bluuebunny/crossref_metadata_2025_split huggingface dataset:
Foreign language teachers’ intercultural competence and legitimacy during an international teaching experience
Authors: Bournot-Trites Monique , Zappa-Hollman Sandra , Spiliotopoulos Valia 
Published: October 2018

AbstractGiven the increase in international mobility opportunities for educators, analyzing how the experience of studying and teaching abroad benefits teachers is of utmost importance in a globalized educational system. UsingDeardorff’s (2009)model of intercultural competence (IC), this study explores how a group of recently graduated Canadian foreign language teachers benefitted from a four-month international teaching experience (ITE). The following questions guided this investigation: In which ways did the ITE contribute to the participants’ IC development? How did the ITE affect the participants’ professional identity and sense of legitimacy? Data were collected, triangulated, and interpreted using thematic content data analysis. This study provides illustrations of the participants’ IC development across all components on Deardorff’s IC model, showing that properly scaffolded ITEs afforded the participants opportunities to develop their IC. The findings also show that the ITE of living and teaching abroad positively impacted their professional identity and feeling of legitimacy.
Acquisition of formulaic sequences in a study abroad context
Authors: Quan Tracy 
Published: October 2018

AbstractResearch (e.g.,Wood, 2010a) suggests that study abroad (SA) and the use of formulaic language (FL), or sequences of words that tend to go together, aid L2 oral fluency. Nonetheless, there is conflicting evidence regarding whether quantity of L2 use abroad is a predictor of language outcomes. This article examines the acquisition of FL by US L2 learners of Spanish (n = 11) who studied abroad in Spain. The study measures the temporal fluency variables and the formula/run ratio of narrative retell tasks pre- and post-SA by L2 learners and native Spanish speakers. The findings indicate that regardless of program type and length, learners produce more FL post-SA, but they are still far from target-like usage. Moreover, participants’ mean length of run is directly related to the formula/run ratio. Lastly, an analysis of language use shows no direct relationship between L2 use abroad and oral fluency outcomes.
Interpreter-mediated investigative interviews with minors
Authors: Böser Ursula , LaRooy David 
Published: October 2018

Abstract
When information is elicited from children in a criminal context, both their ability and willingness to disclose is at stake. In
law, the communicative vulnerability of children is manifest in forensic protocols for interviewing children. These are designed
to retrieve information in a child-aware fashion, as well as to produce evidence with sufficient integrity to stand up under the
scrutiny of the criminal process. This article will consider some of the added challenges of interpreter-mediated interviews for
minors. Drawing on research into monolingual child interviewing, the article proposes how some of the interpreting related aspects
of this challenge may be addressed through the adaptation of elements of reflexive coordination in the widely used NICHD child
interviewing protocol. The authors call for the data-based testing of these adaptations and suggests that modifications of
institutional speech genres for bilingual use may be a component of mainstreaming public service interpreting.
ParGenes: a tool for massively parallel model selection and phylogenetic tree inference on thousands of genes
Authors: Morel Benoit , Kozlov Alexey M , Stamatakis Alexandros 
Published: October 2018

Abstract

Motivation
Coalescent- and reconciliation-based methods are now widely used to infer species phylogenies from genomic data. They typically use per-gene phylogenies as input, which requires conducting multiple individual tree inferences on a large set of multiple sequence alignments (MSAs). At present, no easy-to-use parallel tool for this task exists. Ad hoc scripts for this purpose do not only induce additional implementation overhead, but can also lead to poor resource utilization and long times-to-solution. We present ParGenes, a tool for simultaneously determining the best-fit model and inferring maximum likelihood (ML) phylogenies on thousands of independent MSAs using supercomputers.

Results
ParGenes executes common phylogenetic pipeline steps such as model-testing, ML inference(s), bootstrapping and computation of branch support values via a single parallel program invocation. We evaluated ParGenes by inferring &gt; 20 000 phylogenetic gene trees with bootstrap support values from Ensembl Compara and VectorBase alignments in 28 h on a cluster with 1024 nodes.

Availability and implementation
GNU GPL at https://github.com/BenoitMorel/ParGenes.

