bluuebunny/crossref_metadata_2025_split huggingface dataset:
Do the Youth Olympic Games promote Olympism? Analysing a mission (im)possible from a local youth perspective
Authors: Schnitzer Martin , Walde Janette , Scheiber Sabrina , Nagiller Roman , Tappeiner Gottfried 
Published: April 2018

AbstractOn the basis of the Youth Olympic Games (YOG), we assess if and how the youth in the communities of the YOG host cities have been influenced concerning their perception of the Olympic values (OV) and the Olympic movement (OM). Special attention of the study is paid to the analysis of intervention mechanisms which the local youth underwent (e.g. attending the YOG on‐site, participating in school programmes). Our study was conducted among 1004 adolescents living in the host region three years after the Innsbruck 2012 YOG had been staged. Our analyses extend the corresponding literature by (1) showing that the YOG and the involvement of the local youth in such an event have the power of creating an interest in the OM and its events, but do not have the power to influence the young citizens’ perception of the OV significantly; (2) illustrating that the perception adolescents have of the OV depend mainly on their socio‐demographic background, their a priori interest in sports events, social capital (norms, institutional trust) and the extent to which the youngsters follow the event in the different media; and (3) corroborating the hypothesis that intervention programmes (e.g. school programmes) for promoting (Olympic) values and ideals should not be single, obligatory and isolated activities. We conclude that it is not surprising that the International Olympic Committee has reformulated the goals for the YOG in the Olympic Agenda 2020, as some goals relating to the promotion of the OV might have been a mission impossible.
Deep reinforcement learning of cell movement in the early stage of C.elegans embryogenesis
Authors: Wang Zi , Wang Dali , Li Chengcheng , Xu Yichi , Li Husheng , Bao Zhirong 
Published: April 2018

Abstract

Motivation
Cell movement in the early phase of Caenorhabditis elegans development is regulated by a highly complex process in which a set of rules and connections are formulated at distinct scales. Previous efforts have demonstrated that agent-based, multi-scale modeling systems can integrate physical and biological rules and provide new avenues to study developmental systems. However, the application of these systems to model cell movement is still challenging and requires a comprehensive understanding of regulatory networks at the right scales. Recent developments in deep learning and reinforcement learning provide an unprecedented opportunity to explore cell movement using 3D time-lapse microscopy images.

Results
We present a deep reinforcement learning approach within an agent-based modeling system to characterize cell movement in the embryonic development of C.elegans. Our modeling system captures the complexity of cell movement patterns in the embryo and overcomes the local optimization problem encountered by traditional rule-based, agent-based modeling that uses greedy algorithms. We tested our model with two real developmental processes: the anterior movement of the Cpaaa cell via intercalation and the rearrangement of the superficial left-right asymmetry. In the first case, the model results suggested that Cpaaa’s intercalation is an active directional cell movement caused by the continuous effects from a longer distance (farther than the length of two adjacent cells), as opposed to a passive movement caused by neighbor cell movements. In the second case, a leader-follower mechanism well explained the collective cell movement pattern in the asymmetry rearrangement. These results showed that our approach to introduce deep reinforcement learning into agent-based modeling can test regulatory mechanisms by exploring cell migration paths in a reverse engineering perspective. This model opens new doors to explore the large datasets generated by live imaging.

Availability and implementation
Source code is available at https://github.com/zwang84/drl4cellmovement.

Supplementary information
Supplementary data are available at Bioinformatics online.
Exact Bayesian inference for phylogenetic birth-death models
Authors: Parag Kris V , Pybus Oliver G 
Published: April 2018

Abstract

Motivation
Inferring the rates of change of a population from a reconstructed phylogeny of genetic sequences is a central problem in macro-evolutionary biology, epidemiology and many other disciplines. A popular solution involves estimating the parameters of a birth-death process (BDP), which links the shape of the phylogeny to its birth and death rates. Modern BDP estimators rely on random Markov chain Monte Carlo (MCMC) sampling to infer these rates. Such methods, while powerful and scalable, cannot be guaranteed to converge, leading to results that may be hard to replicate or difficult to validate.

