOL; B = 3.112, P = 0.039, bias-corrected and accelerated (BCa) 95% confidence interval [CI] = 0.371 to 6.014) and greater sensory pain (B = 0.695, P = 0.023, BCa 95% CI = 0.085 to 1.210) were associated with greater aftersensation pain at 15 seconds. Greater sensory pain scores were associated with greater aftersensation pain at 30 seconds (B = 0.286, P = 0.045, BCa 95% CI = 0.008 to 0.513). Depression was not associated with aftersensation pain. The overall models accounted for 44.5% and 40.4% of the variance in aftersensation pain at 15 and 30 seconds, respectively. Conclusions. Longer SOL and higher subjective sensory pain were related to greater aftersensation of experimentally induced pain in women postsurgery for gynecologic cancers. Interventions that improve sleep and subjective sensory pain during the perisurgical period may reduce risk for central sensitization of pain.
Medical Marvels and Professional Medicine: Establishing Scientific Authority in Enlightenment France
Authors: Haas Angela C 
Published: October 2018

Summary
This article examines the investigation of medical marvels—principally reported cases of human bodies that could spontaneously produce rocks, needles, animals or other objects—in Enlightenment France. It argues that published accounts of these investigations served both a pedagogical and propagandistic purpose as they highlighted the benevolence, extensive knowledge, and sceptical approach of the ideal medical practitioner. At a time when medical knowledge was often challenged and the medical community remained insecure about its ability to cure diseases, these accounts provided crucial evidence that medicine was a useful and reliable science. This article examines a critical moment in the professionalisation of medicine when elite physicians in Paris were able to exploit a growing antipathy for the marvellous in order to prove the utility and reliability of medical knowledge, while inextricably linking medical practice with rationalism, scientific reasoning and the Enlightenment campaign against superstition.