Supplementary information
Supplementary material is available at Bioinformatics online.
PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files
Authors: Zhang Chi , Dong Shan-Shan , Xu Jun-Yang , He Wei-Ming , Yang Tie-Lin 
Published: October 2018

Abstract

Motivation
Linkage disequilibrium (LD) decay is of great interest in population genetic studies. However, no tool is available now to do LD decay analysis from variant call format (VCF) files directly. In addition, generation of pair-wise LD measurements for whole genome SNPs usually resulting in large storage wasting files.

Results
We developed PopLDdecay, an open source software, for LD decay analysis from VCF files. It is fast and is able to handle large number of variants from sequencing data. It is also storage saving by avoiding exporting pair-wise results of LD measurements. Subgroup analyses are also supported.

Availability and implementation
PopLDdecay is freely available at https://github.com/BGI-shenzhen/PopLDdecay.
Gut Dysbiosis With Bacilli Dominance and Accumulation of Fermentation Products Precedes Late-onset Sepsis in Preterm Infants
Authors: Graspeuntner S , Waschina S , Künzel S , Twisselmann N , Rausch T K , Cloppenborg-Schmidt K , Zimmermann J , Viemann D , Herting E , Göpel W , Baines J F , Kaleta C , Rupp J , Härtel C , Pagel J 
Published: October 2018

Abstract

Background
Gut dysbiosis has been suggested as a major risk factor for the development of late-onset sepsis (LOS), a main cause of mortality and morbidity in preterm infants. We aimed to assess specific signatures of the gut microbiome, including metabolic profiles, in preterm infants <34 weeks of gestation preceding LOS.

Methods
In a single-center cohort, fecal samples from preterm infants were prospectively collected during the period of highest vulnerability for LOS (days 7, 14, and 21 of life). Following 16S rRNA gene profiling, we assessed microbial community function using microbial metabolic network modeling. Data were adjusted for gestational age and use of probiotics.

Results
We studied stool samples from 71 preterm infants with LOS and 164 unaffected controls (no LOS/necrotizing enterocolitis). In most cases, the bacteria isolated in diagnostic blood culture corresponded to the genera in the gut microbiome. LOS cases had a decelerated development of microbial diversity. Before onset of disease, LOS cases had specific gut microbiome signatures with higher abundance of Bacilli (specifically coagulase-negative Staphylococci) and a lack of anaerobic bacteria. In silico modeling of bacterial community metabolism suggested accumulation of the fermentation products ethanol and formic acid in LOS cases before the onset of disease.

Conclusions
Intestinal dysbiosis preceding LOS is characterized by an accumulation of Bacilli and their fermentation products and a paucity of anaerobic bacteria. Early microbiome and metabolic patterns may become a valuable biomarker to guide individualized prevention strategies of LOS in highly vulnerable populations.
Declining Incident Dementia Rates Across Four Population-Based Birth Cohorts
Authors: Sullivan Kevin J , Dodge Hiroko H , Hughes Tiffany F , Chang Chung-Chou H , Zhu Xinmei , Liu Anran , Ganguli Mary 
Published: October 2018

Abstract

Background
Incidence rates of dementia appear to be declining in high-income countries according to several large epidemiological studies. We aimed to describe declining incident dementia rates across successive birth cohorts in a U.S. population-based sample and to explore the influences of sex and education on these trends.

Methods
We pooled data from two community-sampled prospective cohort studies with similar study aims and contiguous sampling regions: the Monongahela Valley Independent Elders Survey (1987–2001) and the Monongahela-Youghiogheny Healthy Aging Team (2006–Ongoing). We identified four decade-long birth cohorts spanning birth years 1902–1941. In an analysis sample of 3,010 participants (61% women, mean baseline age = 75.7 years, mean follow-up = 7.1 years), we identified 257 cases of incident dementia indicated by a Clinical Dementia Rating of 1.0 or higher. We used Poisson regression to model incident dementia rates by birth cohort, age, sex, education, and interactions of Sex × Cohort and Sex × Education. We further examined whether cohort effects varied by education, testing a Cohort × Education interaction and stratifying the models by education.