Results
We present a conceptually and computationally different parametric BDP inference approach using flexible and easy to implement Snyder filter (SF) algorithms. This method is deterministic so its results are provable, guaranteed and reproducible. We validate the SF on constant rate BDPs and find that it solves BDP likelihoods known to produce robust estimates. We then examine more complex BDPs with time-varying rates. Our estimates compare well with a recently developed parametric MCMC inference method. Lastly, we perform model selection on an empirical Agamid species phylogeny, obtaining results consistent with the literature. The SF makes no approximations, beyond those required for parameter quantization and numerical integration and directly computes the posterior distribution of model parameters. It is a promising alternative inference algorithm that may serve either as a standalone Bayesian estimator or as a useful diagnostic reference for validating more involved MCMC strategies.

Availability and implementation
The Snyder filter is implemented in Matlab and the time-varying BDP models are simulated in R. The source code and data are freely available at https://github.com/kpzoo/snyder-birth-death-code.

Supplementary information
Supplementary data are available at Bioinformatics online.
MetaboDiff: an R package for differential metabolomic analysis
Authors: Mock Andreas , Warta Rolf , Dettling Steffen , Brors Benedikt , Jäger Dirk , Herold-Mende Christel 
Published: April 2018

Abstract

Summary
Comparative metabolomics comes of age through commercial vendors offering metabolomics for translational researchers outside the mass spectrometry field. The MetaboDiff packages aims to provide a low-level entry to differential metabolomic analysis with R by starting off with the table of metabolite measurements. As a key functionality, MetaboDiffs offers the exploration of sample traits in a data-derived metabolic correlation network.

Availability and implementation
The MetaboDiff R package is platform-independent, available at http://github.com/andreasmock/MetaboDiff/ and released under the MIT licence. The package documentation comprises a step-by-step markdown tutorial.

Supplementary information
Supplementary data are available at Bioinformatics online.
RBind: computational network method to predict RNA binding sites
Authors: Wang Kaili , Jian Yiren , Wang Huiwen , Zeng Chen , Zhao Yunjie 
Published: April 2018

AbstractMotivationNon-coding RNA molecules play essential roles by interacting with other molecules to perform various biological functions. However, it is difficult to determine RNA structures due to their flexibility. At present, the number of experimentally solved RNA–ligand and RNA–protein structures is still insufficient. Therefore, binding sites prediction of non-coding RNA is required to understand their functions.ResultsCurrent RNA binding site prediction algorithms produce many false positive nucleotides that are distance away from the binding sites. Here, we present a network approach, RBind, to predict the RNA binding sites. We benchmarked RBind in RNA–ligand and RNA–protein datasets. The average accuracy of 0.82 in RNA–ligand and 0.63 in RNA–protein testing showed that this network strategy has a reliable accuracy for binding sites prediction.Availability and implementationThe codes and datasets are available at https://zhaolab.com.cn/RBind.Supplementary informationSupplementary data are available at Bioinformatics online.
Sequential rank agreement methods for comparison of ranked lists
Authors: Ekstrøm Claus Thorn , Gerds Thomas Alexander , Jensen Andreas Kryger 
Published: April 2018

SummaryThe comparison of alternative rankings of a set of items is a general and common task in applied statistics. Predictor variables are ranked according to magnitude of association with an outcome, prediction models rank subjects according to the personalized risk of an event, and genetic studies rank genes according to their difference in gene expression levels. We propose a sequential rank agreement measure to quantify the rank agreement among two or more ordered lists. This measure has an intuitive interpretation, it can be applied to any number of lists even if some are partially incomplete, and it provides information about the agreement along the lists. The sequential rank agreement can be evaluated analytically or be compared graphically to a permutation based reference set in order to identify changes in the list agreements. The usefulness of this measure is illustrated using gene rankings, and using data from two Danish ovarian cancer studies where we assess the within and between agreement of different statistical classification methods.
Is the plasma aldosterone-to-renin ratio associated with blood pressure response to treatment in general practice?
Authors: Käyser Sabine C , Schalk Bianca W M , de Grauw Wim J C , Schermer Tjard R , Akkermans Reinier P , Lenders Jacques W M , Deinum Jaap , Biermans Marion C J 
Published: April 2018

Abstract

Background
Individualized antihypertensive treatment based on specific biomarkers such as renin may lead to more effective blood pressure control in patients with newly diagnosed essential hypertension. Recent studies suggested that the plasma aldosterone-to-renin ratio (ARR) may also be a candidate predictor for this purpose.

