bluuebunny/crossref_metadata_2025_split huggingface dataset:
CALL in ISLA
Authors: Leow Ronald P. , Cerezo Luis , Caras Allison , Cruz Gorky 
Published: February 2019

Abstract
Despite the current curricular push for hybridization in language programs, research on ISLA provides little guidance as to what and how syllabus content can be migrated online. Cerezo, Caras, and Leow (2016) recently showed that videogames using guided induction (GI) can successfully promote robust learning outcomes and deep processing of a complex L2 grammatical structure, Spanish gustar constructions. This study addressed Cerezo et al.’s various limitations by comparing the effects of two videogame versions (GI vs. deductive instruction or DI) on both learning outcomes and processes of a lexically-driven, L2 form (Spanish para and por prepositions). Different from Cerezo et al. (2016), results showed no significant edge of GI over DI, suggesting that type of linguistic item might moderate the effectiveness of GI and that “one size may not fit all” in the hybridization of syllabus content. Beyond pedagogical and curricular implications, our discussion also focuses on the advantages and challenges of incorporating CALL in ISLA research.
Lexical development in the writing of intensive English program students1
Authors: Juffs Alan 
Published: February 2019

Abstract
This paper focuses on vocabulary development in intensive English program (IEP) students, comparing free writing data from an IEP to previous research in more controlled contexts. These free writing data derive from writing assignments collected from students with three language backgrounds: Arabic (n = 22), Chinese (n = 20) and Korean (n = 19), who studied at the intermediate and subsequently the advanced levels of an IEP in the USA. The main finding was that a purely text-based measure of diversity, vocD, did not capture gains in lexical development, whereas a measure of lexical sophistication, Advanced Guiraud (AG), did show measureable improvement. Discussion focuses on a more theoretically complex conceptualization of lexical development, how experimental methods compare with ‘messy’ classroom corpus data, and the problem of text length. Specific pedagogical recommendations include more focus more on lexical quality (Perfetti & Hart, 2002) and words at lower frequency bands (3000–9000).
The group in the self
Authors: Calzada Pérez María 
Published: February 2019

Abstract
Drawing on theoretical approaches to personal/group behaviour, and informed by Michael Hoey’s priming theory, this paper presents a corpus-assisted discourse study of European Parliament interventions from 2004 to 2011. The study aims to identify the group in the self and the various selves in the individual. For the analysis, three corpora from the European Comparable and Parallel Corpus Archive are explored: EP_EN (with EP interventions: 26,959,446 tokens), HC (with House of Commons interventions: 70,567,728), and SandD_david_martin (with member of European Parliament – MEP – David Martin’s interventions: 116,781). The main tool of analysis is the keyword, as generated by WordSmith 7.0. The analysis proceeds in three stages: stage 1, where the EP_EN and HC wordlists are compared, resulting in EP key priming; stage 2, where the SandD_david_martin and HC wordlists are compared, exposing David Martin’s idiosyncratic productions; and stage 3, where the EP_EN and SandD_david_martin keyword lists are manually compared, leading to the identification of EP priming in David Martin’s interventions.
Home care reimbursement for intravenous ganciclovir therapy
Authors: Mozaffari Essy , Sullivan Sean D. 
Published: February 2019

Variability in reimbursement for home i.v. ganciclovir therapy among three types of payers was investigated.
A survey was developed to estimate reimbursement for drug and medical supplies and nursing services associated with preparing i.v. ganciclovir and administering it to persons with cytomegalovirus (CMV)-associated retinitis in the home care setting. The questionnaire was mailed to 45 home health care agencies and 11 nursing agencies.
Of the 56 surveys mailed, 26 (46%) were returned and considered usable. Of the 26 respondents, 22 were home health care companies, 4 were nursing ageiicies, 22 served patients covered by managed care or state assistance that reimbursed on a per diem trasis, and 9 did not provide care to fee-for-service patients. The mean total daily-reimbursement rate (for ganciclovir, supplies, and nursing services) from managed care per diem plans was $137.69 per patient, compared with $I29.18 from fee-for-service plans and $72.68 from state assistance per diem plans. The dissimilarity may have been due to geographic variations in reimbursement and different mechanisms of reimbursement.
Providers of home i.v. ganciclovir therapy for persons with CMV retinitis received the highest tnean total daily reimbursement from managed care per diem plans, followed by fee-for-service plans and state assistance per diem plans.
SPIM workflow manager for HPC
Authors: Kožusznik Jan , Bainar Petr , Klímová Jana , Krumnikl Michal , Moravec Pavel , Svatoň Václav , Tomančák Pavel 
Published: February 2019