Results
Compared to the earliest birth cohort (1902–1911), each subsequent cohort had a significantly lower incident dementia rate (1912–1921: incidence rate ratio [IRR] = 0.655, 95% confidence interval [95% CI] = 0.477–0.899; 1922–1931: IRR = 0.387, 95% CI = 0.265–0.564; 1932–1941: IRR = 0.233, 95% CI = 0.121–0.449). We observed no significant interactions of either sex or education with birth cohort.

Conclusions
A decline in incident dementia rates was observed across successive birth cohorts independent of sex, education, and age.
Space astrometry of the very massive ∼150 M⊙ candidate runaway star VFTS682
Authors: Renzo M , de Mink S E , Lennon D J , Platais I , van der Marel R P , Laplace E , Bestenlehner J M , Evans C J , Hénault-Brunet V , Justham S , de Koter A , Langer N , Najarro F , Schneider F R N , Vink J S 
Published: October 2018

ABSTRACT
How very massive stars form is still an open question in astrophysics. VFTS682 is among the most massive stars known, with an inferred initial mass of ≳$150\,\text{M}_\odot$. It is located in 30 Doradus at a projected distance of 29 pc from the central cluster R136. Its apparent isolation led to two hypotheses: either it formed in relative isolation or it was ejected dynamically from the cluster. We investigate the kinematics of VFTS682 as obtained by Gaia and Hubble Space Telescope astrometry. We derive a projected velocity relative to the cluster of $38\pm 17{\, \mathrm{km\ s^{-1}}}$ (1σ confidence interval). Although the error bars are substantial, two independent measures suggest that VFTS682 is a runaway ejected from the central cluster. This hypothesis is further supported by a variety of circumstantial clues. The central cluster is known to harbour other stars more massive than $150\, \text{M}_\odot$ of similar spectral type and recent astrometric studies on VFTS16 and VFTS72 provide direct evidence that the cluster can eject some of its most massive members, in agreement with theoretical predictions. If future data confirm the runaway nature, this would make VFTS682 the most massive runaway star known to date.
Emergence of Kaposi’s Sarcoma Herpesvirus-Associated Complications Following Corticosteroid Use in TB-IRIS
Authors: Manion Maura , Uldrick Thomas , Polizzotto Mark N , Sheikh Virginia , Roby Gregg , Lurain Kathryn , Metzger Dorinda , Mican JoAnn M , Pau Alice , Lisco Andrea , Laidlaw Elizabeth , Hammoud Dima A , Whitby Denise , Yarchoan Robert , Sereti Irini 
Published: October 2018

AbstractCorticosteroid use was associated with development of Kaposi’s sarcoma or multicentric Castleman disease in 3 patients with mycobacterial immune reconstitution inflammatory syndrome (IRIS) treated with corticosteroids. Monitoring for development of Kaposi’s sarcoma and alternative treatment may be beneficial for patients with IRIS, especially in the presence of preexisting co-infection with Kaposi’s sarcoma–associated herpesvirus.
Clinical Validation of a Commercial LAMP Test for Ruling out Malaria in Returning Travelers: A Prospective Diagnostic Trial
Authors: Cheaveau James , Nguyen Hong , Chow Barbara , Marasinghe Dewdunee , Mohon Abu Naser , Yuan Hong , Viana Gisele , van Schalkwyk Donelly , Church Deirdre , Chan Wilson , Pillai Dylan R 
Published: October 2018

