bluuebunny/crossref_metadata_2025_split huggingface dataset:
L’expression des procès spatiaux causatifs chez les apprenants francophones du chinois
Authors: Arslangul Arnaud , Hendriks Henriëtte , Hickmann Maya , Demagny Annie-Claude 
Published: January 2019

RésuméCette recherche, située dans le cadre proposé par Talmy (1985,1991,2000), analyse la façon dont des apprenants francophones du chinois langue étrangère (un groupe de niveau intermédiaire et un groupe de niveau avancé) expriment les procès spatiaux causatifs, en comparaison avec des locuteurs natifs du chinois et du français. La procédure utilisée est celle d’une analyse de corpus oraux produits à partir d’une description de séquences animées. Les réponses ont été étudiées au niveau du choix des informations exprimées, de la densité sémantique et de la façon dont les informations ont été encodées. Les résultats révèlent les phénomènes suivants : (1) les apprenants intermédiaires produisent des réponses qui sont en apparence proches de celles des locuteurs natifs du français, mais très différentes de celles des locuteurs natifs du chinois en tous points ; ils ont des difficultés à exprimer un nombre important d’informations dans un seul énoncé grammaticalement correct. En revanche, (2) les apprenants avancés s’éloignent du modèle de leur langue maternelle et montrent une progression nette vers la langue cible au niveau du choix et de la quantité d’informations exprimées ; cependant, les moyens linguistiques utilisés présentent encore des différences avec ceux des locuteurs natifs du chinois.
L’imparfait dans le langage de l’enfant
Authors: Parisse Christophe , de Pontonx Sophie , Morgenstern Aliyah 
Published: January 2019

RésuméPour faire référence à des événements passés ou futurs, l’enfant doit parler d’objets et de situations qui ne sont ni visibles ni audibles, mais mémorisées, imaginaires, ou désirées. L’imparfait est l’un des temps grammaticaux qui permet d’exprimer cette « déconnexion » avec l’ici et maintenant. Notre étude repose sur un suivi longitudinal de deux enfants en situation d’interactions familiales spontanées qui permet d’analyser l’usage des formes de l’imparfait par rapport au présent et au passé composé, en lien avec la déconnexion, l’aspect lexical des verbes utilisés, les situations d’emplois à la fois chez les enfants et les adultes du corpus. Les résultats de nos analyses montrent que les productions d’imparfait de l’enfant sont tardives mais qu’elles se révèlent fortement liées à la déconnexion et aux verbes d’état. Ceci différencie l’imparfait des autres temps analysés. Son usage serait la marque d’une nouvelle étape dans le développement langagier et cognitif de l’enfant.
Agreement/disagreement between caloric and video head impulse tests
Authors: Sinha Sujeet Kumar , Bansal Shalini , Neupane Anuj Kumar 
Published: January 2019

Introduction:
Neuropathies of the eighth nerve may be due to primary demyelination or axonal diseases or by mixed disorder of the two resulting in normal cochlear functioning and affected afferent neural conduction in the auditory pathway. Since vestibular nerve is a part of the eighth nerve, there is a possibility of vestibular nerve also getting affected in individuals with auditory neuropathy.

Aims and objectives:
The aim of the study was to understand the correlation between caloric and video head impulse test (vHIT) results in individuals with auditory neuropathy.

Method:
A total of three participants diagnosed as having auditory neuropathy, with no other otological or neurological problems were taken for the study. Bithermal caloric test and vHIT were administered for all the participants.

Results:
In two of the participants with auditory neuropathy spectrum disorder (ANSD), hypofunctional caloric responses were observed along with reduced vestibuloocular reflex (VOR) gain and refixation saccades. However, third participant had hypofunctional caloric response along with normal VOR gain and absent refixation saccade.

Discussions:
In the present study, the caloric responses were found to be hypofunctional in all three participants suggesting vestibular deficits. Presence of hypofunctional caloric responses reduced VOR gain and refixation saccades suggested greater involvement of vestibular deficit.