Objective
To assess whether the ARR is associated with the blood pressure response to antihypertensive treatment in patients with newly diagnosed hypertension.

Methods
In this prospective cohort study in primary care, we determined the ARR in patients with newly diagnosed hypertension prior to starting treatment. Treatment was categorized in five groups: no medication, use of angiotensin-converting-enzyme inhibitor or angiotensin receptor blocker, use of calcium channel blocker, use of diuretic, or use of beta blocker. We examined the relation between the ARR and blood pressure response within 1 year of treatment, taking into account the type of antihypertensive treatment and adjusting for gender, age, baseline blood pressure, and comorbidity.

Results
Out of 304 patients, we used 947 measurements (727 no medication, 220 medication) for analysis. There was no association between the ARR and the response in blood pressure, and this applied to each treatment group. Target blood pressure, defined as systolic blood pressure &lt;140 mmHg, was reached in 31% of patients. There was no association between the ARR and reaching target blood pressure (OR 1.002, 95% CI 0.983–1.022).

Conclusion
The ARR is not associated with the response in blood pressure within 1 year of antihypertensive treatment in primary care.
Chromosome-scale assembly of the Monopterus genome
Authors: Zhao Xueya , Luo Majing , Li Zhigang , Zhong Pei , Cheng Yibin , Lai Fengling , Wang Xin , Min Jiumeng , Bai Mingzhou , Yang Yulan , Cheng Hanhua , Zhou Rongjia 
Published: April 2018

Abstract

Background
The teleost fish Monopterus albus is emerging as a new model for biological studies due to its natural sex transition and small genome, in addition to its enormous economic and potential medical value. However, no genomic information for the Monopterus is currently available.

Findings
Here, we sequenced and de novo assembled the genome of M. albus and report the de novochromosome assembly by FISH walking assisted by conserved synteny (Cafs). Using Cafs, 328 scaffolds were assembled into 12 chromosomes, which covered genomic sequences of 555 Mb, accounting for 81.3% of the sequences assembled in scaffolds (~689 Mb). A total of 18 ,660 genes were mapped on the chromosomes and showed a nonrandom distribution along chromosomes.

Conclusions
We report the first reference genome of the Monopterus and provide an efficient Cafs strategy for a de novo chromosome-level assembly of the Monopterus genome, which provides a valuable resource, not only for further studies in genetics, evolution, and development, particularly sex determination, but also for breed improvement of the species.
Is Cancer History Associated With Assets, Debt, and Net Worth in the United States?
Authors: Doroudi Maryam , Coughlan Diarmuid , Banegas Matthew P , Han Xuesong , Robin Yabroff K 
Published: April 2018

Abstract

Background
Financial hardships experienced by cancer survivors have become a prominent public health issue in the United States. Few studies of financial hardship have assessed financial holdings, including assets, debts, and their values, associated with a cancer history.

Methods
Using the 2008–2011 Medical Expenditure Panel Survey, we identified 1603 cancer survivors and 34 915 individuals age 18–64 years without a cancer history to assess associations between self-reported cancer history and assets, debts, and net worth. Distributions of self-reported asset and debt ownership, their values, and net worth were compared for adults with and without a cancer history with chi-square statistics. Multivariable ordered probit regression analysis was conducted to assess the association between cancer history and net worth using a two-sided Wald test. All analyses were stratified by age group (18–34, 35–44, 45–54, and 55–64 years). Statistical tests were two-sided.

Results
Among those age 45–54 years, cancer survivors had a lower proportion of home ownership than individuals without a cancer history (59.0% vs 67.1%, P = .0014) and were statistically significantly more likely to have negative net worth (≤–$3000) and less likely to have positive net worth (≥$3000). Cancer survivors were more likely to have debt than individuals without a cancer history, especially among those age 18–34 years (41.3% vs 27.1%, P < .001).