Abstract
The mainstay of malaria diagnosis relies on rapid diagnostic tests (RDTs) and microscopy, both of which lack analytical sensitivity. This leads to repeat testing to rule out malaria. A prospective diagnostic trial of the Meridian illumigene Malaria assay (loop-mediated isothermal amplification [LAMP]) was conducted comparing it with reference microscopy and RDTs (BinaxNOW Malaria) in returning travelers between June 2017 and January 2018. Returning travelers with signs and symptoms of malaria were enrolled in the study. RDTs, microscopy, and LAMP assays were performed simultaneously. A total of 298 patients (50.7% male; mean age, 32.5 years) were enrolled, most visiting friends and relatives (43.3%), presenting with fever (88.9%), not taking prophylaxis (82.9%), and treated as outpatients (84.1%). In the prospective arm (n = 348), LAMP had a sensitivity of 98.1% (95% confidence interval [CI], 90.0%–100%) and a specificity of 97.6% (95% CI, 95.2%–99.1%) vs microscopy. After discrepant resolution with real-time polymerase chain reaction, LAMP had a sensitivity of 100% (95% CI, 93.7%–100%) and a specificity of 100% (95% CI, 98.7%–100%) vs microscopy. After discrepant resolution, RDTs had a sensitivity of 83.3% (95% CI, 58.6%–96.4%) and a specificity of 96.2% (95% CI, 93.2%–98.1%) vs microscopy. When including retrospective specimens (n = 377), LAMP had a sensitivity of 98.8% (95% CI, 93.2%–100%) and a specificity of 97.6% (95% CI, 95.2%–99.1%) vs microscopy, and after discrepant resolution of this set, LAMP had a sensitivity of 100% (95% CI, 95.8%–100%) and a specificity of 100% (95% CI, 98.7%–100%). A cost-benefit analysis of reagents and labor suggests savings of up to USD$13 per specimen using a novel algorithm with LAMP screening.
Ulrich modules over Cohen–Macaulay local rings with minimal multiplicity
Authors: Kobayashi Toshinori , Takahashi Ryo 
Published: October 2018

AbstractLet R be a Cohen–Macaulay local ring. In this paper, we study the structure of Ulrich R-modules mainly in the case where R has minimal multiplicity. We explore generation of Ulrich R-modules and clarify when the Ulrich R-modules are precisely the syzygies of maximal Cohen–Macaulay R-modules. We also investigate the structure of Ulrich R-modules as an exact category.
Oral midodrine is comparable to albumin infusion in cirrhotic patients with refractory ascites undergoing large-volume paracentesis: results of a pilot study
Authors: Yosry Ayman , Soliman Zeinab A. , Eletreby Rasha , Hamza Iman , Ismail Alaa , Elkady Mohammad A. 
Published: October 2018

Background and aims
Albumin infusion reduces the incidence of postparacentesis circulatory dysfunction among patients with cirrhosis and tense ascites compared with no treatment. Less costly treatment alternatives such as vasoconstrictors have been investigated, but the results are controversial. Midodrine, an oral α1-adrenergic agonist, increases effective circulating blood volume and renal perfusion by increasing systemic and splanchnic blood pressure. Our aim is to assess whether or not morbidity in terms of renal dysfunction, hyponatremia, systemic, or portal hemodynamics derangement or mortality differed in patients receiving albumin versus midodrine.

Patients and methods
Seventy-five patients with cirrhosis and refractory ascites were randomized to receive albumin infusion, oral midodrine for 2 days, or oral midodrine for 30 days after therapeutic large volume paracentesis (LVP). The primary endpoints were development of renal impairment or hyponatremia, change in systemic and portal hemodynamics, cost, and mortality in the short-term and long-term follow-up.

Results
No significant difference was found between groups in the development of renal impairment, hyponatremia, or mortality 6 and 30 days after LVP. A significant increase in 24-h urine sodium excretion was noted in the midodrine 30-day group. Renal perfusion improved significantly with the midodrine intake for 30 days only. The cost of midodrine therapy was significantly lower than albumin.

Conclusion
Midodrine is as effective as albumin in reducing morbidity and mortality among patients with refractory ascites undergoing LVP at a significantly lower cost. Long-duration midodrine intake can be more useful than shorter duration intake in terms of improvement of renal perfusion and sodium excretion.
Implications for Breast Cancer Restaging Based on the 8th Edition AJCC Staging Manual
Authors: Plichta Jennifer K. , Ren Yi , Thomas Samantha M. , Greenup Rachel A. , Fayanju Oluwadamilola M. , Rosenberger Laura H. , Hyslop Terry , Hwang E. Shelley 
Published: October 2018

Objective:
We assessed the changes that have resulted from the latest breast cancer staging guidelines and the potential impact on prognosis.

Background:
Contemporary data suggest that combining anatomic staging and tumor biology yields a predictive synergy for determining breast cancer prognosis. This forms the basis for the American Joint Committee on Cancer's (AJCC) Staging Manual, 8th edition. We assessed the changes that have resulted from the new staging guidelines and the potential impact on prognosis.