Abstract

Summary
Here we introduce a Fiji plugin utilizing the HPC-as-a-Service concept, significantly mitigating the challenges life scientists face when delegating complex data-intensive processing workflows to HPC clusters. We demonstrate on a common Selective Plane Illumination Microscopy image processing task that execution of a Fiji workflow on a remote supercomputer leads to improved turnaround time despite the data transfer overhead. The plugin allows the end users to conveniently transfer image data to remote HPC resources, manage pipeline jobs and visualize processed results directly from the Fiji graphical user interface.

Availability and implementation
The code is distributed free and open source under the MIT license. Source code: https://github.com/fiji-hpc/hpc-workflow-manager/, documentation: https://imagej.net/SPIM_Workflow_Manager_For_HPC.

Supplementary information
Supplementary data are available at Bioinformatics online.
Nucleotide Archival Format (NAF) enables efficient lossless reference-free compression of DNA sequences
Authors: Kryukov Kirill , Ueda Mahoko Takahashi , Nakagawa So , Imanishi Tadashi 
Published: February 2019

Abstract

Summary
DNA sequence databases use compression such as gzip to reduce the required storage space and network transmission time. We describe Nucleotide Archival Format (NAF)—a new file format for lossless reference-free compression of FASTA and FASTQ-formatted nucleotide sequences. Nucleotide Archival Format compression ratio is comparable to the best DNA compressors, while providing dramatically faster decompression. We compared our format with DNA compressors: DELIMINATE and MFCompress, and with general purpose compressors: gzip, bzip2, xz, brotli and zstd.

Availability and implementation
NAF compressor and decompressor, as well as format specification are available at https://github.com/KirillKryukov/naf. Format specification is in public domain. Compressor and decompressor are open source under the zlib/libpng license, free for nearly any use.

Supplementary information
Supplementary data are available at Bioinformatics online.
Identification of specific modules and hub genes associated with the progression of gastric cancer
Authors: Gong Congcong , Hu Yang , Zhou Mao , Yao Maojin , Ning Zhengxiang , Wang Zhi , Ren Jiaoyan 
Published: February 2019

AbstractGastric cancer (GC) has high morbidity and mortality rates worldwide. Abundant literature has reported several individual genes and their related pathways intimately involved in tumor progression. However, little is known about GC progression at the gene network level. Therefore, understanding the underlying mechanisms of pathological transition from early stage to late stage is urgently needed. This study aims to identify potential vital genes and modules involved in the progression of GC. To understand the gene regulatory network of GC progression, we analyzed micro RNAs and messenger RNA s expression profiles by using a couple of bioinformatics tools. miR-205 was identified by differentially expressed analysis and was further confirmed through using multiple kernel learning-based Kronecker regularized least squares. Using weighted gene co-expression network analysis, the gastric cancer progression-related module, which has the highest correlation value with cancer progression, was obtained. Kyoto Encyclopedia of Genes and Genomes pathways and biological processes of the GCPR module genes were related to cell adhesion. Meanwhile, large-scale genes of GCPR module were found to be targeted by miR-205, including two hub genes SORBS1 and LPAR1. In brief, through multiple analytical methods, we found that miR-205 and the GCPR module play critical roles in GC progression. In addition, miR-205 might maintain cell adhesion by regulating SORBS1 and LPAR1. To screen the potential drug candidates, the gene expression profile of the GCPR module was mapped connectivity map (Cmap), and the mTOR inhibitor (Sirolimus) was found to be the most promising candidate. We further confirmed that Sirolimus can suppress cell proliferation of GC cell in vitro.
Switching From Fear to No Fear by Different Neural Ensembles in Mouse Retrosplenial Cortex
Authors: Wang Guangyu , Xie Hong , Wang Lun , Luo Wenhan , Wang Yixiang , Jiang Jun , Xiao Chun , Xing Feng , Guan Ji-Song 
Published: February 2019

