bluuebunny/crossref_metadata_2025_split huggingface dataset:
Collecting data for the Rhapsodie treebank
Authors: Lacheret-Dujour Anne , Pietrandrea Paola , Baude Olivier , Obin Nicolas , Simon Anne-Catherine , Tchobanov Atanas 
Published: June 2019

Abstract
This chapter is devoted to the development of the Rhapsodie repository. We describe the selection of data to be annotated, the principles used to document the data and discuss the theoretical assumptions underlying the Rhapsodie project. The aim was to provide a corpus to study the interface between discourse, syntax, and prosody in French and the variation of intonosyntactic features according to discourse genre in the marking of informational structure as well as expressivity in unelicited speech. At the beginning of the Rhapsodie project such data were under-represented and the need for spoken corpora of this type in French was strongly felt. Consequently, several challenges had to be addressed. First, we discuss the different obstacles and challenging questions we faced with respect to the development of a well-balanced corpus of different discourse genres produced in different speech situations, such as the nature of the data and the type of information to include in the metadata. Then, we present the sources from which the samples were extracted, legal and ethical issues, and the methodology adopted to encode the metadata.
The annotation of syllabic prominences and disfluencies
Authors: Avanzi Mathieu , Bordal Guri , Lacheret-Dujour Anne , Obin Nicolas , Sauvage-Vincent Julie 
Published: June 2019

Abstract
This chapter presents the methodology developed to capture syllabic prominences and prosodic disfluencies in the speech flow. Then it describes the protocol used for the 3-point scale labeling of prominences and disfluencies, the choice of annotators, from semi-naive to experts, the inter-annotator reliability and the generation of the final annotation. This step is crucial in the Rhapsodie project, since the annotation of prominences and disfluencies is the cornerstone for the derivation of the internal constituents of the prosodic tree, from the metrical foot to the intonation package. The training and instructions given to the coders should therefore be exhaustive, especially since without a protocol, the annotation is subjective and depends on many acoustic and grammatical cues, which vary according to the competence of each annotator.
Derivation of the prosodic structure
Authors: Lacheret-Dujour Anne , Bordal Guri , Truong Arthur 
Published: June 2019

Abstract
This chapter presents the rules implemented for the automatic generation of the internal prosodic structure of an intonational period based on prominence annotations, from the metrical foot to the intonation package. A special feature of the model is that it accounts for performance features such as filled pauses, interruptions and non-prominent disfluent segments, to differentiate two types of constituents, that we called standard and extended units, at each level of the prosodic hierarchy. Each case is illustrated by examples extracted from the Rhapsodie database. The diversity of the output is discussed in the light of the aim of the project: An exhaustive study of the correlations between situational variables and prosodic constructions implies a detailed characterization of the prosodic objects to be observed. Finally, the issue of the representativeness of each type of unit, standard vs. non standard, is discussed in the context of prosodic performance modeling.
Tools for fundamental frequency estimation in Rhapsodie
Authors: Martin Philippe 
Published: June 2019

Abstract
The quality of the speech recordings in the Rhapsodie project is highly variable, ranging from excellent to very poor. The main enemies of a fundamental frequency analysis are echo, microphone low-pass filtering, overlapping sound sources, creak, etc. As some fundamental frequency tracking algorithms perform better than others on specific speech segments, alternative methods can prove to be more efficient. This chapter describes approaches to identify problems and provides guidelines to select and apply one of the five available fundamental frequency tracking algorithms (spectral comb, AMDF, autocorrelation, Cepstrum, harmonic selection) on specific speech segments. These methods are implemented in a single software program and can be applied to specific recording segments by simple graphic commands. The resulting reliable pitch curves enable automatic stylization and annotation processing, which is usually not possible using a single F0 tracking method.
Macrosyntax at work
Authors: Pietrandrea Paola , Delsart Aline 
Published: June 2019

