bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Prospective Evaluation of a Multisite Cryptococcal Screening and Treatment Program in HIV Clinics in Uganda
Authors: Nalintya Elizabeth , Meya David B. , Lofgren Sarah , Huppler Hullsiek Kathy , Boulware David R. , Rajasingham Radha 
Published: March 2018

Background:

Cryptococcus is a leading cause of AIDS-related mortality. Cryptococcal antigen (CrAg) is detectable in blood before meningitis onset and predicts death. CrAg screening among those with advanced HIV, and treatment of those CrAg+ with fluconazole, has demonstrated survival benefit. However, implementation and widespread uptake have been slow outside clinical trials.

Methods:
We designed a CrAg screening program for routine care that incorporated intensive education and training of clinic staff. We evaluated programmatic implementation, including time to initiation of fluconazole, time to initiation of antiretroviral therapy, and 6-month clinical outcomes.

Results:
Between December 2015 and January 2017, 1440 persons were screened at 11 HIV clinics in Kampala, and CRAG+ prevalence was 6.5% (n = 94/1440) among adults with a CD4 <100 cells/µL. Of those CrAg+, 7 of 94 persons (7%) died or were lost before further clinic evaluation. Fifty-three persons (56%) were asymptomatic and had 6-month survival of 87% (46/53). Of CrAg+ persons, 28% (26/94) were symptomatic at the time of clinic return. Most had confirmed cryptococcal meningitis, and 54% (14/26) of the symptomatic CrAg+ persons were dead or lost at 6 months. Of the 7 symptomatic persons who declined lumbar puncture for further evaluation, all were dead or lost by 6 months.

Conclusion:
All asymptomatic CrAg+ persons identified by our screening program who returned to clinic, initated fluconazole and antiretroviral therapy in a timely manner. Despite this, 27% of CrAg+ (asymptomatic and symptomatic) identified on routine screening were dead or lost to follow-up at 6 months, even with preemptive therapy for those asymptomatic, and standard amphotericin-based treatment for meningitis.
Relationship Between Health-Related Quality of Life and Patient Acceptable Symptom State With Disease Activity and Functional Status in Patients With Ankylosing Spondylitis in Thailand
Authors: Chiowchanwisawakit Praveena , Thaweeratthakul Phakhamon , Wattanamongkolsil Luksame , Srinonprasert Varalak , Koolvisoot Ajchara , Muangchan Chayawee , Nilganuwong Surasak , Arromdee Emvalee , Katchamart Wanruchada 
Published: March 2018

Objective
This study aimed to identify factors associated with EuroQoL–5 Dimensions, 5 Levels and Patient Acceptable Symptom State (PASS) and health utility (HU) in Thai patients with ankylosing spondylitis (AS).

Methods
This was a cross-sectional study of consecutive AS patients visiting Siriraj Hospital between May 31, 2012, and March 31, 2016. Demographic data and outcomes related to HU (Thai version of EuroQoL–5 Dimensions, 5 Levels), disease activity (Bath Ankylosing Spondylitis Disease Activity Index, Ankylosing Spondylitis Disease Activity Score–erythrocyte sedimentation rate or Ankylosing Spondylitis Disease Activity Score–C-reactive protein, number of tender and swollen joints, and enthesitis), and functional status (Bath Ankylosing Spondylitis Functional Index and Health Assessment Questionnaire) were collected. Regression analysis was used to explore factors associated with each EuroQOL–5 Dimensions (EQ-5D) domain, HU, and PASS.

Results
Among 119 AS patients, the mean age was 40.4 years; 61.3% were male. The mean EQ-5D was 0.75. In univariate analysis, lower disease activity and less impaired function were significantly associated with higher HU and not to mild problems in each EQ-5D domain. In multivariate regression analysis, Bath Ankylosing Spondylitis Disease Activity Index, C-reactive protein, and Health Assessment Questionnaire adjusting for age explained 77.4% of the HU variance. Patients answering yes to PASS were significantly older, had higher HU, and lower disease activity compared with those answering no to PASS. Usual activity and pain problems were importantly related to PASS after adjusting for other domains and age.

