bluuebunny/crossref_metadata_2025_split huggingface dataset:
MEXCOwalk: mutual exclusion and coverage based random walk to identify cancer modules
Authors: Ahmed Rafsan , Baali Ilyes , Erten Cesim , Hoxha Evis , Kazan Hilal 
Published: August 2019

AbstractMotivationGenomic analyses from large cancer cohorts have revealed the mutational heterogeneity problem which hinders the identification of driver genes based only on mutation profiles. One way to tackle this problem is to incorporate the fact that genes act together in functional modules. The connectivity knowledge present in existing protein–protein interaction (PPI) networks together with mutation frequencies of genes and the mutual exclusivity of cancer mutations can be utilized to increase the accuracy of identifying cancer driver modules.ResultsWe present a novel edge-weighted random walk-based approach that incorporates connectivity information in the form of protein–protein interactions (PPIs), mutual exclusivity and coverage to identify cancer driver modules. MEXCOwalk outperforms several state-of-the-art computational methods on TCGA pan-cancer data in terms of recovering known cancer genes, providing modules that are capable of classifying normal and tumor samples and that are enriched for mutations in specific cancer types. Furthermore, the risk scores determined with output modules can stratify patients into low-risk and high-risk groups in multiple cancer types. MEXCOwalk identifies modules containing both well-known cancer genes and putative cancer genes that are rarely mutated in the pan-cancer data. The data, the source code and useful scripts are available at: https://github.com/abu-compbio/MEXCOwalk.Supplementary informationSupplementary data are available at Bioinformatics online.
Detection of splicing forgery using differential evolution and wavelet decomposition
Authors: Kashyap Abhishek , Suresh B , Gupta Hariom 
Published: August 2019

Abstract
In this paper, we have proposed a computationally efficient algorithm to detect splicing (copy-create) forgery, our proposed method is developed by using differential evolution and wavelet decomposition, the differential evolution algorithm automatically generates customized parameter values of tampered images, and wavelet decomposition is used to process large-size images under block-based framework. Our proposed method is resilient to distortions, such as the addition of Gaussian noise, scaling and compression of the forged images.
An unusual complication during alcohol septal ablation: severe left anterior descending artery vasospasm causing cardiac arrest: a case report and review of the literature
Authors: Keskin Ömer Faruk , Iyisoy Atila 
Published: August 2019

Abstract

Background
Septal reduction therapy can be considered along the lines of hypertrophic obstructive cardiomyopathy patients who have drug-refractory symptoms. This can be applied either surgical myectomy or either alcohol septal ablation (ASA). Alcohol septal ablation has been performed successfully since the first announcement of ASA in 1995.

Case summary
We present a case report of coronary artery vasospasm that occurred in the left anterior descending artery (LAD) during ASA. We performed ASA via first septal artery. Two cubic centimetre of 99% ethanol was slowly injected and 10 min later balloon was withdrawn. Then the patient felt severe chest pain; his systolic blood pressure went down quickly and fibrillated. We started the cardiopulmonary resuscitation (CPR). After CPR, the rhythm was achieved total 4 min later cardiac arrest but blood pressure was low. Emergent coronary angiography showed that coronary spasm caused severe occlusion in the LAD segment just after the first septal artery and impaired coronary flow nearly totally in the LAD just after septal artery. At that time, we decided to implant a stent due to the patient’s serious condition and a 3.5 × 18 mm drug-eluting stent was implanted. We performed control angiography to patient 3 days later of the procedure and LAD flow was TIMI 3.

