bluuebunny/crossref_metadata_2025_split huggingface dataset:
Drifting of the line-tied footpoints of CME flux-ropes
Authors: Aulanier Guillaume , Dudík Jaroslav 
Published: November 2018

Context. Bridging the gap between heliospheric and solar observations of eruptions requires the mapping of interplanetary coronal mass ejection (CME) footpoints down to the Sun’s surface. But this not straightforward. Improving the understanding of the spatio-temporal evolutions of eruptive flares requires a comprehensive standard model. But the current model is only two-dimensional and cannot address the question of interplanetary CME footpoints.
Aims. Existing 3D extensions to the standard model show that flux-rope footpoints are surrounded by curved-shaped quasi-separatrix layer (QSL) footprints that can be related with hook-shaped flare-ribbons. We build upon this finding and further address the joint questions of their time-evolution, and of the formation of flare loops at the ends of the flaring polarity inversion line (PIL) of the erupting bipole, which are both relevant for flare understanding in general and for interplanetary CME studies in particular.
Methods. We calculated QSLs and relevant field lines in an MHD simulation of a torus-unstable flux-rope. The evolving QSL footprints are used to define the outer edge of the flux rope at different times, and to identify and characterize new 3D reconnection geometries and sequences that occur above the ends of the flaring PIL. We also analyzed flare-ribbons as observed in the extreme ultraviolet by SDO/AIA and IRIS during two X-class flares.
Results. The flux-rope footpoints are drifting during the eruption, which is unexpected due to line-tying. This drifting is due to a series of coronal reconnections that erode the flux rope on one side and enlarge it on the other side. Other changes in the flux-rope footpoint-area are due to multiple reconnections of individual field lines whose topology can evolve sequentially from arcade to flux rope and finally to flare loop. These are associated with deformations and displacements of QSL footprints, which resemble those of the studied flare ribbons.
Conclusions. Our model predicts continuous deformations and a drifting of interplanetary CME flux-rope footpoints whose areas are surrounded by equally evolving hooked-shaped flare-ribbons, as well as the formation of flare loops at the ends of flaring PILs which originate from the flux-rope itself, both of which being due to purely three-dimensional reconnection geometries. The observed evolution of flare-ribbons in two events supports the model, but more observations are required to test all its predictions.
Predictable gene expression related to behavioral variation in parenting
Authors: Benowitz Kyle M , McKinney Elizabeth C , Cunningham Christopher B , Moore Allen J 
Published: November 2018

AbstractDifferential gene expression has been associated with transitions between behavioral states for a wide variety of organisms and behaviors. Heterochrony, genetic toolkits, and predictable pathways underlying behavioral transitions have been hypothesized to explain the relationship between transcription and behavioral changes. Less studied is how variation in transcription is related to variation within a behavior, and if the genes that are associated with this variation are predictable. Here, we adopt an evolutionary systems biology perspective to address 2 hypotheses relating differential expression to changes within and between behavior. We predicted fewer genes will be associated with variation within a behavior than with transitions between states, and the genes underlying variation within a behavior will represent a narrower set of biological functions. We tested for associations with parenting variation within a state with a set of genes known a priori to be differentially expressed (DE) between parenting states in the burying beetle Nicrophorus vespilloides. As predicted, we found that far fewer genes are DE related to variation within parenting. Moreover, these were not randomly distributed among categories or pathways in the gene set we tested and primarily involved genes associated with neurotransmission. We suggest that this means candidate genes will be easier to identify for associations within a behavior, as descriptions of behavioral state may include more than a single phenotype.
DeeReCT-PolyA: a robust and generic deep learning method for PAS identification
Authors: Xia Zhihao , Li Yu , Zhang Bin , Li Zhongxiao , Hu Yuhui , Chen Wei , Gao Xin 
Published: November 2018

Abstract

Motivation
Polyadenylation is a critical step for gene expression regulation during the maturation of mRNA. An accurate and robust method for poly(A) signals (PASs) identification is not only desired for the purpose of better transcripts’ end annotation, but can also help us gain a deeper insight of the underlying regulatory mechanism. Although many methods have been proposed for PAS recognition, most of them are PAS motif- and human-specific, which leads to high risks of overfitting, low generalization power, and inability to reveal the connections between the underlying mechanisms of different mammals.