Conclusions
Disease activity and functional status in AS patients were significant factors related to HU and PASS. To improve quality of life, treatment goals should be achieving remission, improving function, and controlling pain.
LAP-VEGaS Practice Guidelines for Reporting of Educational Videos in Laparoscopic Surgery
Authors: Celentano Valerio , Smart Neil , McGrath John , Cahill Ronan A. , Spinelli Antonino , Obermair Andreas , Hasegawa Hirotoshi , Lal Pawanindra , Almoudaris Alex M. , Hitchins Charlotte R. , Pellino Gianluca , Browning Matthew G. , Ishida Takashi , Luvisetto Federico , Cingiloglu Pinar , Gash Katherine , Harries Rhiannon , Harji Deena , Di Candido Francesca , Cassinotti Elisa , McDermott Frank D. , Berry James E. A. , Battersby Nick J. , Platt Esther , Campain Nicholas J. , Keeler Barrie D. , Boni Luigi , Gupta Sharmila , Griffith John P. , Acheson Austin G. , Cecil Tom D. , Coleman Mark G. 
Published: March 2018

Objective:
Consensus statement by an international multispecialty trainers and trainees expert committee on guidelines for reporting of educational videos in laparoscopic surgery.

Summary of Background Data:
Instructive laparoscopy videos with appropriate exposition could be ideal for initial training in laparoscopic surgery, but there are no guidelines for video annotation or procedural educational and safety evaluation.

Methods:
Delphi questionnaire of 45 statements prepared by a steering group and voted on over 2 rounds by committee members using an electronic survey tool. Committee selection design included representative surgical training experts worldwide across different laparoscopic specialties, including general surgery, lower and upper gastrointestinal surgery, gynecology and urology, and a proportion of aligned surgical trainees.

Results:
All 33 committee members completed both the first and the second round of the Delphi questionnaire related to 7 major domains: Video Introduction/Authors’ information; Patient Details; Procedure Description; Procedure Outcome; Associated Educational Content; Peer Review; and Use in Educational Curriculae. The 17 statements that did not reach at least 80% agreement after the first round were revised and returned into the second round. The committee consensus approved 37 statements to at least an 82% agreement.

Conclusion:
Consensus guidelines on how to report laparoscopic surgery videos for educational purposes have been developed. We anticipate that following our guidelines could help to improve video quality.
These reporting guidelines may be useful as a standard for reviewing videos submitted for publication or conference presentation.
A Telephone Call to Decrease Patient Anxiety Before Urodynamic Testing: A Randomized Controlled Trial
Authors: Warda Hussein , Hacker Michele R. , Haviland Miriam J. , Hota Lekha S. 
Published: March 2018

Objective
The aim of this study was to determine if a telephone call before undergoing urodynamic study (UDS) would decrease test-related anxiety compared with standard care.

Methods
We performed a randomized controlled trial at a single practice from April 2016 to June 2017. Patients at least 18 years old with lower urinary tract dysfunction and undergoing UDS for the first time were eligible. All participants received standard counseling; participants randomized to the intervention group also received a telephone call before their UDS appointment to answer any questions regarding their upcoming test. All participants completed surveys before and after testing to assess anxiety, preparedness, and satisfaction. The primary outcome was anxiety level immediately before UDS. Secondary outcomes included self-reported patient preparedness, pain, and satisfaction with counseling. Data were compared using χ2, Fisher exact, and Wilcoxon rank sum tests.

Results
One hundred two participants were included in this as-treated analysis: 52 in the intervention group and 50 in the standard care group. The 2 groups were similar in age, ethnicity, and the proportion seeking additional information before testing. There were no statistically significant differences between groups with respect to overall anxiety, anxiety regarding specific elements of the test, or anticipated pain (all P ≥ 0.19). Participant satisfaction with pre-UDS counseling was significantly higher in the intervention group (80.8%) compared with the standard care group (54.0%; P = 0.002).