Methods:
Women with stages I to III breast cancer from 2010 to 2014 in the National Cancer Data Base were pathologically staged according to the 7th and 8th editions of the AJCC Staging Manual. Patient characteristics and restaging outcomes were summarized. Unadjusted overall survival (OS) was estimated, and differences were assessed. Cox proportional-hazards models were utilized to estimate the adjusted association of stage with OS.

Results:
After restaging the 493,854 women identified, 6.8% were upstaged and 29.7% were downstaged. The stage changes varied by tumor histology, receptor status, tumor grade, and Oncotype DX scores (all P < 0.0001). Applying the 8th edition criteria yielded an incremental reduction in survival for each increase in stage, which was not consistently seen in the 7th edition. In a subgroup analysis based on hormone receptor (HR) status, those with stages II and III, and HR− disease had a worse OS than those with HR+ disease.

Conclusions:
Applying the 8th edition staging criteria resulted in a stage change for >35% of patients diagnosed with invasive breast cancer and refined OS estimates. Overall, the transition to the 8th edition is expected to better drive clinical care, treatment recommendations, and future research.
Alcohol Use Thresholds for Identifying Alcohol-related Problems Before and Following Roux-en-Y Gastric Bypass
Authors: White Gretchen E. , Courcoulas Anita P. , Richardson Gale A. , Mair Christina , King Wendy C. 
Published: October 2018

Objective:
The aim of this study was to determine the sensitivity and specificity of potential thresholds of alcohol use for identifying alcohol-related problems in women post-Roux-en-Y gastric bypass (RYGB).

Background:
Despite evidence that RYGB alters alcohol pharmacokinetics and is associated with an increased risk for alcohol-related problems, the level of alcohol use that should prompt further screening for alcohol-related problems following RYGB is unclear.

Methods:
The Longitudinal Assessment of Bariatric Surgery-2 is a prospective cohort study. Before surgery and annually for ≤7 years following surgery, participants completed the 10-item Alcohol Use Disorder Identification Test (AUDIT), which assesses past-year frequency and quantity of alcohol, frequency of consuming ≥6 drinks, and alcohol-related problems (ie, symptoms of alcohol dependence and/or alcohol-related harm). The AUDIT-Consumption (AUDIT-C) score was determined from the first 3 AUDIT items.

Results:
Post-RYGB, 835 women reported current drinking at 1 or more annual assessment(s). Compared with higher frequency thresholds, drinking ≥2 times/month had the highest combined sensitivity (85.3%) and specificity (61.4%) for identifying alcohol-related problems. Compared with higher quantity thresholds, drinking ≥3 drinks/drinking day had the highest combined sensitivity (64.2%) and specificity (87.2%). An AUDIT-C score ≥3, versus other thresholds, had the highest combined sensitivity (76.4%) and specificity (81.6%).

Conclusion:
The sensitivity and specificity of these thresholds indicate assessment of alcohol consumption alone may be inadequate for identifying women at risk for alcohol-related problems post-RYGB. Additional screening tools for alcohol-related problems, which assess symptoms of alcohol-related problems, should be conducted in this population.
Classifying cold stress responses of inbred maize seedlings using RGB imaging
Authors: Enders Tara A. , St. Dennis Susan , Oakland Justin , Callen Steven T. , Gehan Malia A. , Miller Nathan D. , Spalding Edgar P. , Springer Nathan M. , Hirsch Cory D. 
Published: October 2018

AbstractIncreasing the tolerance of maize seedlings to low temperature episodes could mitigate the effects of increasing climate variability on yield. To aid progress toward this goal, we established a growth chamber-based system for subjecting seedlings of 40 maize inbred genotypes to a defined, temporary cold stress while collecting digital profile images over a 9-day time course. Image analysis performed with PlantCV software quantified shoot height, shoot area, 14 other morphological traits, and necrosis identified by color analysis. Hierarchical clustering of changes in growth rates of morphological traits and quantification of leaf necrosis over two time intervals resulted in three clusters of genotypes, which are characterized by unique responses to cold stress. For any given genotype, the set of traits with similar growth rates is unique. However, the patterns among traits are different between genotypes. Cold sensitivity was not correlated with the latitude where the inbred varieties were released suggesting potential further improvement for this trait. This work will serve as the basis for future experiments investigating the genetic basis of recovery to cold stress in maize seedlings.