Results
In this work, we propose a robust, PAS motif agnostic, and highly interpretable and transferrable deep learning model for accurate PAS recognition, which requires no prior knowledge or human-designed features. We show that our single model trained over all human PAS motifs not only outperforms the state-of-the-art methods trained on specific motifs, but can also be generalized well to two mouse datasets. Moreover, we further increase the prediction accuracy by transferring the deep learning model trained on the data of one species to the data of a different species. Several novel underlying poly(A) patterns are revealed through the visualization of important oligomers and positions in our trained models. Finally, we interpret the deep learning models by converting the convolutional filters into sequence logos and quantitatively compare the sequence logos between human and mouse datasets.

Availability and implementation
https://github.com/likesum/DeeReCT-PolyA

Supplementary information
Supplementary data are available at Bioinformatics online.
Healthcare Costs and Life-years Gained From Treatments Within the Advancing Cryptococcal Meningitis Treatment for Africa (ACTA) Trial on Cryptococcal Meningitis: A Comparison of Antifungal Induction Strategies in Sub-Saharan Africa
Authors: Chen Tao , Mwenge Lawrence , Lakhi Shabir , Chanda Duncan , Mwaba Peter , Molloy Síle F , Gheorghe Adrian , Griffiths Ulla K , Heyderman Robert S , Kanyama Cecilia , Kouanfack Charles , Mfinanga Sayoki , Chan Adrienne K , Temfack Elvis , Kivuyo Sokoine , Hosseinipour Mina C , Lortholary Olivier , Loyse Angela , Jaffar Shabbar , Harrison Thomas S , Niessen Louis W ,   ACTA Trial Team
Published: November 2018

Abstract

Background
Mortality from cryptoccocal meningitis remains high. The ACTA trial demonstrated that, compared with 2 weeks of amphotericin B (AmB) plus flucystosine (5FC), 1 week of AmB and 5FC was associated with lower mortality and 2 weeks of oral flucanozole (FLU) plus 5FC was non-inferior. Here, we assess the cost-effectiveness of these different treatment courses.

Methods
Participants were randomized in a ratio of 2:1:1:1:1 to 2 weeks of oral 5FC and FLU, 1 week of AmB and FLU, 1 week of AmB and 5FC, 2 weeks of AmB and FLU, or 2 weeks of AmB and 5FC in Malawi, Zambia, Cameroon, and Tanzania. Data on individual resource use and health outcomes were collected. Cost-effectiveness was measured as incremental costs per life-year saved, and non-parametric bootstrapping was done.

Results
Total costs per patient were US $1442 for 2 weeks of oral FLU and 5FC, $1763 for 1 week of AmB and FLU, $1861 for 1 week of AmB and 5FC, $2125 for 2 weeks of AmB and FLU, and $2285 for 2 weeks of AmB and 5FC. Compared to 2 weeks of AmB and 5FC, 1 week of AmB and 5FC was less costly and more effective and 2 weeks of oral FLU and 5FC was less costly and as effective. The incremental cost-effectiveness ratio for 1 week of AmB and 5FC versus oral FLU and 5FC was US $208 (95% confidence interval $91–1210) per life-year saved.

Clinical Trials Registration
ISRCTN45035509.

Conclusions
Both 1 week of AmB and 5FC and 2 weeks of Oral FLU and 5FC are cost-effective treatments.
Associations between general practice characteristics with use of urgent referrals for suspected cancer and endoscopies: a cross-sectional ecological study
Authors: Mendonca Silvia C , Abel Gary A , Gildea Carolynn , McPhail Sean , Peake Michael D , Rubin Greg , Singh Hardeep , Hamilton Willie , Walter Fiona M , Roland Martin O , Lyratzopoulos Georgios 
Published: November 2018

Abstract

Background
Large variation in measures of diagnostic activity has been described previously between English general practices, but related predictors remain understudied.

Objective
To examine associations between general practice population and characteristics, with the use of urgent referrals for suspected cancer, and use of endoscopy.

Methods
Cross-sectional observational study of English general practices. We examined practice-level use (/1000 patients/year) of urgent referrals for suspected cancer, gastroscopy, flexible sigmoidoscopy and colonoscopy. We used mixed-effects Poisson regression to examine associations with the sociodemographic profile of practice populations and other practice attributes, including the average age, sex and country of qualification of practice doctors.