Abstract
Fear extinction is generally considered a form of new learning that inhibits previously acquired fear memories. Here, by tracking immediate early gene expression in vivo, we found that contextual fear extinction training evoked distinct neural ensembles in mouse retrosplenial cortex (RSC). The optogenetic reactivation of these extinction-activated neurons in the RSC was sufficient to suppress a fear response, while the reactivation of conditioning-activated neurons in the same area promoted a fear response. The generation of such an extinction-memory-related neural ensemble was associated with adult neurogenesis, as abolishing newborn neurons in the adult hippocampus via X-ray irradiation eliminated both the extinction-activated neurons in the RSC and the optogenetic-reactivation-induced suppression of contextual fear memory. Therefore, switching from fear to no fear in response to the same context is modulated by the RSC through an extinction-activated neural ensemble, the generation of which might require adult neurogenesis in the hippocampus.
The Role of Redox Dysregulation in the Effects of Prenatal Stress on Embryonic Interneuron Migration
Authors: Bittle Jada , Menezes Edenia C , McCormick Michael L , Spitz Douglas R , Dailey Michael , Stevens Hanna E 
Published: February 2019

AbstractMaternal stress during pregnancy is associated with increased risk of psychiatric disorders in offspring, but embryonic brain mechanisms disrupted by prenatal stress are not fully understood. Our lab has shown that prenatal stress delays inhibitory neural progenitor migration. Here, we investigated redox dysregulation as a mechanism for embryonic cortical interneuron migration delay, utilizing direct manipulation of pro- and antioxidants and a mouse model of maternal repetitive restraint stress starting on embryonic day 12. Time-lapse, live-imaging of migrating GAD67GFP+ interneurons showed that normal tangential migration of inhibitory progenitor cells was disrupted by the pro-oxidant, hydrogen peroxide. Interneuron migration was also delayed by in utero intracerebroventricular rotenone. Prenatal stress altered glutathione levels and induced changes in activity of antioxidant enzymes and expression of redox-related genes in the embryonic forebrain. Assessment of dihydroethidium (DHE) fluorescence after prenatal stress in ganglionic eminence (GE), the source of migrating interneurons, showed increased levels of DHE oxidation. Maternal antioxidants (N-acetylcysteine and astaxanthin) normalized DHE oxidation levels in GE and ameliorated the migration delay caused by prenatal stress. Through convergent redox manipula-tions, delayed interneuron migration after prenatal stress was found to critically involve redox dysregulation. Redox biology during prenatal periods may be a target for protecting brain development.
Performance of Acoustic Radiation Force Impulse Elastography for Staging Liver Fibrosis in Patients With Chronic Hepatitis C After Viral Eradication
Authors: Chen Sheng-Hung , Lai Hsueh-Chou , Chiang I-Ping , Su Wen-Pang , Lin Chia-Hsin , Kao Jung-Ta , Chuang Po-Heng , Hsu Wei-Fan , Wang Hung-Wei , Chen Hung-Yao , Huang Guan-Tarn , Peng Cheng-Yuan 
Published: February 2019

Abstract

Background
Data on noninvasive liver fibrosis staging after viral eradication are unclear. This histology-based study validated the performance of liver stiffness (LS) measurements after viral eradication.

Methods
Consecutive participants with chronic hepatitis C (CHC) who received concomitant LS measurements through acoustic radiation force impulse (ARFI) elastography and percutaneous liver biopsy were prospectively screened and analyzed.