Discussion
The causes of LAD occlusion are alcohol leakage, dissection, and vasospasm. It is important to detect the correct reason for appropriate treatment. Alcohol leakage impairs and causes coronary flow disruption; this can cause ventricular wall motion abnormalities. In our case, there was severe spasm in the LAD coronary artery and LAD flow was severely impaired. On echocardiogram, there was no myocardial wall motion abnormality. So alcohol leakage was ruled out. Left anterior descending artery image was not typical dissection. As a result of these findings, we concluded that the cause of LAD occlusion was coronary artery vasospasm.
‘The Nation Rejoices or Mourns’: Literary and Cultural Ambivalences in Wendy Cope’s Making Cocoa for Kingsley Amis (1986)
Authors: Waterman Rory 
Published: August 2019

Abstract
The poet Wendy Cope gained a huge reputation in the early 1980s mainly for a series of witty and incisive parodies, often under the name of her desperate fictional poète maudit Jake Strugnell, and these poems were collected, along with others, in her hugely successful and influential debut collection, Making Cocoa for Kingsley Amis, which appeared in 1986. This book sold almost 200,000 copies, but has been the subject of a very small body of criticism. Many of her contemporary poet-critics were dismissive: in one contemporary review, Peter Riley epitomized a not uncommon reaction when he claimed that no ‘poetic import can be claimed for the book’, and railed against ‘a new audience for poetry, one which must be presumed to have previously fought shy of it as too difficult or too deep’. Certainly, Making Cocoa for Kingsley Amis is not a work of avant garde complexity, but Cope’s debut is not as cosily complacent as such critics indicate. It is in fact highly allusive and resistant to orthodoxies – and was a thorn in the side of the literary and cultural establishment into which she was instantly propelled. This essay assesses the ways in which Cope’s debut collection takes an ambivalent, nuanced, and parodic response to British institutions, and to the orthodoxies of the male-dominated literary world she was entering.
The Impact of Natural Selection on the Evolution and Function of Placentally Expressed Galectins
Authors: Ely Zackery A , Moon Jiyun M , Sliwoski Gregory R , Sangha Amandeep K , Shen Xing-Xing , Labella Abigail L , Meiler Jens , Capra John A , Rokas Antonis 
Published: August 2019

Abstract
Immunity genes have repeatedly experienced natural selection during mammalian evolution. Galectins are carbohydrate-binding proteins that regulate diverse immune responses, including maternal–fetal immune tolerance in placental pregnancy. Seven human galectins, four conserved across vertebrates and three specific to primates, are involved in placental development. To comprehensively study the molecular evolution of these galectins, both across mammals and within humans, we conducted a series of between- and within-species evolutionary analyses. By examining patterns of sequence evolution between species, we found that primate-specific galectins showed uniformly high substitution rates, whereas two of the four other galectins experienced accelerated evolution in primates. By examining human population genomic variation, we found that galectin genes and variants, including variants previously linked to immune diseases, showed signatures of recent positive selection in specific human populations. By examining one nonsynonymous variant in Galectin-8 previously associated with autoimmune diseases, we further discovered that it is tightly linked to three other nonsynonymous variants; surprisingly, the global frequency of this four-variant haplotype is ∼50%. To begin understanding the impact of this major haplotype on Galectin-8 protein structure, we modeled its 3D protein structure and found that it differed substantially from the reference protein structure. These results suggest that placentally expressed galectins experienced both ancient and more recent selection in a lineage- and population-specific manner. Furthermore, our discovery that the major Galectin-8 haplotype is structurally distinct from and more commonly found than the reference haplotype illustrates the significance of understanding the evolutionary processes that sculpted variants associated with human genetic disease.
Current and Promising Approaches to Identify Horizontal Gene Transfer Events in Metagenomes
Authors: Douglas Gavin M , Langille Morgan G I 
Published: August 2019

AbstractHigh-throughput shotgun metagenomics sequencing has enabled the profiling of myriad natural communities. These data are commonly used to identify gene families and pathways that were potentially gained or lost in an environment and which may be involved in microbial adaptation. Despite the widespread interest in these events, there are no established best practices for identifying gene gain and loss in metagenomics data. Horizontal gene transfer (HGT) represents several mechanisms of gene gain that are especially of interest in clinical microbiology due to the rapid spread of antibiotic resistance genes in natural communities. Several additional mechanisms of gene gain and loss, including gene duplication, gene loss-of-function events, and de novo gene birth are also important to consider in the context of metagenomes but have been less studied. This review is largely focused on detecting HGT in prokaryotic metagenomes, but methods for detecting these other mechanisms are first discussed. For this article to be self-contained, we provide a general background on HGT and the different possible signatures of this process. Lastly, we discuss how improved assembly of genomes from metagenomes would be the most straight-forward approach for improving the inference of gene gain and loss events. Several recent technological advances could help improve metagenome assemblies: long-read sequencing, determining the physical proximity of contigs, optical mapping of short sequences along chromosomes, and single-cell metagenomics. The benefits and limitations of these advances are discussed and open questions in this area are highlighted.
Potential Effect of Immunotherapy Agents on Cognitive Function in Cancer Patients
Authors: Joly Florence , Castel Hélène , Tron Laure , Lange Marie , Vardy Janette 
Published: August 2019