Abstract
In this chapter we conduct a quantitative analysis of the distribution of macrosyntactic structures in the Rhapsodie corpus. The analysis shows that there is a strong tendency to massively reuse only a small number of macrosyntactic patterns and that simple utterances predominate in the corpus. The analysis also shows that French spoken discourse is not at all characterized by the lack of microsyntactic cohesion, as is usually claimed. Rather than a strategy used to compensate for an alleged lack of microsyntactic cohesion in spoken discourse, macrosyntax is better regarded as an additional level of cohesion that ensures the interface between the internal structure of an utterance and the global structure of the discourse in which that utterance occurs.
Otoplasty Using the Combined Mustardé-Furnas Technique: Satisfaction and Objective Results
Authors: García-Purriños Francisco , Raposo Alberto , Guilllén Alberto , Calero Juan , Giribet Ana , Barrios Andrés 
Published: June 2019

Abstract

Background
To understand the level of satisfaction among patients undergoing otoplasty using the combined Mustardé-Furnas technique. To evaluate surgery outcomes using McDowell/Wright (MW) criteria.

Objectives
The authors sought to analyze any possible correlation between satisfaction level and surgery outcome.

Methods
The authors conducted a retrospective study on patients who underwent combined Mustardé and Furnas otoplasty between 1996 and 2016. All patients were assessed 12 months after surgery employing MW goals and satisfaction surveys.

Results
The study includes 172 patients who underwent 343 otoplasty procedures. There were 134 patients (77.9%) who had all 6 of the criteria for surgical success as defined by MW 12 months after surgery, reporting satisfaction levels of 9 to 10. Fifteen patients (9.3%) had 5 of the 6 MW criteria, reporting satisfaction levels of 9 to 10, and 22 patients (12.79%) had only 4 MW objectives and reported satisfaction levels of 7 to 10. The Spearman rho coefficient was 0.545 and the Kendall coefficient was 0.375, with a statistically significant association (P &lt; 0.001).

Conclusions
Patient satisfaction increases as the number of MW goals are met, although the correlation is moderate to low. Patients perceive the results of the surgery as satisfactory or very satisfactory, even when ENT surgeons consider outcomes to be poor according to MW criteria.

Level of Evidence: 4
RERconverge: an R package for associating evolutionary rates with convergent traits
Authors: Kowalczyk Amanda , Meyer Wynn K , Partha Raghavendran , Mao Weiguang , Clark Nathan L , Chikina Maria 
Published: June 2019

AbstractMotivationWhen different lineages of organisms independently adapt to similar environments, selection often acts repeatedly upon the same genes, leading to signatures of convergent evolutionary rate shifts at these genes. With the increasing availability of genome sequences for organisms displaying a variety of convergent traits, the ability to identify genes with such convergent rate signatures would enable new insights into the molecular basis of these traits.ResultsHere we present the R package RERconverge, which tests for association between relative evolutionary rates of genes and the evolution of traits across a phylogeny. RERconverge can perform associations with binary and continuous traits, and it contains tools for visualization and enrichment analyses of association results.Availability and implementationRERconverge source code, documentation and a detailed usage walk-through are freely available at https://github.com/nclark-lab/RERconverge. Datasets for mammals, Drosophila and yeast are available at https://bit.ly/2J2QBnj.Supplementary informationSupplementary data are available at Bioinformatics online.
Hepatitis B virus X protein enhances the development of liver fibrosis and the expression of genes associated with epithelial-mesenchymal transitions and tumor progenitor cells
Authors: Ahodantin James , Lekbaby Bouchra , Bou Nader Myriam , Soussan Patrick , Kremsdorf Dina 
Published: June 2019

Abstract
The hepatitis B virus X protein (HBx) has pleiotropic biological effects, which underlies its potential role in cell transformation. However, its involvement in hepatic fibrosis remains unclear. In this study, we wanted to clarify, in vivo, the role of HBx protein in the development of liver fibrosis. Mice transgenic for the full-length HBx (FL-HBx) were used. To create liver fibrosis, FL-HBx transgenic and control mice were chronically exposed to carbon tetrachloride (CCl4). Modulation of the expression of proteins involved in matrix remodeling, hepatic metabolism and epithelial-mesenchymal transition (EMT) were investigated. In transgenic mice, FL-HBx expression potentiates CCl4-induced liver fibrosis with increased expression of proteins involved in matrix remodeling (Collagen1a, α-Sma, PdgfR-β, MMP-13). In FL-HBx transgenic mice, an increase in EMT was observed with a higher transcription of two inflammatory cytokines (TNF-α and TGF-β) and a decrease of glutamine synthetase expression level. This was associated with a sustained cell cycle and hepatocyte polyploidy alteration consistent with p38 and ERK1/2 overactivation, increase of PLK1 transcription, accumulation of SQSTM1/p62 protein and increase expression of Beclin-1. This correlates with a higher expression of tumor progenitor cell markers (AFP, Ly6D and EpCam), indicating a higher risk of progression from fibrosis to hepatocellular carcinoma (HCC) in the presence of FL-HBx protein. In conclusion, our results show that FL-HBx protein enhances the development of liver fibrosis and contributes to the progression of liver disease from chronic hepatitis to HCC.
Liquid chromatography tandem mass spectrometry for the quantification of steroid hormone profiles in blubber from stranded humpback whales (Megaptera novaeangliae)
Authors: Dalle Luche Greta , Bengtson Nash Susan , Kucklick John R , Mingramm Fletcher M J , Boggs Ashley S P 
Published: June 2019