Results
Of the 644 patients, 521 (80.9%) underwent a biopsy at treatment baseline, and the remaining 123 (19.1%) underwent a biopsy at 3 years (median; interquartile range, 0.1) after the sustained virological response (SVR) to pegylated interferon–based and direct-acting antiviral treatments. The proportions of histological fibrosis stages did not differ significantly between the pretreatment and post-SVR groups (P = .0615). However, the LS values differed significantly (P &lt; .0001). The median LS values (presented as shear wave velocities in meters per second) were 1.51 (0.92) for the pretreatment group and 1.22 (0.77) for the post-SVR group. The cutoffs (areas under the receiver operating characteristic curve, obtained using the bootstrap method) to dichotomize between METAVIR fibrosis stage F1 versus stages F2–F4, F1–F2 versus F3–F4, and F1–F3 versus F4 were 1.47 (0.8333, 95% confidence interval [CI] 0.7981–0.8663), 1.81 (0.8763, 95% CI 0.8376–0.9107), and 1.86 (0.8811, 95% CI 0.8378–0.9179) in the pretreatment group, respectively, and 1.22 (0.7872, 95% CI 0.7001–0.8624), 1.59 (0.8808, 95% CI 0.8034–0.9422), and 1.75 (0.9018, 95% CI 0.8201–0.9644) in the post-SVR group, respectively.

Conclusions
The performance of LS measurements through ARFI elastography is promising to determine the liver fibrosis stage on necroinflammation-resolved histology in CHC after viral eradication.
Machine Learning Support for EU Funding Project Categorization
Authors: Zamazal Ondřej 
Published: February 2019

Abstract
European Union reallocates its money to their member states using different kinds of funding. EU member states categorize EU funding projects using their own categorization system. While EU prepared an integrated European categorization system, many EU members do not use it in their reports. This hinders a straightforward fiscal analysis. The article aims at an automatic support for categorization of EU funding projects by Machine Learning. The experiments showed that Support Vector Machines (SVM) is the top performance Machine Learning algorithm for this task. We experimented with the SVM classifier and the results disclosed that by employing this approach we can classify EU funding projects using a lexical description better than a baseline (i.e. the classification to a major class). Further, we experienced that the approach using the natural language translator outperforms the approach using the word sense disambiguation. Finally, we investigated the influence of the length of project description on the performance of the classifier. The results showed that while there was a positive correlation between the length of project description and the classifier performance for project descriptions in English, in the case of project description in Non-English languages the classifier performed better for shorter project descriptions. In future, we plan to build a new online application which would use the classifier on the back-end and a user would get a category recommendation on the front-end using a visualization of the EU categorization system.
Understanding local adaptation in a freshwater salmonid fish: evolution of a research programme
Authors: Vøllestad L Asbjørn , Primmer Craig R 
Published: February 2019

AbstractLinking ecology and evolution can be challenging, particularly as these fields evolve rapidly tracking technological and theoretical developments. Thus, it is important for practitioners of different biological disciplines to understand new opportunities and challenges. Since theory and methods evolve, so will research programmes—often tracking opportunity. Here, we describe a research programme where we have investigated the population biology of grayling Thymallus thymallus in a Norwegian alpine landscape over three decades. Starting with classical ecological studies, we identified a set of populations that had evolved population-specific phenotypic traits over a relatively short time span (10–30 generations). These observations led us into evolutionary studies at various levels of biological organization, using population and quantitative genetic, transcriptomic and proteomic approaches. Overall, the results show that the populations exhibit evolutionary responses to local-scale differences in environment (mainly water temperature during early development). Further, plastic responses are important in the early phase of population diversification. Population genomic studies are now becoming possible following the completion of an annotated genome. This will help us and others in addressing questions about the genetic architecture of traits important for local adaptation, thus emphasizing that combining ecological and evolutionary approaches is more important and interesting than ever.
Non-compliance and Non-response in Randomised School Meals Experiment: Evidence from Rural Senegal†
Authors: Azomahou Théophile T , Diagne Abdoulaye , Diallo Fatoumata L 
Published: February 2019

Abstract
School meals have been introduced as an important policy tool to improve education outcomes and pupil’s nutritional status. This study uses a unique and large-scale randomised field experiment to assess the effectiveness of such programmes on pupils’s performance (test scores in French, mathematics and the aggregate) and on the internal efficiency of schools (enrolment, promotion, repetition and dropout) in rural Senegal. We show that attrition and non-compliance occurred not at random in the experiment. Relying on the average treatment effect and the complier effects, we find that the programme has a positive and significant impact on pupils’ scores and on the enrolment rate. However, the repetition rate increased. The intervention has a marked gender effect. Cost-effectiveness analysis shows that deworming intervention is more cost-effective than school meals.
The relevant market in competition law: a legal concept
Authors: Robertson Viktoria H S E 
Published: February 2019