Results
The sociodemographic characteristics of registered patients explained much of the between-practice variance in use of urgent referrals (32%) and endoscopic investigations (18–25%), all being higher in practices with older and more socioeconomically deprived patients. Practice-level attributes explained a substantial amount of between-practice variance in urgent referral (19%) but little of the variance in endoscopy (3%-4%). Adjusted urgent referral rates were higher in training practices and those with younger GPs. Practices with mean doctor ages of 41 and 57 years (at the 10th/90th centiles of the national distribution) would have urgent referral rates of 24.1 and 19.1/1000 registered patients, P < 0.001.

Conclusion
Most between-practice variation in use of urgent referrals and endoscopies seems to reflect health need. Some practice characteristics, such as the mean age of GPs, are associated with appreciable variation in use of urgent referrals, though these associations do not seem strong enough to justify targeted interventions.
Factors influencing healthy eating and physical activity amongst school staff
Authors: Huse Oliver , Palermo Claire , Evans Monica , Peeters Anna 
Published: November 2018

Summary
Limited research has explored teachers’ perceptions of the role that schools can play in supporting staff members’ healthy eating and physical activity. We aimed to identify barriers to healthy eating and physical activity within the school context, and to conclude on potential strategies for supporting staff to pursue these healthier behaviours. A convenience sampling strategy was used to recruit eleven schools from across Victoria to participate in this study, through contacts known to the researchers. The researchers facilitated focus groups involving staff from schools. Focus groups ranged in size from 3 to 12 participants (total 82) and lasted between 40 and 75 min. Thematic analysis was used to identify themes and sub-themes which were identified by staff as being important for healthy eating and physical activity. Schools that were perceived by staff to support healthy eating and physical activity offered opportunities, through initiatives and the physical environment, to support staff in accessing environments and facilities that supported them in being healthy. Further supportive elements were identified as a culture of health behaviours amongst staff members and leadership which supported health behaviours. Workplace stressors were reported to impact many aspects of staff health and wellbeing. Potential actions by schools to better support staff to pursue healthy eating and physical activity were identified from the themes emerging from this study. Alignment between these themes and elements of the World Health Organisation’s healthy workplace framework suggest it will be important for health promotion models to account for these themes.
Valency and English learners’ thesauri
Authors: Gao Jun , Liu Haitao 
Published: November 2018

AbstractLearners’ thesauri do not simply offer an inventory of semantically related lexical items but explicate their nuances and furnish users with rich syntactic, semantic, and pragmatic information. Adopting the theoretical framework of valency, this study examines the distinctive features of two English learners’ thesauri, the Oxford Learner’s Thesaurus: A Dictionary of Synonyms (OLT) and the Longman Language Activator (LLA). Furthermore, the study, supported by learner corpus evidence, empirically assesses the usefulness of OLT and LLA in Chinese learners’ writing. The results demonstrate that learners’ thesauri can generally meet the practical needs of users in writing through providing a range of synonyms and syntactic patterns, including abundant information on semantic collocations, and offering rich pragmatic information regarding registers and emotive variables. The results also show some defects in OLT and LLA, such as their failure to present specific syntactic patterns, including those frequently used in Chinese learners’ compositions. It is then suggested that the compilation of learners’ thesauri draw upon the ways in which lexical information is presented in the English Valency Dictionary, and that learner corpora and native speaker corpora be combined to improve their usefulness.
Les collections royales de raretés sous François Ier et Henri II
Authors: Trébosc Delphine 
Published: November 2018

Abstract
François Ier, qui fonda la collection royale de raretés, en instaura non seulement le regroupement, mais aussi la fonction politique, la collection de singularités prenant part à la fois au projet encyclopédique royal et à la magnificence royale. Sous son règne, ainsi que sous celui d’Henri II, le château de Fontainebleau devint le lieu privilégié du rassemblement et de la présentation de cette collection, en particulier au sein de plusieurs espaces associés au logis du roi.
Short-term effect of the New Nordic Renal Diet on phosphorus homoeostasis in chronic kidney disease Stages 3 and 4
Authors: Salomo Louise , Rix Marianne , Kamper Anne-Lise , Thomassen Jesper Q , Sloth Jens J , Astrup Arne 
Published: November 2018

Abstract

Background
The New Nordic Diet is a food concept favouring organically produced food items, fruits, vegetables, whole grains and fish. We investigated the short-term effects of a modified phosphorus-reduced New Nordic Renal Diet (NNRD) in chronic kidney disease (CKD) patients on important parameters of phosphorus homoeostasis.