AbstractMarine mammal blubber is known to have quantifiable concentrations of steroid hormones and is increasingly chosen as a matrix for the detection of these reproductive and stress biomarkers. Steroid hormones act through complex cascades, often in concert, yet studies conducted on cetaceans have rarely measured more than two steroids simultaneously. Due to the role of steroid hormones in multiple physiological processes, and variability in concentration among individuals, data on single compounds are often difficult to interpret. Here a liquid chromatography tandem mass spectrometry method for the simultaneous analyses of multiple steroid hormones in cetacean blubber was validated and applied to samples from 10 stranded humpback whales (Megaptera novaeangliae). Progesterone, 17α-hydroxyprogesterone, testosterone, androstenedione, oestrone, oestradiol, cortisone, cortisol, corticosterone and 11-deoxycorticosterone were reliably (relative standard deviation on six replicates <15%) and accurately (recovery of an amended sample between 70% and 120%) quantified, but not 11-deoxycortisol. With the exception of progesterone, testosterone, oestradiol and cortisol, these compounds were quantified for the first time in humpback whales. Given that blubber is frequently collected from free-swimming cetaceans in ongoing research programs, the technique developed here could substantially strengthen understanding and monitoring of the physiological condition of these species.
Self-reported Vision Impairment and Subjective Well-being in Older Adults: A Longitudinal Mediation Analysis
Authors: Xiang Xiaoling , Freedman Vicki A , Shah Khushali , Hu Rita X , Stagg Brian C , Ehrlich Joshua R 
Published: June 2019

Abstract

Background
Vision impairment (VI) in older adults is associated with declines in well-being. However, the pathways through which poor vision leads to declines in well-being have not been well-described. The purpose of this study was to determine whether activity limitations and social participation restrictions mediate the impact of self-reported VI on subjective well-being.

Methods
The National Health and Aging Trends Study (NHATS) is a nationally representative longitudinal study of Medicare beneficiaries 65 and older that includes detailed measures of the disablement process. A longitudinal mediation model was conceptualized linking self-reported VI and subjective well-being. Structural equation modeling was used to test the mediating effects of activity limitations and social participation restrictions while adjusting for relevant covariates.

Results
The final sample included 5,431 respondents. At baseline, 8.0% of Medicare beneficiaries had self-reported VI. Subjective well-being scores were significantly lower among respondents with self-reported VI (15.7; 95% confidence interval [CI]: 15.2, 16.2) compared with those without VI (17.6; 95% CI: 17.5, 17.7). Self-reported VI had a significant indirect effect on subjective well-being through limiting mobility (β = −0.04; 95% CI: −0.07, −0.03) and household activities (β = −0.05; 95% CI: −0.08, −0.03), but not self-care limitations (β = 0.0; 95% CI = 0.0, 0.0) or participation restrictions (β = 0.0; 95% CI = −0.01, 0.00). Total indirect effects from all mediation paths accounted for 42% of the effect of VI on well-being.