Abstract
A paradigm shift is occurring in cancer therapy, where instead of targeting tumor cells, immunotherapy agents (IA) target the immune system to overcome cancer tolerance and to stimulate an antitumor immune response. IA using immune checkpoint inhibitors (CPI) or chimeric antigen receptor T-cells have emerged as the most encouraging approaches to treat cancer patients. CPI are reported to induce moderate-to-severe neurologic immune-related adverse events in less than 1% of patients, whereas chimeric antigen receptor T-cell therapy is associated with frequent neurological toxicities that can be severe or even fatal. Cognitive difficulties have been described following chemotherapy and targeted therapy, but not specifically explored in patients receiving IA. The aim of this review is to establish a picture of the first published studies suggesting some biological and physiopathological effects of IA on cognitive functions among cancer patients. The first results originate from a preclinical study evaluating the role of CPI associated with peripheral radiation on cognitive dysfunction and the recent discovery of the central nervous lymphatic system allowing leukocytes to penetrate the central nervous system. Evaluating possible side effects of IA on cognitive function will be an important challenge for future clinical trials and for better understanding the underlying mechanisms through preclinical animal models.
Beliefs About HPV Vaccine’s Success at Cervical Cancer Prevention Among Adult US Women
Authors: Fokom Domgue Joël , Chido-Amajuoyi Onyema G , Yu Robert K , Shete Sanjay 
Published: August 2019

AbstractBackgroundBeliefs are known to be a key determinant in vaccines’ uptake. However, little is known about beliefs surrounding the success of the human papillomavirus (HPV) vaccine in preventing cervical cancer in the United States.MethodsData from the Health Information National Trends Survey 5 Cycle 1 (2017) were analyzed for 1851 female respondents aged 18 years and older. Weighted multinomial logistic regression was employed to determine predictors of beliefs in the success of the HPV vaccine in preventing cervical cancer.ResultsOverall, 29.8% of women believed that HPV vaccine is successful in preventing cervical cancer, 6.6% believed it is not successful, and 63.6% did not know if the HPV vaccine is successful. Non-Hispanic blacks (adjusted odds ratio [aOR] = 1.80, 95% confidence interval [CI] = 1.16 to 2.79), women with no more than 12 years of education (aOR = 2.05, 95% CI = 1.17 to 3.60), those who did not know if they were advised by a health-care provider to get an HPV shot within the last 12 months (aOR = 4.19, 95% CI = 1.39 to 12.60), and those unaware of a family cancer history (aOR = 5.17, 95% CI = 1.48 to 18.21) were more likely to not know whether the HPV vaccine prevents cervical cancer. Women younger than 65 years were more likely than elderly to believe that the HPV vaccine is not successful at preventing cervical cancer.ConclusionsA substantial proportion of US women are uninformed about the HPV vaccine. To accelerate progress in the HPV vaccine’s uptake, future interventions should incorporate educational programs, particularly targeting Non-Hispanic blacks, women with a lower level of education, and those younger than 65 years. Health-care providers’ participation in promotion of patient education about HPV vaccination should also be increased.
Measuring the growth of structure by matching dark matter haloes to galaxies with VIPERS and SDSS
Authors: Granett Benjamin R , Favole Ginevra , Montero-Dorta Antonio D , Branchini Enzo , Guzzo Luigi , de la Torre Sylvain 
Published: August 2019