Conclusions
Our study showed that a telephone call before undergoing UDS did not decrease anxiety compared with standard care; however, the telephone call was associated with higher satisfaction with pre-UDS counseling.
A Scoping Study of Psychosocial Factors in Women Diagnosed With and/or Treated for Pelvic Organ Prolapse
Authors: Touza Kaitlin K. , Rand Kevin L. , Carpenter Janet S. , Chen Chen X. , Heit Michael H. 
Published: March 2018

Objective
Pelvic organ prolapse (POP) is prevalent and can impact women's physical and psychosocial health. To develop interventions that support this population, an understanding of the state of research on psychosocial factors related to POP is essential. We conducted a scoping study focused on the psychosocial experience of women with POP. The purpose of this review was to (1) inventory and describe the current state of knowledge of the psychosocial experience of women with POP, (2) identify gaps in knowledge, and (3) identify targets for future research.

Method
Electronic databases PsycINFO, PubMed, EMBASE, and CINAHL were searched through November 1, 2017.

Results
Of 524 titles reviewed, 103 articles met all inclusion criteria. Articles were grouped by the disease period (ie, prediagnosis, diagnosis/preintervention, intervention, follow-up, and mixed) and psychosocial factors. Most articles (n = 73) focused on women undergoing intervention. Articles focusing on the preintervention period was the next largest category (n = 14). Follow-up after intervention (n = 8) and samples of mixed disease periods (n = 7) were less common. One article focused on women before diagnosis. Articles focused on quality of life (QOL; n = 79), sexual function (n = 51), satisfaction (n = 16), body image (n = 13), psychological distress (n = 4), and knowledge (n = 3).

Conclusions
Research on the psychosocial experience of POP has largely focused on changes in QOL and sexual function. Future research should target emotional experience of women with POP; relationships among QOL, psychological distress, body image, and sexual function; and psychosocial factors related to treatment outcomes.
Stability of nonlinear waves and patterns and related topics
Authors: Ghazaryan Anna , Lafortune Stephane , Manukian Vahagn 
Published: March 2018

Periodic and localized travelling waves such as wave trains, pulses, fronts and patterns of more complex structure often occur in natural and experimentally built systems. In mathematics, these objects are realized as solutions of nonlinear partial differential equations. The existence, dynamic properties and bifurcations of those solutions are of interest. In particular, their stability is important for applications, as the waves that are observable are usually stable. When the waves are unstable, further investigation is warranted of the way the instability is exhibited, i.e. the nature of the instability, and also coherent structures that appear as a result of an instability of travelling waves. A variety of analytical, numerical and hybrid techniques are used to study travelling waves and their properties.
This article is part of the theme issue ‘Stability of nonlinear waves and patterns and related topics’.
The UBR-1 Ubiquitin Ligase Regulates Glutamate Metabolism to Generate Coordinated Motor Pattern inC. elegans
Authors: Chitturi Jyothsna , Hung Wesley , Abdel Rahman Anas M. , Wu Min , Lim Maria A. , Calarco John , Baran Renee , Huang Xun , Dennis James W. , Zhen Mei 
Published: March 2018

AbstractUBR1 is an E3 ubiquitin ligase best known for its ability to target protein degradation by the N-end rule. The physiological functions of UBR family proteins, however, remain not fully understood. We found that the functional loss ofC. elegansUBR-1 leads to a specific motor deficit: when adult animals generate reversal movements, A-class motor neurons exhibit synchronized activation, preventing body bending. This motor deficit is rescued by removing GOT-1, a transaminase that converts aspartate to glutamate. Both UBR-1 and GOT-1 are expressed and critically required in premotor interneurons of the reversal motor circuit to regulate the motor pattern.ubr-1andgot-1mutants exhibit elevated and decreased glutamate level, respectively. These results raise an intriguing possibility that UBR proteins regulate glutamate metabolism, which is critical for neuronal development and signaling.Author SummaryUbiquitin-mediated protein degradation is central to diverse biological processes. The selection of substrates for degradation is carried out by the E3 ubiquitin ligases, which target specific groups of proteins for ubiquitination. The human genome encodes hundreds of E3 ligases; many exhibit sequence conservation across animal species, including one such ligase called UBR1. Patients carrying mutations inUBR1exhibit severe systemic defects, but the biology behinds UBR1’s physiological function remains elusive. Here we found that theC. elegansUBR-1 regulates glutamate level. When UBR-1 is defective,C. elegansexhibits increased glutamate; this leads to synchronization of motor neuron activity, hence defective locomotion when animals reach adulthood. UBR1-mediated glutamate metabolism may contribute to the physiological defects ofUBR1mutations.
crsra: A package for Cleaning and Analyzing Coursera Research Export Data
Authors: Hadavand Aboozar , Leek Jeffrey 
Published: March 2018