Methods
The NNRD contained a total of 850 mg phosphorus/day. A total of 18 patients, CKD Stages 3 and 4 were studied in a randomized crossover trial comparing a 1-week control period of the habitual diet with a 1-week period of the NNRD. Data were obtained at baseline and during 1 week of dietary intervention (habitual diet versus NNRD) by collecting fasting blood samples and 24-h urine collections. The primary outcome was the difference in the change in 24-h urine phosphorus excretion from baseline to Day 7 between the NNRD and habitual diet periods. Secondary outcomes were changes in the fractional excretion of phosphorus, fibroblast growth factor 23 (FGF23) and plasma phosphate.

Results
As compared with the habitual diet, 24-h urine phosphorus excretion was reduced in the NNRD by 313 mg/day (P &lt; 0.001). The mean baseline phosphorus was 875 ± 346 mg/day and was decreased by 400 ± 256 mg/day in the NNRD and 87 ± 266 mg/day in the habitual diet. The 24-h urine fractional excretion of phosphorus decreased by 11% (P &lt; 0.001) and FGF23 decreased by 30 pg/mL (P = 0.03) with the NNRD compared with the habitual diet. Plasma phosphate did not change.

Conclusion
This study demonstrates that dietary phosphorus restriction in the context of the NNRD is feasible and has positive effects on phosphorus homeostasis in CKD patients.
Physician Responses to Enhanced Prescription Drug Monitoring Program Profiles
Authors: Leichtling Gillian , Hildebran Christi , Novak Kevin , Alley Lindsey , Doyle Sheri , Reilly Cynthia , Weiner Scott G 
Published: November 2018

Abstract

Objective
Many states have begun implementing enhancements to PDMP patient profiles such as summaries or graphics to highlight issues of concern and enhance comprehension. The purpose of this study was to examine how physicians respond to sample enhanced PDMP profiles based on patient vignettes.

Design
Brief semistructured interviews with physicians.

Setting
Three national medical conferences for targeted specialties.

Subjects
Ninety-three physicians practicing in primary care, emergency medicine, or pain management.

Methods
We presented participants with one of three patient vignettes with corresponding standard and enhanced PDMP profiles and conducted brief interviews.

Results
Findings indicated that enhanced profiles could increase ease of comprehension, reduce time burden, and aid in communicating with patients about opioid risks. Physicians also expressed concern about liability for prescribing when the enhanced profile indicates risk and cautioned against any implication that risk warnings should override clinical judgment based on the patient’s complete medical history or presenting condition. Physicians emphasized the need for transparency of measures and evidence of validation of risk scores. We found little indication that enhanced profiles would change opioid prescribing decisions, though decisions varied by physician.

Conclusions
Our study underscores the importance of involving prescribers in developing and testing PDMP profile enhancements, as well as providing guidance in the interpretation and clinical use of enhanced profiles. Reduced time burden is an important benefit to consider as the number of states mandating PDMP use increases.
Regional Transfer Multipliers
Authors: Corbi Raphael , Papaioannou Elias , Surico Paolo 
Published: November 2018

AbstractA series of discontinuities in the allocation mechanism of federal transfers to municipal governments in Brazil allow us to identify the causal effect of public spending on local labour markets, using a “fuzzy” Regression Discontinuity Design (RDD). Our estimates imply a cost per job of about 8,000 US dollars per year and a local income multiplier around two. The effect comes mostly from employment in services and is more pronounced among less financially developed municipalities.
A content analysis of smartphone apps for adolescent smoking cessation
Authors: Robinson Cendrine D , Seaman Elizabeth L , Grenen Emily , Montgomery LaTrice , Yockey R Andrew , Coa Kisha , Prutzman Yvonne , Augustson Erik 
Published: November 2018