ABSTRACT
We test the history of structure formation from redshift 1 to today by matching galaxies from the VIMOS Public Extragalactic Redshift Survey (VIPERS) and Sloan Digital Sky Survey (SDSS) with dark matter haloes in the MultiDark, Small MultiDark Planck (SMDPL), N-body simulation. We first show that the standard subhalo abundance matching (SHAM) recipe implemented with MultiDark fits the clustering of galaxies well both at redshift 0 for SDSS and at redshift 1 for VIPERS. This is an important validation of the SHAM model at high redshift. We then remap the simulation time steps to test alternative growth histories and infer the growth index γ = 0.6 ± 0.3. This analysis demonstrates the power of using N-body simulations to forward model galaxy surveys for cosmological inference. The data products and code necessary to reproduce the results of this analysis are available online (https://github.com/darklight-cosmology/vipers-sham).
Machine-assisted Semi-Simulation Model (MSSM): Estimating Galactic Baryonic Properties from Their Dark Matter Using A Machine Trained on Hydrodynamic Simulations
Authors: Jo Yongseok , Kim Ji-hoon 
Published: August 2019

Abstract
We present a pipeline to estimate baryonic properties of a galaxy inside a dark matter (DM) halo in DM-only simulations using a machine trained on high-resolution hydrodynamic simulations. As an example, we use the IllustrisTNG hydrodynamic simulation of a (75  h−1Mpc)3 volume to train our machine to predict e.g., stellar mass and star formation rate in a galaxy-sized halo based purely on its DM content. An extremely randomized tree (ERT) algorithm is used together with multiple novel improvements we introduce here such as a refined error function in machine training and two-stage learning. Aided by these improvements, our model demonstrates a significantly increased accuracy in predicting baryonic properties compared to prior attempts — in other words, the machine better mimics IllustrisTNG’s galaxy-halo correlation. By applying our machine to the MultiDark-Planck DM-only simulation of a large (1  h−1Gpc)3 volume, we then validate the pipeline that rapidly generates a galaxy catalogue from a DM halo catalogue using the correlations the machine found in IllustrisTNG. We also compare our galaxy catalogue with the ones produced by popular semi-analytic models (SAMs). Our so-called machine-assisted semi-simulation model (MSSM) is shown to be largely compatible with SAMs, and may become a promising method to transplant the baryon physics of galaxy-scale hydrodynamic calculations onto a larger-volume DM-only run. We discuss the benefits that machine-based approaches like this entail, as well as suggestions to raise the scientific potential of such approaches.
Smaller stellar disc scale lengths in rich environments
Authors: Demers Melanie L , Parker Laura C , Roberts Ian D 
Published: August 2019

Abstract
We investigate the dependence of stellar disc scale lengths on environment for a sample of Sloan Digital Sky Survey Data Release 7 galaxies with published photometric bulge-disc decompositions. We compare disc scale lengths at fixed bulge mass for galaxies in an isolated field environment to galaxies in X-ray rich and X-ray poor groups. At low bulge mass, stellar disc scale lengths in X-ray rich groups are smaller compared to discs in both X-ray poor groups and in isolated field environments. This decrease in disc scale length is largely independent of halo mass, though shows some dependence on group-centric distance. We also find that stellar disc scale lengths are smaller in X-ray rich environments for a subset of star-forming galaxies and for galaxies of different morphological types. We note that disc scale lengths of low mass galaxies are known to have large systematic uncertainties, however we focus on differences between samples with the same measurement biases. Our results show that stellar disc scale lengths depend on X-ray brightness, a tracer of IGM density, suggesting a role for hydrodynamic processes such as ram-pressure stripping and/or starvation.
The Association Between Tobacco Outlet Density and Smoking Among Young People: A Systematic Methodological Review
Authors: Nuyts Paulien A W , Davies Lisa E M , Kunst Anton E , Kuipers Mirte A G 
Published: August 2019

Abstract

Aim
Evidence on the association between tobacco outlet density and proximity and smoking behavior among youth is inconsistent, which may be due to methodological problems in some studies. We assessed the association of outlet density or proximity with smoking behavior among young people while taking into account the methodological quality of studies.

Methods
MEDLINE, EMBASE, and Google Scholar were systematically searched for studies on the relationship between outlet density or proximity and smoking behavior among 12- to 25-year-olds, published between 1997 and 2017. Methodological quality of the included studies was evaluated independently by two reviewers.