Abstract
In competition law, the relevant market acts as a filter that delineates that part of commerce within which competition law assesses companies’ market behaviour. This contribution considers how competition law can reconcile the legal concept of the relevant market with its economic roots. It argues that for market definition—like for many an economic concept—a spectrum opens up between law and economics. On the economics side of the spectrum, economics may take on a more determinative role almost amounting to normative force. This places considerable pressure on the integrity of economics. On the law side of the spectrum, the relevant market is looked at through the prism of the law and is seen as a legal concept building upon an economic one. Here, economics is assigned an interpretive role. A plethora of different positions are possible along the spectrum, and different actors may place themselves at different locations under different circumstances or at different points in time. If it is acknowledged that the relevant market concept acquires a distinct legal conception through its incorporation into the competition laws, then this has far-reaching repercussions on our entire conception of competition law. This view effectively calls into question not only competition law’s understanding of the relevant market, but also the prevailing understanding of other shared legal and economic concepts.
Clinical impact of intraoperative electronic health record downtime on surgical patients
Authors: Harrison Andrew M , Siwani Rizwan , Pickering Brian W , Herasevich Vitaly 
Published: February 2019

Abstract

Objective
Despite increased use of electronic health records (EHRs), the clinical impact of system downtime is unknown.

Materials and Methods
This retrospective matched cohort study evaluated the impact of EHR downtime episodes lasting more than 60 minutes over a 6-year study period. Patients age 18 years or older who underwent surgical procedures at least 60 minutes in duration with an inpatient stay exceeding 24 hours within the study period were eligible for inclusion. Out of 4115 patients exposed to 1 of 176 EHR downtime episodes, 4103 patients were matched to an unexposed cohort in a 1:1 ratio. Multivariable regression analysis, as well as trend analysis for effect of duration of downtime on outcomes, was performed.

Results
Downtime-exposed patients had operating room duration 1.1 times longer (p &lt; .001) and postoperative length of stay 1.04 times longer (p = .007) compared to unexposed patients. The 30-day mortality rates were similar between these groups (odds ratio 1.26, p &gt; .05). In trend analysis, there was no association between duration of downtime with respect to evaluated outcomes, postoperative length of stay, and 30-day mortality.

Conclusion
EHR downtime had no impact on 30-day mortality. Potential associations for increased postoperative length of stay and duration of time spent in the operating room were observed among downtime-exposed patients. No trend effect was observed with respect to duration of downtime and postoperative length of stay and 30-day mortality rates.
Small Price Responses to Large Demand Shocks
Authors: Gagnon Etienne , López-Salido David 
Published: February 2019

Abstract
We study the pricing response of U.S. supermarkets to large demand shocks triggered by labor conflicts, mass population displacement, and shopping sprees around major snowstorms and hurricanes. We find that these large swings in demand have, at best, modest effects on the level of retail prices, consistent with flat short- to medium-term supply curves. This finding holds even when shocks are highly persistent and despite the fact that stores adjust prices frequently. We also provide evidence that retailers maintain frequent promotional sales even as their demand varies and that they seek to match movements in their local competitors’ recourse to promotional sales.
Creating the empire
Authors: Falcucci Beatrice 
Published: February 2019

Abstract
The Istituto Agricolo Coloniale Italiano was established in Florence in 1904 by Professor Gino Bartolommei Gioli, whose aim was to create a study centre that would support Italian colonial policy, contribute to the training of experts on tropical agriculture, and inspire admiration and love for Italy’s colonies. The nation's overseas empire was, in the opinion of many intellectuals, greatly neglected both by the Italian population at large and by the industrial leaders, who commonly disregarded the potential and richness of the colonies. The museum formed an essential part of the colonial project, displaying the material aspect of the African territories, presenting their economic potential, addressing the colonies as a place where Italians could invest and stimulating their imperial vocations. This article interrogates the museum and its evolution as an educational tool, from the first decade of the twentieth century to the post-colonial era, focusing on the history of the colonial collection and on how it was exhibited.