Conclusions:
Findings of the study suggest that in addition to the auditory system, the vestibular system may also be affected in ANSD.
T-cell receptor mimic (TCRm) antibody therapeutics against intracellular proteins
Authors: Xu Yixiang , Salazar Georgina To’a , Zhang Ningyan , An Zhiqiang 
Published: January 2019

AbstractT-cell receptor mimic (TCRm) antibodies combine the capacity of a T cell to target intracellular antigens with other capacities unique to antibodies. Neoantigens are abnormal proteins that arise as a consequence of somatic mutations. Technological advances promote the development of neoantigen-targeting therapies including TCRm antibody therapies. This review summarizes key characteristics of TCRm antibodies, in particular those targeting neoantigens, and further introduces discussion of obstacles that must be overcome to advance TCRm therapeutics.
The Value of Biodiversity as an Insurance Device
Authors: Augeraud‐Véron Emmanuelle , Fabbri Giorgio , Schubert Katheline 
Published: January 2019

AbstractThis paper presents a benchmark stochastic endogenous growth model of an agricultural economy. Producing food requires land, and increasing the share of total land devoted to farming mechanically reduces the share of land devoted to biodiversity conservation. However, safeguarding a greater number of species guarantees better ecosystem services, which in turn ensure lower volatility of agricultural productivity. The optimal conversion/conservation rule is explicitly characterized. Value of biodiversity is considered in its function of hedging against the volatility of agricultural production. Two aspects of biodiversity's value are examined. We first consider the total value of biodiversity as the welfare gain from biodiversity conservation, that is, the percentage increase in consumption that the society is willing to accept to give up the optimal level of biodiversity in favor of no biodiversity at all. We then consider the insurance value of biodiversity, extending the usual concepts to our stochastic dynamic framework, defining the insurance value of biodiversity as the change of the risk premium due to a marginal change in the level of biodiversity. To highlight the impact of risk on the optimal decision as in the value of biodiversity, we use the Epstein‐Zin‐Weil specification of preferences and represent preferences by a recursive utility function. This allows us to disentangle the effects of risk aversion and aversion to fluctuations. Thus, the preference for some rather uncertain outcomes and the propensity to smooth consumption over time are represented by two distinct parameters, and the effect of each of them are studied.
Varanto: variant enrichment analysis and annotation
Authors: Timonen Oskari , Särkkä Mikko , Fülöp Tibor , Mattsson Anton , Kekäläinen Juha , Paananen Jussi 
Published: January 2019

AbstractSummaryGenome-wide association studies (GWAS) aim to identify associations of genetic variations such as single-nucleotide polymorphisms (SNPs) to a specific trait or a disease. Identifying common themes such as pathways, biological processes and diseases associations is needed to further explore and interpret these results. Varanto is a novel web tool for annotating, visualizing and analyzing human genetic variations using diverse data sources. Varanto can be used to query a set of input variations, retrieve their associated variation and gene level annotations, perform annotation enrichment analysis and visualize the results.Availability and implementationVaranto web app is developed with R and implemented as Shiny app with PostgreSQL database and is freely available at http://bioinformatics.uef.fi/varanto. Source code for the tool is available at https://github.com/oqe/varanto.Supplementary informationSupplementary data are available at Bioinformatics online.
Tracing the ancestry of operons in bacteria
Authors: Nguyen Huy N , Jain Ashish , Eulenstein Oliver , Friedberg Iddo 
Published: January 2019

Abstract

Motivation
Complexity is a fundamental attribute of life. Complex systems are made of parts that together perform functions that a single component, or subsets of components, cannot. Examples of complex molecular systems include protein structures such as the F1Fo-ATPase, the ribosome, or the flagellar motor: each one of these structures requires most or all of its components to function properly. Given the ubiquity of complex systems in the biosphere, understanding the evolution of complexity is central to biology. At the molecular level, operons are classic examples of a complex system. An operon’s genes are co-transcribed under the control of a single promoter to a polycistronic mRNA molecule, and the operon’s gene products often form molecular complexes or metabolic pathways. With the large number of complete bacterial genomes available, we now have the opportunity to explore the evolution of these complex entities, by identifying possible intermediate states of operons.