Conclusions
Mobility and household activity limitations are significant mediators that explain a considerable portion of the impact of poor vision on well-being. Interventions to promote successful accommodation may result in greater overall well-being for older adults with poor vision.
A Coordinated Multi-study Analysis of the Longitudinal Association Between Handgrip Strength and Cognitive Function in Older Adults
Authors: Zammit Andrea R , Piccinin Andrea M , Duggan Emily C , Koval Andriy , Clouston Sean , Robitaille Annie , Brown Cassandra L , Handschuh Philipp , Wu Chenkai , Jarry Valérie , Finkel Deborah , Graham Raquel B , Muniz-Terrera Graciela , Praetorius Björk Marcus , Bennett David , Deeg Dorly J , Johansson Boo , Katz Mindy J , Kaye Jeffrey , Lipton Richard B , Martin Mike , Pederson Nancy L , Spiro Avron , Zimprich Daniel , Hofer Scott M 
Published: June 2019

Abstract

Objective
Handgrip strength, an indicator of overall muscle strength, has been found to be associated with slower rate of cognitive decline and decreased risk for cognitive impairment and dementia. However, evaluating the replicability of associations between aging-related changes in physical and cognitive functioning is challenging due to differences in study designs and analytical models. A multiple-study coordinated analysis approach was used to generate new longitudinal results based on comparable construct-level measurements and identical statistical models and to facilitate replication and research synthesis.

Methods
We performed coordinated analysis on 9 cohort studies affiliated with the Integrative Analysis of Longitudinal Studies of Aging and Dementia (IALSA) research network. Bivariate linear mixed models were used to examine associations among individual differences in baseline level, rate of change, and occasion-specific variation across grip strength and indicators of cognitive function, including mental status, processing speed, attention and working memory, perceptual reasoning, verbal ability, and learning and memory. Results were summarized using meta-analysis.

Results
After adjustment for covariates, we found an overall moderate association between change in grip strength and change in each cognitive domain for both males and females: Average correlation coefficient was 0.55 (95% CI = 0.44–0.56). We also found a high level of heterogeneity in this association across studies.

Discussion
Meta-analytic results from nine longitudinal studies showed consistently positive associations between linear rates of change in grip strength and changes in cognitive functioning. Future work will benefit from the examination of individual patterns of change to understand the heterogeneity in rates of aging and health-related changes across physical and cognitive biomarkers.
An anti-RANKL treatment reduces muscle inflammation and dysfunction and strengthens bone in dystrophic mice
Authors: Hamoudi Dounia , Marcadet Laetitia , Piette Boulanger Antoine , Yagita Hideo , Bouredji Zineb , Argaw Anteneh , Frenette Jérôme 
Published: June 2019

AbstractDuchenne muscular dystrophy (DMD) is the most severe form of muscular dystrophy which leads to progressive muscle degeneration and inflammation. The receptor activator of nuclear factor NF-κB ligand (RANKL) and its receptor (RANK), which are expressed in bone and skeletal and cardiac muscles, form a signaling network upstream from nuclear factor-kappa B (NF-κB). We thus hypothesized that prolonged silencing RANKL/RANK signaling would significantly improve DMD. We showed that RANK and RANKL protein levels were increased in the microenvironment of myofibers of 5-month-old utrophin haploinsufficient mdx (mdx/utrn+/−) mice and that a 4 mg/kg dose of anti-RANKL antibody every 3 d for 28 days is optimal and more effective than 1 mg/kg every 3 d for improving the ex vivo maximum specific force (sP0) of dystrophic EDL muscles from mdx/utrn+/− mice. This functional improvement was associated with a reduction in muscle edema, damage, and fibrosis and a marked reduction in serum CK levels. The anti-RANKL treatment inhibited the NF-κB pathway, increased the proportion of anti-inflammatory and non-cytotoxic M2 macrophages, and reduced the number of centrally-nucleated myofibers and the frequency of small myofibers, suggesting that anti-RANKL inhibits the cycle of degeneration/regeneration in dystrophic mice. A three-point bending test showed that a 28-d anti-RANKL treatment increases the mechanical properties of bone in mdx/utrn+/− dystrophic mice. In conclusion, the anti-RANKL treatment protected against skeletal muscle dysfunctions while enhancing bone mechanical properties, filling two needs with one deed in the context of muscular dystrophy.
Low ivermectin use among 5- to 6-year-old children: observations from door-to-door surveys in onchocerciasis-endemic regions in Africa
Authors: Siewe Fodjo J N , Mubiru F , Ukaga C , Logora M Y , Mmbando B P , Mandro M , Njamnshi A K , Colebunders R 
Published: June 2019