AbstractDue to the fundamental differences between traditional education and Massive Open Online Courses (MOOCs) and the ever-increasing popularity of MOOCs more research is needed to under- stand current and future trends in education. Although research in the field has rapidly grown in recent years, one of the main challenges facing researchers remains to be the complexity and messiness of the data. Therefore, it is imperative to provide tools that pave the way for more research on the new subject of MOOCs. This paper introduces a package called crsra based on the statistical software R to help clean and analyze massive loads of data provided by Coursera. The advantages of the package are as follows: a) faster loading and organizing data for analysis, b) an efficient method for combining data from multiple courses and even across institutions, and c) provision of a set of functions for analyzing student behaviors.
The contribution of parent-to-offspring transmission of telomeres to the heritability of telomere length in humans
Authors: Delgado Dayana A. , Zhang Chenan , Demanelis Kathryn , Chen Lin S. , Gao Jianjun , Roy Shantanu , Shinkle Justin , Sabarinathan Mekala , Argos Maria , Tong Lin , Ahmed Alauddin , Islam Tariqul , Rakibuz-Zaman Muhammad , Sarwar Golam , Shahriar Hasan , Rahman Mahfuzar , Yunus Muhammad , Doherty Jennifer A. , Jasmine Farzana , Kibriya Muhammad G. , Ahsan Habibul , Pierce Brandon L. 
Published: March 2018

ABSTRACTLeukocyte telomere length (LTL) is a heritable trait with two potential sources of heritability (h2): inherited variation in non-telomeric regions (e.g., SNPs that influence telomere maintenance) and variability in the lengths of telomeres in gametes that produce offspring zygotes (i.e., “direct” inheritance). Prior studies of LTL h2have not attempted to disentangle these two sources. Here, we use a novel approach for detecting the direct inheritance of telomeres by studying the association between identity-by-descent (IBD) sharing at chromosome ends and phenotypic similarity in LTL. We measured genome-wide SNPs and LTL for a sample of 5,069 Bangladeshi adults with substantial relatedness. For each of the 7,254 relative pairs identified, we used SNPs near the telomeres to estimate the number of chromosome ends shared IBD, a proxy for the number of telomeres shared IBD (Tshared). We then estimated the association between Tsharedand the squared pairwise difference in LTL ((ΔLTL)2) within various classes of relatives (siblings, avuncular, cousins, and distant), adjusting for overall genetic relatedness (ϕ). The association between Tsharedand (ΔLTL)2was inverse among all relative pair types. In a meta-analysis including all relative pairs (ϕ >0.05), the association between Tsharedand (ΔLTL)2(P=0.002) was stronger than the association between ϕ and (ΔLTL)2(P=0.45). Our results provide strong evidence that telomere length (TL) in parental germ cells impacts TL in offspring cells and contributes to LTL h2despite telomere “reprogramming” during embryonic development. Applying our method to larger studies will enable robust estimation of LTL h2attributable to direction transmission.
Accelerometry data in health research: challenges and opportunities
Authors: Karas Marta , Bai Jiawei , Strączkiewicz Marcin , Harezlak Jaroslaw , Glynn Nancy W. , Harris Tamara , Zipunnikov Vadim , Crainiceanu Ciprian , Urbanek Jacek K. 
Published: March 2018