Results
In this work, we developed a maximum parsimony algorithm to reconstruct ancestral operon states, and show a simple vertical evolution model of how operons may evolve from the individual component genes. We describe several ancestral states that are plausible functional intermediate forms leading to the full operon. We also offer Reconstruction of Ancestral Gene blocks Using Events or ROAGUE as a software tool for those interested in exploring gene block and operon evolution.

Availability and implementation
The software accompanying this paper is available under GPLv3 license on: https://github.com/nguyenngochuy91/Ancestral-Blocks-Reconstruction.

Supplementary information
Supplementary data are available at Bioinformatics online.
Children With Cystic Fibrosis Are Infected With Multiple Subpopulations of Mycobacterium abscessus With Different Antimicrobial Resistance Profiles
Authors: Shaw Liam P , Doyle Ronan M , Kavaliunaite Ema , Spencer Helen , Balloux Francois , Dixon Garth , Harris Kathryn A 
Published: January 2019

Abstract

Background
Children with cystic fibrosis (CF) can develop life-threatening infections of Mycobacterium abscessus. These present a significant clinical challenge, particularly when the strains involved are resistant to antibiotics. Recent evidence of within-patient subclones of M. abscessus in adults with CF suggests the possibility that within-patient diversity may be relevant for the treatment of pediatric CF patients.

Methods
We performed whole-genome sequencing (WGS) on 32 isolates of M. abscessus that were taken from multiple body sites of 2 patients with CF who were undergoing treatment at Great Ormond Street Hospital, United Kingdom, in 2015.

Results
We found evidence of extensive diversity within patients over time. A clustering analysis of single nucleotide variants revealed that each patient harbored multiple subpopulations, which were differentially abundant between sputum, lung samples, chest wounds, and pleural fluid. The sputum isolates did not reflect the overall within-patient diversity and did not allow for the detection of subclones with mutations previously associated with macrolide resistance (rrl 2058/2059). Some variants were present at intermediate frequencies before the lung transplants. The time of the transplants coincided with extensive variation, suggesting that this event is particularly disruptive for the microbial community, but the transplants did not clear the M. abscessus infections and both patients died as a result of these infections.

Conclusions
Isolates of M. abscessus from sputum do not always reflect the entire diversity present within the patient, which can include subclones with differing antimicrobial resistance profiles. An awareness of this phenotypic variability, with the sampling of multiple body sites in conjunction with WGS, may be necessary to ensure the best treatment for this vulnerable patient group.
Emergence of Low-level Delamanid and Bedaquiline Resistance During Extremely Drug-resistant Tuberculosis Treatment
Authors: Polsfuss Silke , Hofmann-Thiel Sabine , Merker Matthias , Krieger David , Niemann Stefan , Rüssmann Holger , Schönfeld Nicolas , Hoffmann Harald , Kranzer Katharina 
Published: January 2019

Abstract
Two new drugs, delamanid and bedaquiline, have recently been approved for treatment of multidrug-resistant and extensively drug-resistant (XDR) tuberculosis. Here, we report a case of clofazimine, bedaquiline, and low-level delamanid resistances acquired during treatment of a patient with XDR tuberculosis.
Relationship between changes in pericoronary adipose tissue attenuation and coronary plaque burden quantified from coronary computed tomography angiography
Authors: Goeller Markus , Tamarappoo Balaji K , Kwan Alan C , Cadet Sebastien , Commandeur Frederic , Razipour Aryabod , Slomka Piotr J , Gransar Heidi , Chen Xi , Otaki Yuka , Friedman John D , Cao J Jane , Albrecht Moritz H , Bittner Daniel O , Marwan Mohamed , Achenbach Stephan , Berman Daniel S , Dey Damini 
Published: January 2019

Abstract

Aims
Increased attenuation of pericoronary adipose tissue (PCAT) around the proximal right coronary artery (RCA) from coronary computed tomography angiography (CTA) has been shown to be associated with coronary inflammation and improved prediction of cardiac death over plaque features. Our aim was to investigate whether PCAT CT attenuation is related to progression of coronary plaque burden.

