bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acceptable outcomes after fundoplication—different views are held by patients, GPs, and surgeons
Authors: Currie Andrew C , Bright Tim , Thompson Sarah K , Smith Lorelle , Devitt Peter G , Watson David I 
Published: April 2019

SUMMARY
Antireflux surgery aims to improve quality of life. However, whether patients and clinicians agree on what this means, and what is an acceptable outcome following fundoplication, is unknown. This study used clinical scenarios pertinent to laparoscopic fundoplication for gastroesophageal reflux to define acceptable outcomes from the perspective of patients, surgeons, and general practitioners (GPs). Patients who had previously undergone a laparoscopic fundoplication, general practitioners, and esophagogastric surgeons were invited to rank 11 clinical scenarios of outcomes following laparoscopic fundoplication for acceptability. Clinicopathological and practice variables were collated for patients and clinicians, respectively. GPs and esophagogastric surgeons additionally were asked to estimate postfundoplication outcome probabilities. Descriptive and multivariate statistical analyses were undertaken to examine for associations with acceptability. Reponses were received from 331 patients (36.4% response rate), 93 GPs (13.4% response), and 60 surgeons (36.4% response). Bloating and inability to belch was less acceptable and dysphagia requiring intervention more acceptable to patients compared to clinicians. On regression analysis, female patients found bloating to be less acceptable (OR: 0.51 [95%CI: 0.29–0.91]; P = 0.022), but dysphagia more acceptable (OR: 1.93 [95%CI: 1.17–3.21]; P = 0.011). Postfundoplication estimation of reflux resolution was higher and that of bloating was lower for GPs compared to esophagogastric surgeons. Patients and clinicians have different appreciations of an acceptable outcome following antireflux surgery. Female patients are more concerned about wind-related side effects than male patients. The opposite holds true for dysphagia. Surgeons and GPs differ in their estimation of event probability for patient recovery following antireflux surgery, and this might explain their differing considerations of acceptable outcomes.
Independent role of low-density lipoprotein cholesterol in subclinical coronary atherosclerosis in the absence of traditional cardiovascular risk factors
Authors: Won Ki-Bum , Park Gyung-Min , Yang Yu Jin , Ann Soe Hee , Kim Yong-Giun , Yang Dong Hyun , Kang Joon-Won , Lim Tae-Hwan , Kim Hong-Kyu , Choe Jaewon , Lee Seung-Whan , Kim Young-Hak , Kim Shin-Jae , Lee Sang-Gon 
Published: April 2019

Abstract

Aims
Individuals without traditional cardiovascular risk factors (CVRFs) still experience adverse events in clinical practice. This study evaluated the predictors of subclinical coronary atherosclerosis in individuals without traditional CVRFs.

Methods and results
A total of 1250 (52.8 ± 6.5 years, 46.9% male) asymptomatic individuals without CVRFs who underwent coronary computed tomographic angiography for a general health examination were analysed. The following were considered as traditional CVRFs: systolic/diastolic blood pressure ≥140/90 mmHg; fasting glucose ≥126 mg/dL; total cholesterol ≥240 mg/dL; low-density lipoprotein cholesterol (LDL-C) ≥160 mg/dL; high-density lipoprotein cholesterol <40 mg/dL; body mass index ≥25.0 kg/m2; current smoking status; and previous medical history of hypertension, diabetes, and dyslipidaemia. Subclinical atherosclerosis, defined as the presence of any coronary plaque, was present in 20.6% cases; the incidences of non-calcified, calcified, and mixed plaque were 9.6%, 12.6%, and 2.6%, respectively. Multivariate regression analysis showed that LDL-C level [odds ratio (OR): 1.008; 95% confidence interval (CI): 1.001–1.015], together with age (OR: 1.101; 95% CI: 1.075–1.128) and male sex (OR: 5.574; 95% CI: 3.310–9.388), was associated with the presence of subclinical atherosclerosis (All P < 0.05). LDL-C level was significantly associated with an increased risk of calcified plaques rather than non-calcified or mixed plaques.