AbstractWearable accelerometers provide detailed, objective, and continu-ous measurements of physical activity (PA). Recent advances in technology and the decreasing cost of wearable devices led to an explosion in the popula-rity of wearable technology in health research. An ever increasing number of studies collect high-throughput, sub-second level raw acceleration data. In this paper we discuss problems related to the collection and analysis of raw acce-lerometry data and provide insights into potential solutions. In particular, we describe the size and complexity of the data, the within- and between-subject variability and the effects of sensor location on the body. We also provide a short tutorial for dealing with sampling frequency, device calibration, data labeling and multiple PA monitors synchronization. We illustrate these po-ints using the Developmental Epidemiological Cohort Study (DECOS), which collected raw accelerometry data on individuals both in a controlled and the free-living environment.
Differential variation and expression analysis
Authors: Bar Haim , Schifano Elizabeth D. 
Published: March 2018

AbstractWe propose an empirical Bayes approach using a three-component mixture model, the L2N model, that may be applied to detect both differential expression (mean) and variation. It consists of two log-normal components (L2) for the differentially expressed (dispersed) features (one component for under-expressed [dispersed] and the other for over-expressed [dispersed] features), and a single normal component (N) for the null features (i.e., non-differentially expressed [dispersed] features). Simulation results show that L2N can capture asymmetries in the numbers of over-and under-expressed (dispersed) features (e.g., genes) when they exist, can provide a better fit to data in which the distributions of the null and non-null features are not well-separated, but can also perform well under symmetry and separation. Thus the L2N model is particularly appealing when no a priori biological knowledge about the mixture density is available. The L2N model is implemented in an R package called DVX, for Differential Variation and eXpression analysis. The package also includes an implementation of differential expression analysis via the limma package, and a differential variation and expression analysis using a three-way normal mixture model. DVX is a user-friendly, graphical interface implemented via the ‘Shiny’ package [6], so that a user is not required to have R programming knowledge. It offers a set of diagnostics plots, data transformation tools, and report generation in Microsoft Excel- and Word-compatible formats. The package is available on the web, at https://haim-bar.uconn.edu/software/DVX/.
Where and how our brain represents the temporal structure of observed action
Authors: Thomas R.M. , Sanctis T. De , Gazzola V. , Keysers C. 
Published: March 2018

AbstractReacting faster to the behavior of others provides evolutionary advantages. Reacting to unpredictable events takes hundreds of milliseconds. Understanding where and how the brain represents what actions are likely to follow one another is therefore important. Everyday actions are predictable sequences of acts, yet neuroscientists focus on how brains responds to unexpected, individual motor acts. Using fMRI we show the brain encodes sequence-specific information in the motor system. Using EEG, we show visual responses were faster and smaller for predictable sequences that recruit the motor system. This study shifts the study of action observation from single acts to motor sequences, informs how we adapt to the actions of others and suggests the motor system may implement perceptual predictive coding.
The AOPOntology: A Semantic Artificial Intelligence Tool for Predictive Toxicology
Authors: Burgoon Lyle D. 
Published: March 2018

AbstractIntroductionToxicology needs artificial intelligence tools that can automate the prediction of toxicity. Today we are at an interesting nexus. We have thousands of chemicals in the environment that lack regulatory thresholds for determining risk. New high throughput in vitro testing methods are becoming available to test these chemicals. Causal Adverse Outcome Pathway Networks (CAOPN) are emerging that will allow us to make predictions based on perturbations of specific key events within the network. The AOPOntology was developed as infrastructure for this nexus, providing the ability to model and marry the data from the in vitro tests for the thousands of chemicals and place them within the CAOPN framework to facilitate adverse outcome predictions.Materials and MethodsThe AOPN is a functional specialized ontology that creates classes that model biological pathways and CAOPNs. Adverse outcome predictions are based on mathematical determinations of key events that are sufficient to infer adverse outcomes will occur, or biological information. These sufficiency relationships are captured in the AOPOntology and used by the semantic reasoners to make predictions.ResultsThe AOPOntology version 1.0 architecture is in place, and a CAOPN for steatosis demonstrates how causal network theory is used to make predictions. The AOPOntology is available at https://github.com/DataSciBurgoon/aop-ontology.DiscussionThe AOPOntology is a knowledge base for CAOPNs that one can use to make predictions about a chemical’s potential toxicity using in vitro high throughput and other assays.ConclusionsUsing CAOPNs and causal network theory one is able to predict potential toxicity for chemicals using in vitro high throughput and various high content screens.