bluuebunny/crossref_metadata_2025_split huggingface dataset:
Niacin deficiency modulates genes involved in cancer: Are smokers at higher risk?
Authors: Lohani Mohtashim , Dhasmana Anupam , Haque Shafiul , Dar Sajad A. , Jawed Arshad , Wahid Mohd , Mandal Raju K. , Akhter Naseem , Farasani Abdullah , Hobani Yahya Hassan , Singh Ankita , Hussain Showket 
Published: September 2018

AbstractThe role of niacin’s metabolite, nicotinamide adenine dinucleotide (NAD), in DNA repair via base‐excision repair pathway is well documented. We evaluated if niacin deficiency results in genetic instability in normal human fetal lung fibroblasts (MRC‐5), and further, does it leads to enhanced accumulation of cigarette smoke–induced genetic damage? MRC‐5 cells were grown discretely in niacin‐proficient/deficient media, and exposed to nicotine‐derived nitrosamine ketone (NNK, a cigarette smoke carcinogen). Niacin deficiency abated the NAD polymerization, augmented the spontaneous induction of micronuclei (MN) and chromosomal aberrations (CA) and raised the expression of 10 genes and suppressed 12 genes involved in different biological functions. NNK exposure resulted in genetic damage as measured by the induction of MN and CA in cells grown in niacin‐proficient medium, but the damage became practically marked when niacin‐deficient cells were exposed to NNK. NNK exposure raised the expression of 16 genes and suppressed the expression of 56 genes in cells grown in niacin‐proficient medium. NNK exposure to niacin‐deficient cells raised the expression of eight genes including genes crucial in promoting cancer such as FGFR3 and DUSP1 and suppressed the expression of 33 genes, including genes crucial in preventing the onset and progression of cancer like RASSF2, JUP, and IL24, in comparison with the cells grown in niacin‐proficient medium. Overall, niacin deficiency interferes with the DNA damage repair process induced by chemical carcinogens like NNK, and niacin‐deficient population are at the higher risk of genetic instability caused by cigarette smoke carcinogen NNK.
Exploring the concentration‐dependent actions of interferon‐τ on bovine neutrophils to understand the process of implantation
Authors: Manjari P. , Hyder Iqbal , Kapoor Suresh , Senthilnathan M. , Dang A. K. 
Published: September 2018

AbstractInterferon‐τ (IFNT) is a major cytokine produced by the ruminant trophoectoderm during the peri‐implantation period exerting immunomodulatory actions on various cells including neutrophils. The current in vitro study was undertaken to analyze the concentration‐dependent effects of IFNT on neutrophil gene dynamics to understand its possible role in implantation process. The neutrophils were isolated from the blood of heifers and were cultured subjecting them to different IFNT concentrations (1, 5, or 10 ng/mL). The gene‐expression patterns of different interferon‐stimulated genes, l‐selectin, CD31, CD11b, and progesterone‐induced blocking factor (PIBF) were analyzed by quantitative real‐time PCR. It was observed that at lower concentrations of IFNT, the IFI16, l‐selectin, ISG15, and PIBF were upregulated, whereas at higher concentrations the same were down regulated. At all the experimental concentrations, IFI44, OAS1, MX genes were significantly upregulated and CD31, CD11b were significantly downregulated. At lower concentrations of IFNT, the neutrophil activity with respect to chemoattraction is stimulated, whereas at higher concentrations the same is reduced. Hence, it can be concluded that IFNT exerts concentration‐dependent actions on neutrophil gene‐expression dynamics indicating a fine modulation of its activity depending upon the temporal variation in its destined functions ultimately leading to successful implantation.
PNPLA3 variant M148 causes resistance to starvation‐mediated lipid droplet autophagy in human hepatocytes
Authors: Negoita Florentina , Blomdahl Julia , Wasserstrom Sebastian , Winberg Martin E. , Osmark Peter , Larsson Sara , Stenkula Karin G. , Ekstedt Mattias , Kechagias Stergios , Holm Cecilia , Jones Helena A. 
Published: September 2018