Abstract
Adolescent cigarette smokers have an increased risk of sustained smoking into adulthood. Smartphone applications (apps) for smoking cessation are a promising treatment resource. However, research on apps for adolescent smoking cessation is limited. This study compared smoking cessation mobile apps targeting an adolescent audience with popular cessation apps for a general audience. Adolescent and general-audience apps were identified by searching the Google Play and Apple App Stores (November 2016). Two coders assessed each app for adherence to clinical practice guidelines for tobacco and adolescent-specific content (2016–2017) and developed a summary score that summed all adherence and adolescent content criteria. Eight adolescent apps were identified and compared with the top 38 general apps (as ranked by Apple and Google). Both general and adolescent apps commonly had adherence content related to developing a quit plan (general: 73.68 per cent; adolescent: 87.50 per cent) and enhancing motivation by describing the rewards of not smoking (general: 76.32 per cent; adolescent: 62.50 per cent). Adolescent-specific content such as peer influence on smoking was common in adolescent apps but not in general apps (general: 5.26 per cent; adolescent: 62.50 per cent). Adolescent apps had a higher general adherence content summary score [t (44) = 2.55, p = .01] and a higher adolescent content summary score [t (7.81) = 2.47, p = .04] than the general apps. On average, adolescent cessation apps included more adherence content and adolescent-specific content than general apps. Future research is needed to determine the extent to which adolescents engage with the adherence content available in these apps.
IQGAP1 Maintains Pancreatic Ductal Adenocarcinoma Clonogenic Growth and Metastasis
Authors: Li Joey H. , McMillan Ross H. , Begum Asma , Gocke Christian B. , Matsui William 
Published: November 2018

Objectives
IQ motif containing GTPase-activating protein 1 (IQGAP1) acts as a scaffold for aberrant mitogen-activated protein kinase (MAPK) signaling driven by KRAS mutations in pancreatic ductal adenocarcinoma (PDAC). We determined the role of IQGAP1 in clonogenic growth and metastasis in PDAC.

Methods
We inhibited IQGAP1 expression using shRNA and assessed clonogenic growth, cell migration, and MAPK signaling in vitro and tumor initiation and metastasis in vivo. The efficacy of a peptide mimicking the IQGAP1 WW domain that binds and inhibits ERK1/2 was determined in vitro and in vivo.

Results
IQGAP1 loss inhibited clonogenic growth and migration of KRAS-dependent PDAC cells by disrupting MAPK signaling. In mice, IQGAP1 knockdown decreased tumor-initiating cell frequency and metastasis. WW peptide treatment inhibited clonogenic growth and in vivo tumor growth.

Conclusions
Pancreatic ductal adenocarcinoma clonogenic growth, metastasis, and tumor initiation are dependent on MAPK signaling via IQGAP1. Treatment with a WW peptide disrupts IQGAP1 function and represents a novel targeting strategy for PDAC.
Changing Epidemiology of Liver Involvement in Children With Celiac Disease
Authors: Benelli Elisa , Naviglio Samuele , De Leo Luigina , Stera Giacomo , Giangreco Manuela , Ronfani Luca , Villanacci Vincenzo , Martelossi Stefano , Ventura Alessandro , Not Tarcisio 
Published: November 2018

ABSTRACTObjectives:Available data indicate that liver involvement is present in a significant proportion of children with celiac disease (CD) at the diagnosis (elevated transaminases 15%–57%, autoimmune liver disease 1%–2%). We sought to evaluate prevalence, clinical course, and risk factors for liver involvement in a large cohort of children with CD.Methods:Children (age 0–18 years) diagnosed with CD from March 2010 to April 2016 were enrolled. Liver involvement was considered to be present when alanine transaminase (ALT) levels were >40 U/L (hypertransaminasemia [HTS]). Patients with HTS were re‐evaluated after at least 12 months of a gluten‐free diet.Results:CD was diagnosed in 806 patients during the study period; of these, ALT levels were available for 700 patients (86.9%), and were elevated in 27 (3.9%, HTS group); median ALT and aspartate transaminase levels in the HTS group were 57 U/L (interquartile range 49–80 U/L) and 67 U/L (interquartile range 53–85 U/L), respectively. Younger age, malabsorption symptoms, and low hemoglobin or ferritin were significantly more common in the HTS group at univariate analysis. At multivariate analysis, only age ⩽4.27 years correlated with risk of liver involvement (odds ratio 3.73; 95% confidence interval: 1.61–8.66). When retested on a gluten‐free diet, all but 3 patients normalized ALT levels; of these, 1 was diagnosed with sclerosing cholangitis.Conclusions:Liver involvement in celiac children is now less frequent than previously reported, possibly due to changing CD epidemiology. Younger age is the only risk factor. Associated autoimmune liver disease is rare.