Methods and results
We analysed CTA studies of 111 stable patients (age 59.2 ± 9.8 years, 77% male) who underwent sequential CTA (3.4 ± 1.6 years between scans) with identical acquisition protocols. Total plaque (TP), calcified plaque (CP), non-calcified plaque (NCP), and low-density non-calcified plaque (LD-NCP) volumes and corresponding burden (plaque volume × 100%/vessel volume) were quantified using semi-automated software. PCAT CT attenuation (HU) was measured around the proximal RCA, the most standardized method for PCAT analysis. Patients with an increase in NCP burden (n = 51) showed an increase in PCAT attenuation, whereas patients with a decrease in NCP burden (n = 60) showed a decrease {4.4 [95% confidence interval (CI) 2.6–6.2] vs. −2.78 (95% CI −4.6 to −1.0) HU, P < 0.0001}. Changes in PCAT attenuation correlated with changes in the burden of NCP (r = 0.55, P < 0.001) and LD-NCP (r = 0.24, P = 0.01); but not CP burden (P = 0.3). Increased baseline PCAT attenuation ≥−75 HU was independently associated with increase in NCP (odds ratio 3.07, 95% CI 1.4–7.0; P < 0.008) and TP burden on follow-up CTA.

Conclusion
PCAT attenuation measured from routine CTA is related to the progression of NCP and TP burden. This imaging biomarker may help to identify patients at increased risk of high-risk plaque progression and allow monitoring of beneficial changes from medical therapy.
Whole Stand Volume and Green Weight Equations for Loblolly Pine in the Western Gulf Region of the United States through Age 15
Authors: Gallagher Derrick A , Bullock Bronson P , Montes Cristian R , Kane Michael B 
Published: January 2019

AbstractThree whole stand equations were evaluated for best prediction performance of loblolly pine volume and green weight in three physiographic regions of the Western Gulf through age 15 using remeasured permanent research plots from a spacing study. The equations evaluated are two nonlinear forms of the Schumacher yield equation that predict yield from dominant height, stand basal area, and age with or without stand tree density, and a logistic parameterization of the Chapman–Richards equation that uses only basal area and age. The nonlinear form of the Schumacher yield equations (Equations 2 and 3) performed better than the Chapman–Richards model (Equation 4), indicating a more appropriate mathematical model to describe forest yield. The sixfold cross-validation residual standard error for volume prediction in the Lower Coastal Plain, Upper Coastal Plain, and Interior Flatwoods was 109, 179, and 71 cubic feet per acre, respectively. The residual standard error of green weight prediction for the Lower Coastal Plain, Upper Coastal Plain, and Interior Flatwoods was 4, 2, and 3 tons per acre, respectively. The presented whole stand yield models provide physiographic region-specific estimates of yield for genetically improved loblolly pine under intensive management regimes.
Metformin use and risk of cancer in patients with type 2 diabetes: a cohort study of primary care records using inverse probability weighting of marginal structural models
Authors: Farmer Ruth E , Ford Deborah , Mathur Rohini , Chaturvedi Nish , Kaplan Rick , Smeeth Liam , Bhaskaran Krishnan 
Published: January 2019

Abstract

Background
Previous studies provide conflicting evidence on whether metformin is protective against cancer. When studying time-varying exposure to metformin, covariates such as body mass index (BMI) and glycated haemoglobin (HbA1c) may act as both confounders and causal pathway variables, and so cannot be handled adequately by standard regression methods. Marginal structural models (MSMs) with inverse probability of treatment weights (IPTW) can correctly adjust for such confounders. Using this approach, the main objective of this study was to estimate the effect of metformin on cancer risk compared with risk in patients with T2DM taking no medication.

Methods
Patients with incident type 2 diabetes (T2DM) were identified in the Clinical Practice Research Datalink (CPRD), a database of electronic health records derived from primary care in the UK. Patients entered the study at diabetes diagnosis or the first point after this when they had valid HbA1c and BMI measurements, and follow-up was split into 1-month intervals. Logistic regression was used to calculate IPTW; then the effect of metformin on all cancers (including and excluding non-melanoma skin cancer) and breast, prostate, lung, colorectal and pancreatic cancers was estimated in the weighted population.