Conclusion
LDL-C, even at levels currently considered within normal range, is independently associated with the presence of subclinical coronary atherosclerosis in individuals without traditional CVRFs. Our results suggest that a stricter control of LDL-C levels may be necessary for primary prevention in individuals who are conventionally considered healthy.
Why Kill Deposed Leaders? Regime Types and Post-tenure Fates
Authors: Radtke Mitchell Thomas 
Published: April 2019

AbstractPast research has argued that leaders care about their post-tenure fates and that consideration of these circumstances can motivate policy choices. But, so far, there has been little theorizing on why some successors let leaders walk away while others meet more dismal ends. I provide a regime-based argument for this variation that predicts that personalist leaders will be more likely to experience negative post-tenure fates (exile, imprisonment, and death) than democratic and other autocratic counterparts. The reason is that personalist leaders’ legitimacy is uniquely tied to their personal traits. So long as the former despot is living and near, he poses a threat to his successors. I test my argument on a sample of leaders (1945–2004) and find that the legitimacy argument predicts leader outcomes even while accounting for rival arguments such as a need for retribution, means of exit, militarization of regime, and past history.
Force balance in numerical geodynamo simulations: a systematic study
Authors: Schwaiger T , Gastine T , Aubert J 
Published: April 2019

SUMMARY
Dynamo action in the Earth’s outer core is expected to be controlled by a balance between pressure, Coriolis, buoyancy and Lorentz forces, with marginal contributions from inertia and viscous forces. Current numerical simulations of the geodynamo, however, operate at much larger inertia and viscosity because of computational limitations. This casts some doubt on the physical relevance of these models.
Our work aims at finding dynamo models in a moderate computational regime which reproduce the leading-order force balance of the Earth. By performing a systematic parameter space survey with Ekman numbers in the range 10−6 ≤ E ≤ 10−4, we study the variations of the force balance when changing the forcing (Rayleigh number, Ra) and the ratio between viscous and magnetic diffusivities (magnetic Prandtl number, Pm). For dipole-dominated dynamos, we observe that the force balance is structurally robust throughout the investigated parameter space, exhibiting a quasi-geostrophic (QG) balance (balance between Coriolis and pressure forces) at zeroth order, followed by a first-order Magneto-Archimedean-Coriolis (MAC) balance between the ageostrophic Coriolis, buoyancy and Lorentz forces. At second order, this balance is disturbed by contributions from inertia and viscous forces. Dynamos with a different sequence of the forces, where inertia and/or viscosity replace the Lorentz force in the first-order force balance, can only be found close to the onset of dynamo action and in the multipolar regime. To assess the agreement of the model force balance with that expected in the Earth’s core, we introduce a parameter quantifying the distance between the first- and second-order forces. Analysis of this parameter shows that the strongest-field dynamos can be obtained close to the onset of convection (Ra close to critical) and in situations of reduced magnetic diffusivity (high Pm). Decreasing the Ekman number gradually expands this regime towards higher supercriticalities and lower values of Pm.
Our study illustrates that most classical numerical dynamos are controlled by a QG-MAC balance, while cases where viscosity and inertia play a dominant role are the exception rather than the norm.
Households or Hotspots? Defining Intervention Targets for Malaria Elimination in Ratanakiri Province, Eastern Cambodia
Authors: Bannister-Tyrrell Melanie , Krit Meryam , Sluydts Vincent , Tho Sochantha , Sokny Mao , Mean Vanna , Kim Saorin , Menard Didier , Grietens Koen Peeters , Abrams Steven , Hens Niel , Coosemans Marc , Bassat Quique , van Hensbroek Michael Boele , Durnez Lies , Van Bortel Wim 
Published: April 2019

Abstract

Background
Malaria “hotspots” have been proposed as potential intervention units for targeted malaria elimination. Little is known about hotspot formation and stability in settings outside sub-Saharan Africa.

Methods
Clustering of Plasmodium infections at the household and hotspot level was assessed over 2 years in 3 villages in eastern Cambodia. Social and spatial autocorrelation statistics were calculated to assess clustering of malaria risk, and logistic regression was used to assess the effect of living in a malaria hotspot compared to living in a malaria-positive household in the first year of the study on risk of malaria infection in the second year.

Results
The crude prevalence of Plasmodium infection was 8.4% in 2016 and 3.6% in 2017. Living in a hotspot in 2016 did not predict Plasmodium risk at the individual or household level in 2017 overall, but living in a Plasmodium-positive household in 2016 strongly predicted living in a Plasmodium-positive household in 2017 (Risk Ratio, 5.00 [95% confidence interval, 2.09–11.96], P < .0001). There was no consistent evidence that malaria risk clustered in groups of socially connected individuals from different households.