Abstract
During door-to-door surveys in onchocerciasis-endemic regions in Africa, the age-specific ivermectin coverage in 29 722 individuals was assessed. Children 5–6 y of age had significantly lower coverage compared with older participants. Insufficient ivermectin intake among young children could prolong onchocerciasis elimination prospects, as they may serve as human reservoirs of Onchocerca volvulus; moreover, it increases the risk of developing onchocerciasis-associated epilepsy (OAE). The causes of the low ivermectin coverage observed among children 5–6 y of age need to be explored. Integrating ivermectin distribution into chemoprophylaxis strategies for other neglected diseases could increase coverage in a cost-effective manner.
The association between specific sports activities and sport performance following hip arthroscopy for femoroacetabular impingement syndrome: A secondary analysis of a cross-sectional cohort study including 184 athletes
Authors: Ishøi Lasse , Thorborg Kristian , Kraemer Otto , Hölmich Per 
Published: June 2019

Abstract
The main purpose of this secondary analysis was to compare the proportion of athletes with moderate-to-extreme difficulties in eight specific sport activities in athletes with optimal versus impaired sport performance after a hip arthroscopy for femoroacetabular impingement syndrome. Subjects were identified in a nationwide registry and invited to answer a return to sport and performance questionnaire, and the Copenhagen Hip and Groin Outcome Score Sport subscale investigating difficulties in eight specific sports activities (HAGOS sport items) as; none, mild, moderate, severe or extreme. Subjects were divided into two groups based on sport performance (optimal or impaired). The proportion of athletes with none-to-mild versus moderate-to-extreme difficulties in the eight specific sport activities was compared between groups. The association between difficulties in sport activities and sport performance were investigated using logistic regression analysis. One hundred and eighty-four athletes (31 athletes with optimal and 153 athletes with impaired sport performance) were included at a mean follow-up of 33.1 ± 16.3 months. Up to six athletes (<20%) with optimal sport performance had moderate-to-extreme difficulties in sport activities. Contrary, 43–108 athletes (28.1–70.6%) with impaired performance had moderate-to-extreme difficulties in sport activities. Furthermore, moderate-to-extreme difficulties in HAGOS sport items: ‘running as fast as you can’ and ‘kicking, skating etc.’ increased the odds (14.7 and 6.1 times, respectively) of having impaired sport performance. Many athletes with impaired sport performance reported moderate-to-extreme difficulties in sport activities, specifically moderate-to-extreme difficulties in ‘running as fast as you can’ and ‘kicking, skating etc.’ were associated with patients having impaired sport performance.
In search for drought-tolerant soybean: is the slow-wilting phenotype more than just a curiosity?
Authors: Kunert Karl , Vorster Barend J 
Published: June 2019

This article comments on:Ye H, Song L, Schapaugh WT, Ali MDL, Sinclair TR, Riar MK, Raymond RN, Li Y, Vuong T, Valliyodan B, Neto PA, Klepadlo M, Song Q, Shannon JG, Chen P, Nguyen HT. 2019. The importance of slow canopy wilting in drought tolerance in soybean, Journal of Experimental Botany 71, 642–652.
Cooling of hypernuclear compact stars: Hartree–Fock models and high-density pairing
Authors: Raduta Adriana R , Li Jia Jie , Sedrakian Armen , Weber Fridolin 
Published: June 2019

ABSTRACT
The thermal evolution of hypernuclear compact stars is studied for stellar models constructed on the basis of covariant density functional theory in Hartree and Hartree–Fock approximation. Parametrizations of both types are consistent with the astrophysical mass constraints on compact stars and available hypernuclear data. We discuss the differences of these density functionals and highlight the effects they have on the composition and on the cooling of hypernuclear stars. It is shown that hypernuclear stars computed with density functional models that have a low symmetry energy slope, L, are fairly consistent with the cooling data of observed compact stars. The class of stellar models based on larger L values gives rise to the direct Urca process at low densities, which leads to significantly faster cooling. We conjecture high-density pairing for protons and Λ’s in the P-wave channel and provide simple scaling arguments to obtain these gaps. As a consequence the most massive stellar models with masses 1.8 ≤ M/M⊙ ≤ 2 experience slower cooling by hyperonic dUrca processes which involve Λ’s and protons.