Conclusions
Cancer history is associated with lower asset ownership, more debt, and lower net worth, especially in survivors age 45–54 years. Longitudinal studies of financial holdings will be important to inform development of interventions to reduce financial hardship.
Oxytocin Reduces Cigarette Consumption in Daily Smokers
Authors: Van Hedger Kathryne , Kushner Meredith J , Lee Royce , de Wit Harriet 
Published: April 2018

Abstract

Introduction
Despite widespread knowledge of the dangers of cigarette consumption, smoking continues to be a public health concern. One compound that has shown potential for treatment in preclinical models is the neuropeptide oxytocin (OT). The purpose of the present study was to examine the effects of intranasal oxytocin on cigarette craving, behavioral economic demand for cigarettes, and cigarette consumption, in regular smokers after 18 hours of abstinence.

Method
Otherwise healthy daily smokers (n = 35) completed two sessions where they received OT (40 IU intranasal) or placebo (PBO) and completed measures of craving and cigarette demand, and they were given six opportunities to smoke partial cigarettes in exchange for money.

Results
On average participants smoked few cigarettes after receiving OT than after receiving PBO, and they reported less desire for additional cigarettes during the smoking period. OT did not affect cigarette demand or standardized measures of cigarette craving.

Conclusions
This study suggests that OT decreases some indices of smoking desire and consumption, providing modest support for the idea that OT might be effective for reducing cigarette smoking.

Implications
This study provides new evidence that oxytocin might have clinical value in the treatment of addictive disorders, in this case tobacco addiction. The study adds to a growing literature suggesting that this neuropeptide, which is mainly known for its role in social bonding and attachment, may also affect mood and motivational states relevant to addiction.
Health Care Utilization Behaviors Predict Disengagement From HIV Care: A Latent Class Analysis
Authors: Okeke Nwora Lance , Clement Meredith E , McKellar Mehri S , Stout Jason E 
Published: April 2018

Abstract

Background
The traditional definition of engagement in HIV care in terms of only clinic attendance and viral suppression provides a limited understanding of how persons living with HIV (PLWH) interact with the health care system.

Methods
We conducted a retrospective analysis of patients with ≥1 HIV clinic visits at the Duke Adult Infectious Diseases Clinic between 2008 and 2013. Health care utilization was characterized by 4 indicators: clinic attendance in each half of the year (yes/no), number of emergency department (ED) visits/year (0, 1, or 2+), inpatient admissions/year (0, 1, 2+), and viral suppression (never, intermittent, always). Health care engagement patterns were modeled using latent class/latent transition analysis.

Results.
A total of 2288 patients (median age, 46.4 years; 59% black, 71% male) were included in the analysis. Three care engagement classes were derived from the latent class model: “adherent” “nonadherent,” and “sick.” Patients age ≤40 years were more likely to be in the nonadherent class (odds ratio, 2.64; 95% confidence interval, 1.38–5.04) than other cohort members. Whites and males were more likely to transition from nonadherent to adherent the following year. Nonadherent patients were significantly more likely to disengage from care the subsequent year than adherent patients (23.6 vs 0.2%, P &lt; .001).

Conclusions
A broader definition of health care engagement revealed distinct and dynamic patterns among PLWH that would have been hidden had only previous HIV clinic attendance had been considered. These patterns may be useful for designing engagement-targeted interventions.
Evolution of clinical trials for rheumatoid arthritis and spondyloarthritis
Authors: van de Sande Marleen G.H. , van Vollenhoven Ronald F. 
Published: April 2018

Purpose of review
The present review presents an overview of the evolution in trial design from mainly randomized placebo-controlled efficacy trials to more strategic clinical trials in rheumatoid arthritis and spondyloarthritis. Additionally, it relates to how these differently designed trials have affected clinical practice.