Results
A total of 55 629 T2DM patients were alive and cancer-free at their study entry; 2530 people had incident cancer during a median follow-up time of 2.9 years [interquartile range (IQR) 1.3–5.4 years]. Using the MSM approach, the hazard ratio (HR) for all cancers, comparing treatment with metformin with no glucose-lowering treatment, was 1.02 (0.88–1.18). Results were robust to a range of sensitivity analyses and remained consistent when estimating the treatment effect by length of exposure. We also found no evidence of a protective effect of metformin on individual cancer outcomes.

Conclusions
We find no evidence that metformin has a causal association with cancer risk.
Changes in millennial adolescent mental health and health-related behaviours over 10 years: a population cohort comparison study
Authors: Patalay Praveetha , Gage Suzanne H 
Published: January 2019

Abstract

Background
There is evidence that mental health problems are increasing and substance use behaviours are decreasing. This paper aimed to investigate recent trends in mental ill health and health-related behaviours in two cohorts of UK adolescents in 2005 and 2015.

Methods
Prevalences in mental health (depressive symptoms, self-harm, anti-social behaviours, parent-reported difficulties) and health-related behaviours (substance use, weight, weight perception, sleep, sexual intercourse) were examined at age 14 in two UK birth cohorts; Avon Longitudinal Study of Parents and Children (ALSPAC, N = 5627, born 1991–92) and Millennium Cohort Study (MCS, N = 11 318, born 2000–02). Prevalences and trend estimates are presented unadjusted and using propensity score matching and entropy balancing to account for differences between samples.

Results
Depressive symptoms (9% to 14.8%) and self-harm (11.8% to 14.4%) were higher in 2015 compared with 2005. Parent-reported emotional difficulties, conduct problems, hyperactivity and peer problems were higher in 2015 compared with 2005 (5.7–8.9% to 9.7–17.7%). Conversely, substance use (tried smoking, 9.2% to 2.9%; tried alcohol, 52.1% to 43.5%, cannabis, 4.6% to 3.9%), sexual activity (2% to 0.9%) and anti-social behaviours (6.2–40.1% to 1.6–27.7%) were less common or no different. Adolescents in 2015 were spending less time sleeping (&lt;8 h 5.7% to 11.5%), had higher body mass index (BMI) (obese, 3.8% to 7.3%) and a greater proportion perceived themselves as overweight (26.5% to 32.9%). The findings should be interpreted bearing in mind limitations in ability to adequately harmonize certain variables and account for differences in attrition rates and generalizability of the two cohorts.

Conclusions
Given health-related behaviours are often cited as risk factors for poor mental health, our findings suggest relationships between these factors might be more complex and dynamic in nature than currently understood. Substantial increases in mental health difficulties, BMI and poor sleep-related behaviours highlight an increasing public health challenge.
Evaluation of a mandatory phishing training program for high-risk employees at a US healthcare system
Authors: Gordon William J , Wright Adam , Glynn Robert J , Kadakia Jigar , Mazzone Christina , Leinbach Elizabeth , Landman Adam 
Published: January 2019

Abstract

Objective
The study sought to understand the impact of a phishing training program on phishing click rates for employees at a single, anonymous US healthcare institution.

Materials and Methods
We stratified our population into 2 groups: offenders and nonoffenders. Offenders were defined as those that had clicked on at least 5 simulated phishing emails and nonoffenders were those that had not. We calculated click rates for offenders and nonoffenders, before and after a mandatory training program for offenders was implemented.

Results
A total of 5416 unique employees received all 20 campaigns during the intervention period; 772 clicked on at least 5 emails and were labeled offenders. Only 975 (17.9%) of our set clicked on 0 phishing emails over the course of the 20 campaigns; 3565 (65.3%) clicked on at least 2 emails. There was a decrease in click rates for each group over the 20 campaigns. The mandatory training program, initiated after campaign 15, did not have a substantial impact on click rates, and the offenders remained more likely to click on a phishing simulation.

Discussion
Phishing is a common threat vector against hospital employees and an important cybersecurity risk to healthcare systems. Our work suggests that, under simulation, employee click rates decrease with repeated simulation, but a mandatory training program targeted at high-risk employees did not meaningfully decrease the click rates of this population.

Conclusions
Employee phishing click rates decrease over time, but a mandatory training program for the highest-risk employees did not decrease click rates when compared with lower-risk employees.