Conclusions
Malaria risk clustered more clearly in households than in hotspots over 2 years. Household-based strategies should be prioritized in malaria elimination programs in this region.
Dysregulation of miR484-TUSC5 axis takes part in the progression of hepatocellular carcinoma
Authors: Wang Shanzong , Wang Weijuan , Han Xiaoguang , Wang Youli , Ge Yunzhen , Tan Zhen 
Published: April 2019

Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related death worldwide. miR-484 is previously reported to be a crucial modulator during the process from precancerous lesion to cancer. Tumour suppressor candidate 5 (TUSC5) is a potential tumour suppressor, but its expression and function in HCC are obscure. In this study, we aimed to explore the roles of miR-484 and TUSC5 in HCC, and clarify the relationship between them. We demonstrated that miR-484 was significantly up-regulated in HCC, while TUSC5 was down-regulated. TUSC5 was validated as the target gene of miR-484 and both of them were associated with the prognosis of HCC patients. miR-484 mimics markedly promoted the malignant phenotypes while TUSC5 plasmid had the opposite effect. In conclusion, miR-484/TUSC5 is potential diagnostic biomarkers and therapy targets for HCC.
Comparison of the Efficacy and Phytotoxicity of Phosphine and Ethyl Formate for Controlling Pseudococcus longispinus (Hemiptera: Pseudococcidae) and Pseudococcus orchidicola on Imported Foliage Nursery Plants
Authors: Kyung Yejin , Kim Hyun Kyung , Cho Sung Woo , Kim Bong-Su , Yang Jeong-Oh , Koo Hyun-Na , Kim Gil-Hah 
Published: April 2019

Abstract
The fumigation activity of phosphine (PH3) and ethyl formate (EF) and their phytotoxicity to 13 imported foliage nursery plant species were evaluated. The lethal concentration and time (LCT99) values of the PH3 indicated that the susceptibility of the nymphs (3.95 and <0.45 mg·h/liter, respectively) was higher than that of the adults (5.29 and 3.66 mg·h/liter, respectively) of two mealybugs [Pseudococcus longispinus (Targioni-Tozzetti) and P. orchidicola Takahashi]. The highest concentration reduction rate of PH3 and EF on the 13 foliage nursery plants in the 12-liter desiccator was 41.5% for Heteropanax fragrans and 71.7% for Schefflera arboricola, respectively, which indicates that PH3 has a lower sorption rate than EF. The phytotoxicities of PH3-treated foliage nursery plants did not significantly differ from those of the nontreated plants, but EF caused phytotoxicity in 11 foliage nursery plants a week after treatment. When the exposure time of PH3 increased to 24 h, the adults and nymphs of both mealybug species showed 100% mortality in the 0.5 m3 fumigation chamber. In the 10 m3 fumigation container used in the field, there was 100% mortality of both mealybugs after treatment with 2 g/m3 PH3 for 24 h at 16°C. These results indicate that EF is not a suitable mealybug fumigant due to its high sorption and phytotoxicity to foliage nursery plants, despite fumigation activity against the two species. However, PH3 seems to be suitable for mealybug fumigation in foliage nursery plants and can be used as a substitute for methyl bromide.
Separating prestack diffractions with SVMF in the flattened shot domain
Authors: Zhao Jingtao , Sun Xiuli , Peng Suping , Wei Wei , Liu Tao 
Published: April 2019

Abstract
Separating weak diffractions in the prestack domain plays a vital role in high-resolution imaging small-scale discontinuities or inhomogeneities, which are associated with the migration paths and storage spaces for carbonate fracture-cave reservoirs. A shot-domain diffraction separation method is proposed with a SVMF (space-varying media filter) in the flattened shot domain. The diffractions with fast dynamic changings, including damping amplitudes and phase reversal, are filtered out by the spacing-varying median filter along the prediction-step directions of the flattened shot domain. The proposed method opens a possibility for separating diffractions in the shot domain and has an advantage in the traditional common-offset diffraction separation method. A numerical experiment illustrates the good performance of the proposed method in eliminating reflections and separating diffractions in the shot domain, and the field application further verifies its potential value in resolving the hidden small-scale cavities and tiny faults in carbonate reservoirs.
Vegetation and environment changes inferred from pollen records since 3000 cal. yr BP in Kanas wetland, Xinjiang
Authors: Li Yumei , Zhang Yun , Kong Zhaochen , Zhao Long , Wang Li , Li Yuanyuan , Chen Lixin 
Published: April 2019