Results
Twenty studies were included in the review. The quality assessment identified five primary sources of potential bias: overadjustment for mediators (problems identified in 14 studies), underadjustment for confounders (six studies), poor statistical model fit (four studies), selection bias (three studies), and misclassification of exposure measurements (eight studies). Four studies were of high methodological quality. In studies with relatively high quality, 10 associations were reported, of which seven were nonsignificant, two positive, and one negative. Similarly, the complete body of evidence demonstrated mostly nonsignificant associations, but a larger proportion of positive associations than negative.

Conclusion
Although there is some support for a positive direction, current literature does not provide consistent evidence for a positive association between outlet density and smoking among youth. This is not necessarily due to bias in specific studies, but more to fundamental challenges in study design and exposure measurements. These issues need to be addressed in future studies using more rigorous methods.

Implications
Our findings suggest that, although there is some evidence for a positive association, current scientific literature does not provide consistent support to claim an effect of tobacco outlet density or proximity on youth smoking. This underlines the need for more research with improved methodology. There is a need for quasiexperimental studies, in which the outlet density changes substantially, studies measuring the actual exposure of youth to tobacco outlets, and qualitative research on the mechanisms underlying any association.
Effect of supplementing a Saccharomyces cerevisiae fermentation product during a preconditioning period prior to transit on receiving period performance, nutrient digestibility, and antioxidant defense by beef steers
Authors: Deters Erin L , Hansen Stephanie L 
Published: August 2019

Abstract:
Forty-eight newly weaned crossbred beef steers from a single-source were used to determine the effects of feeding a Saccharomyces cerevisiae fermentation product (SCFP; NaturSafe, Diamond V) on receiving period performance, nutrient digestibility, and antioxidant defense. Seven days after arrival, steers were stratified by BW (257 ± 18 kg), sorted into pens (n = 1 pen/treatment), and pens assigned to dietary treatments: SCFP at 0 (CON), 12 (SCFP12), 18 (SCFP18), or 0 g·steer−1·d−1 during preconditioning (PRE; days −19 to 0), then 18 g·steer−1·d−1 during receiving (REC; days 0 to 58; CON18). On day −1 BW and blood were collected, steers were loaded onto a semitruck and transported 1,748 km over 19 h. Upon return, steers were weighed, stratified by BW within treatment and sorted into pens with GrowSafe bunks (n = 12 steers/treatment). Steers were weighed on days −1, 0, 29, 30, 57, and 58. Blood was collected from all steers on days −1, 1, and 8 and liver biopsies were performed on all steers on days −20, −3, and 59. Titanium dioxide was included as an indigestible marker in the diet of all steers from days 14 through 29 to determine total tract nutrient digestibility. Data were analyzed as a completely randomized design using ProcMixed of SAS with the fixed effect of treatment. Steer was the experimental unit for REC period variables. Contrast statements compared the linear and quadratic effects of feeding SCFP throughout the trial (CON, SCFP12, and SCFP18) and the effect of supplementation at 18 g·steer−1·d−1 for the entire trial or starting in REC (SCFP18 vs. CON18). Steers fed SCFP12 exhibited the greatest ADG and G:F from days 0 to 30 (quadratic P ≤ 0.04). Total tract digestibility of NDF and ADF was linearly decreased by SCFP (linear P ≤ 0.03). On day −3, SCFP12-fed steers tended to have the greatest liver concentrations of total, oxidized, and reduced glutathione (quadratic P = 0.06). Red blood cell lysate Mn:total-superoxide dismutase activity was 16% greater 1 d posttransit compared with pretransit values (day P ≤ 0.01). Timing of SCFP supplementation (SCFP18 vs. CON18) did not affect any of the variables assessed herein (P ≥ 0.19). Supplementing SCFP at 12 g·steer−1·d−1 tended to affect antioxidant capacity prior to transit and improved early receiving period performance; however, overall receiving period performance was not affected by SCFP supplementation. Further research is necessary to determine the optimal dose and timing of SCFP supplementation for beef cattle.