Recent findings
Placebo-controlled clinical trials, comparing a new agent to placebo on a stable background, have resulted in the development of a wide array of therapeutic agents in rheumatoid arthritis and spondyloarthritis. However, these kind of trials do have some down sides as they do not provide evidence on the optimal strategy to use this multitude of treatments in daily clinical practice and the ethics concerning a placebo phase are often discussed. These and other concerns resulted in the emergence of various different types of trials in rheumatoid arthritis. A similar change of focus is now observed in spondyloarthritis clinical trials. We address literature on direct comparison (’head-to-head’), noninferiority trials, induction-maintenance, discontinuation, and treat-to-target/tight control clinical trials.

Summary
In recent years various clinical trials have been published with a design different from placebo-controlled clinical trials. These novel trial designs aimed to provide guidance on the optimal way to use the full range of targeted treatments available and to make it possible, in some design, to leave out the placebo. In rheumatoid arthritis, some of these more strategic type of trials have had a large impact on common practice. In spondyloarthritis, the first steps toward trials with a more strategic design have been taken, and it stands to reason that more will follow
Epidemiology and Impact of Health Care Provider–Diagnosed Anxiety and Depression Among US Children
Authors: Bitsko Rebecca H. , Holbrook Joseph R. , Ghandour Reem M. , Blumberg Stephen J. , Visser Susanna N. , Perou Ruth , Walkup John T. 
Published: April 2018

Objective:
This study documents the prevalence and impact of anxiety and depression in US children based on the parent report of health care provider diagnosis.

Methods:
National Survey of Children's Health data from 2003, 2007, and 2011–2012 were analyzed to estimate the prevalence of anxiety or depression among children aged 6 to 17 years. Estimates were based on the parent report of being told by a health care provider that their child had the specified condition. Sociodemographic characteristics, co-occurrence of other conditions, health care use, school measures, and parenting aggravation were estimated using 2011–2012 data.

Results:
Based on the parent report, lifetime diagnosis of anxiety or depression among children aged 6 to 17 years increased from 5.4% in 2003 to 8.4% in 2011–2012. Current anxiety or depression increased from 4.7% in 2007 to 5.3% in 2011–2012; current anxiety increased significantly, whereas current depression did not change. Anxiety and depression were associated with increased risk of co-occurring conditions, health care use, school problems, and having parents with high parenting aggravation. Children with anxiety or depression with effective care coordination or a medical home were less likely to have unmet health care needs or parents with high parenting aggravation.

Conclusion:
By parent report, more than 1 in 20 US children had current anxiety or depression in 2011–2012. Both were associated with significant comorbidity and impact on children and families. These findings may inform efforts to improve the health and well-being of children with internalizing disorders. Future research is needed to determine why child anxiety diagnoses seem to have increased from 2007 to 2012.
Possible Ameliorative Effect of Ivabradine on the Autonomic and Left Ventricular Dysfunction Induced by Doxorubicin in Male Rats
Authors: El-Naggar Amany E. , El-Gowilly Sahar M. , Sharabi Fouad M. 
Published: April 2018

Abstract:
Heart failure is a common adverse effect associated with doxorubicin treatment. The aim of this study is to investigate the effect of ivabradine treatment on doxorubicin-induced heart failure in conscious rats. Rats were treated with doxorubicin (2.5 mg/kg/d) or ivabradine (10 mg/kg/d) alone or along with doxorubicin injections. Changes in heart rate variability (HRV), baroreflex sensitivity, left ventricular (LV) function, serum cardiac troponin T, and cardiac histological features were taken as index parameters for the development of heart failure. Ivabradine significantly reduced the elevated heart rate; normalized the parameters of LV function, dP/dtmax and the relaxation time constant (Tau); reduced the elevated serum level of cardiac troponin T; and minimized the cardiac structural abnormalities in doxorubicin-treated rats. Moreover, ivabradine significantly increased the diminished time domain parameters of HRV, SDNN and rMSSD, and decreased the elevated low frequency power and the low frequency/high frequency while having no effect on the reduced high frequency power. Consistently, ivabradine significantly lowered the elevated baroreflex sensitivity measured by sodium nitroprusside. In conclusion, ivabradine ameliorated the LV dysfunction induced by doxorubicin. Moreover, ivabradine increased the overall HRV and restored the autonomic balance by reducing the sympathetic over activation. Therefore, ivabradine may have a possible therapeutic potential against doxorubicin-induced heart failure.