AbstractAimsClimate change can significantly affect the vegetation worldwide. Thus, paleovegetation and paleoclimate reconstruction should consider the quantitative relationship between modern vegetation and climate. The specific objectives of this study were (i) to assess the influence of environmental variables on pollen assemblages in the Kanas region, (ii) to reconstruct the evolution of vegetation over the past 3000 years using pollen records and (iii) to quantify historical climate change (including mean annual temperature and total annual precipitation) using a weighted averaging partial least squares regression method (WAPLS) applied to fossil pollen data from the Kanas wetland in Xinjiang, China.MethodsA total of 65 surface and 50 fossil samples were collected from the Kanas wetland and analysed for 14C, pollen and grain size. By combining these data with those obtained from 214 samples of surface pollen assemblages in north Xinjiang, the late Holocene climate was reconstructed using a WAPLS model.Important FindingsThe vegetation in Kanas was dominated by forest for the past 3000 years, undergoing an arbour-vegetation transition from predominantly pine to spruce over that period. The WAPLS model showed that the paleoclimate progressed from cold-wet to warm-dry and subsequently back to cold-wet. Prior to 1350 calibrated years before the present (cal. yr BP), the climate of Kanas was cold and wet, and conditions became increasingly warm and dry until 870 cal. yr BP. The temperature reconstruction model indicated that a ‘Little Ice Age’ occurred ~380 cal. yr BP. These data will help us improve the understanding of abrupt climate change and provide important information regarding the prediction of climate.
Diverticulitis of isolated jejunal diverticulum complicated by small bowel obstruction secondary to de novo enterolith formation
Authors: Aispuro Ivan O , Yazzie Nazhone P 
Published: April 2019

ABSTRACT
Jejunoileal diverticula (JD) are an uncommon condition most prevalent in the sixth and seventh decade of life. Although mostly asymptomatic, JD can be complicated by perforation, diverticulitis, abscess, bleeding, fistula, and small bowel obstruction (SBO) secondary to enterolith formation. There are a limited number of cases describing JD complicated by SBO secondary to enterolith formation. Most of these cases are not associated with diverticulitis and multiple JD are present in all but one previously reported case. We present a case of diverticulitis of a large, isolated jejunal diverticulum complicated by de novo enterolith-induced SBO initially diagnosed as intussusception based on computerized tomography (CT) imaging. Our main objective is to increase awareness that isolated JD are not as readily evident on imaging as cases presenting with multiple JD, but nevertheless should be considered as possible etiology of acute abdomen.
What drives the velocity dispersion of ionized gas in star-forming galaxies?
Authors: Yu Xiaoling , Shi Yong , Chen Yanmei , Law David R , Bizyaev Dmitry , Bing Longji , Li Songlin , Zhou Luwenjia , Chen Jianhang , Riffel Rogemar A , Riffel Rogério , Zhang Kai , Chen Yongyun , Pan Kaike 
Published: April 2019

Abstract
We analyse the intrinsic velocity dispersion properties of 648 star-forming galaxies observed by the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey, to explore the relation of intrinsic gas velocity dispersions with star formation rates (SFRs), SFR surface densities ($\rm {\Sigma _{SFR}}$), stellar masses, and stellar mass surface densities ($\rm {\Sigma _{*}}$). By combining with high z galaxies, we found that there is a good correlation between the velocity dispersion and the SFR as well as $\rm {\Sigma _{SFR}}$. But the correlation between the velocity dispersion and the stellar mass as well as $\rm {\Sigma _{*}}$ is moderate. By comparing our results with predictions of theoretical models, we found that the energy feedback from star formation processes alone and the gravitational instability alone cannot fully explain simultaneously the observed velocity–dispersion/SFR and velocity–dispersion/$\rm {\Sigma _{SFR}}$ relationships.
CPGAVAS2, an integrated plastome sequence annotator and analyzer
Authors: Shi Linchun , Chen Haimei , Jiang Mei , Wang Liqiang , Wu Xi , Huang Linfang , Liu Chang 
Published: April 2019

AbstractWe previously developed a web server CPGAVAS for annotation, visualization and GenBank submission of plastome sequences. Here, we upgrade the server into CPGAVAS2 to address the following challenges: (i) inaccurate annotation in the reference sequence likely causing the propagation of errors; (ii) difficulty in the annotation of small exons of genes petB, petD and rps16 and trans-splicing gene rps12; (iii) lack of annotation for other genome features and their visualization, such as repeat elements; and (iv) lack of modules for diversity analysis of plastomes. In particular, CPGAVAS2 provides two reference datasets for plastome annotation. The first dataset contains 43 plastomes whose annotation have been validated or corrected by RNA-seq data. The second one contains 2544 plastomes curated with sequence alignment. Two new algorithms are also implemented to correctly annotate small exons and trans-splicing genes. Tandem and dispersed repeats are identified, whose results are displayed on a circular map together with the annotated genes. DNA-seq and RNA-seq data can be uploaded for identification of single-nucleotide polymorphism sites and RNA-editing sites. The results of two case studies show that CPGAVAS2 annotates better than several other servers. CPGAVAS2 will likely become an indispensible tool for plastome research and can be accessed from http://www.herbalgenomics.org/cpgavas2.
modEnrichr: a suite of gene set enrichment analysis tools for model organisms
Authors: Kuleshov Maxim V , Diaz Jennifer E L , Flamholz Zachary N , Keenan Alexandra B , Lachmann Alexander , Wojciechowicz Megan L , Cagan Ross L , Ma’ayan Avi 
Published: April 2019

Abstract
High-throughput experiments produce increasingly large datasets that are difficult to analyze and integrate. While most data integration approaches focus on aligning metadata, data integration can be achieved by abstracting experimental results into gene sets. Such gene sets can be made available for reuse through gene set enrichment analysis tools such as Enrichr. Enrichr currently only supports gene sets compiled from human and mouse, limiting accessibility for investigators that study other model organisms. modEnrichr is an expansion of Enrichr for four model organisms: fish, fly, worm and yeast. The gene set libraries within FishEnrichr, FlyEnrichr, WormEnrichr and YeastEnrichr are created from the Gene Ontology, mRNA expression profiles, GeneRIF, pathway databases, protein domain databases and other organism-specific resources. Additionally, libraries were created by predicting gene function from RNA-seq co-expression data processed uniformly from the gene expression omnibus for each organism. The modEnrichr suite of tools provides the ability to convert gene lists across species using an ortholog conversion tool that automatically detects the species. For complex analyses, modEnrichr provides API access that enables submitting batch queries. In summary, modEnrichr leverages existing model organism databases and other resources to facilitate comprehensive hypothesis generation through data integration.
Role of fruit juice in achieving the 5-a-day recommendation for fruit and vegetable intake
Authors: Benton David , Young Hayley A 
Published: April 2019

Abstract
Although there is strong evidence that consumption of fruit and vegetables is associated with a reduced rate of all-cause mortality, only a minority of the population consumes 5 servings a day, and campaigns to increase intake have had limited success. This review examines whether encouraging the consumption of fruit juice might offer a step toward the 5-a-day target. Reasons given for not consuming whole fruit involve practicalities, inconvenience, and the effort required. Psychologically, what is important is not only basic information about health, but how individuals interpret their ability to implement that information. It has been argued that fruit juice avoids the problems that commonly prevent fruit consumption and thus provides a practical means of increasing intake and benefitting health through an approach with which the population can readily engage. Those arguing against consuming fruit juice emphasize that it is a source of sugar lacking fiber, yet juice provides nutrients such as vitamin C, carotenoids, and polyphenols that offer health-related benefits. Actively encouraging the daily consumption of fruit juice in public health policy could help populations achieve the 5-a-day recommendation for fruit and vegetable intake.
An Annealed Sequential Monte Carlo Method for Bayesian Phylogenetics
Authors: Wang Liangliang , Wang Shijia , Bouchard-Côté Alexandre 
Published: April 2019

AbstractWe describe an “embarrassingly parallel” method for Bayesian phylogenetic inference, annealed Sequential Monte Carlo (SMC), based on recent advances in the SMC literature such as adaptive determination of annealing parameters. The algorithm provides an approximate posterior distribution over trees and evolutionary parameters as well as an unbiased estimator for the marginal likelihood. This unbiasedness property can be used for the purpose of testing the correctness of posterior simulation software. We evaluate the performance of phylogenetic annealed SMC by reviewing and comparing with other computational Bayesian phylogenetic methods, in particular, different marginal likelihood estimation methods. Unlike previous SMC methods in phylogenetics, our annealed method can utilize standard Markov chain Monte Carlo (MCMC) tree moves and hence benefit from the large inventory of such moves available in the literature. Consequently, the annealed SMC method should be relatively easy to incorporate into existing phylogenetic software packages based on MCMC algorithms. We illustrate our method using simulation studies and real data analysis.