AbstractThe mechanism of how patatin‐like phospholipase domain‐containing protein 3 (PNPLA3) variant M148 is associated with increased risk of development of hepatic steatosis is still debated. Here, we propose a novel role of PNPLA3 as a key player during autophagosome formation in the process of lipophagy. A human hepatocyte cell line, HepG2 cells, expressing recombinant I148 or 148M, was used to study lipophagy under energy deprived conditions, and lipid droplet morphology was investigated using florescence microscopy, image analysis and biochemical assays. Autophagic flux was studied using the golden‐standard of LC3‐II turnover in combination with the well characterized GFP‐RFP‐LC3 vector. To discriminate between, perturbed autophagic initiation and lysosome functionality, lysosomes were characterized by Lysotracker staining and LAMP1 protein levels as well as activity and activation of cathepsin B. For validation, human liver biopsies genotyped for I148 and 148M were analyzed for the presence of LC3‐II and PNPLA3 on lipid droplets. We show that the M148‐PNPLA3 variant is associated with lipid droplets that are resistant to starvation‐mediated degradation. M148 expressing hepatocytes reveal decreased autophagic flux and reduced lipophagy. Both I148‐PNPLA3 and M148‐PNPLA3 colocalize and interact with LC3‐II, but the M148‐PNPLA3 variant has lower ability to bind LC3‐II. Together, our data indicate that PNPLA3 might play an essential role in lipophagy in hepatocytes and furthermore that the M148‐PNPLA3 variant appears to display a loss in this activity, leading to decreased lipophagy.
Constructions of augmented orthogonal arrays
Authors: Wang Xin , Ji Lijun , Li Yun , Liang Miao 
Published: September 2018

AbstractAugmented orthogonal arrays (AOAs) were introduced by Stinson, who showed the equivalence between ideal ramp schemes and AOAs (Discrete Math. 341 (2018), 299–307). In this paper, we show that there is an AOAif and only if there is an OAwhich can be partitioned intosubarrays, each being an OA, and that there is a linear AOAif and only if there is a linear maximum distance separable (MDS) code of lengthand dimensionover, which contains a linear MDS subcode of lengthand dimensionover. Some constructions for AOAs and some new infinite classes of AOAs are also given.
Shear stress promotes anoikis resistance of cancer cells via caveolin‐1‐dependent extrinsic and intrinsic apoptotic pathways
Authors: Li Shun , Chen Yu , Zhang Yuehui , Jiang Xiaomin , Jiang Ying , Qin Xiang , Yang Hong , Wu Chunhui , Liu Yiyao 
Published: September 2018

AbstractCirculating tumor cells (CTCs) need to acquire resistance to anoikis to survive after they experience fluid shear stress in the circulatory and lymphatic systems. However, the mechanism by which tumor cells resist anoikis under shear stress conditions remains unknown. Here, we found that the application of low shear stress (LSS; 2 dyn/cm2) to human breast carcinoma cells (MDA‐MB‐231) resulted in increased anoikis resistance when tumor cells were grown under anchorage‐independent conditions. Caveolin‐1 (Cav‐1), the major component of plasma membrane caveolae, was overexpressed in LSS‐treated cells and prevented tumor cells from anoikis, while depletion of Cav‐1 restored sensitivity to anoikis. LSS‐induced dissociation of Cav‐1–Fas inhibited formation of the death‐inducing signaling complex, caspase‐8 activation, and rendered tumor cells resistant to anoikis. Likewise, LSS blocked the mitochondrial pathway through promotion of integrin β1–focal adhesion kinase‐mediated multicellular aggregation and suppression of truncated BID translocation mediated crosstalk between the extrinsic and intrinsic apoptotic pathways. Our findings provide insights into the mechanisms by which LSS induces anoikis resistance in breast carcinoma cells through inhibition of Cav‐1‐dependent extrinsic and intrinsic apoptotic pathways, and serves as a potential therapeutic target for CTCs and metastatic breast cancer.
Interest of neuroimaging of social exclusion in suicide
Authors: Olié Emilie , Courtet Philippe 
Published: September 2018

AbstractWith one million deaths worldwide, suicide is a major health issue. The frequency of life events preceding suicidal act is high and raises the question of their role in suicidal process. At biological level, dysfunctional neural processing of social exclusion may participate in suicidal risk through an increased perception of social adversity in vulnerable subjects. The purpose of this narrative review is to discuss neuroimaging findings related to social exclusion and loneliness, and to open new perspectives to investigate sensitivity to social stress in suicide.
Evaluation of Normal and Varicocele‐Bearing Testes Using Real‐time Strain Elastography
Authors: Salama Nader , Samir Mohamed , Blgozah Saeed 
Published: September 2018

ObjectivesTo evaluate testes in patients with varicocele using real‐time strain elastography and to correlate the results with the patients' clinical, seminal, and hormonal profiles.MethodsFifty patients with left varicocele and 20 age‐matched control participants were included in the study. All participants were evaluated via a historical interview, clinical examination, including testicular volume and varicocele grade, hormonal assay (total and free testosterone, luteinizing hormone, and follicle‐stimulating hormone), computer‐assisted semen analysis, and testicular assessment using real‐time strain elastography to define the strain ratio and elasticity score.ResultsTesticular volume and sperm parameters were significantly lower (P < .001), whereas the follicle‐stimulating hormone level, strain ratio, and elasticity score were significantly higher (P < .01; P < .001; P < .001, respectively), in the varicocele group. Other hormone levels in the endocrine profile were not significantly different between the groups. Significant negative correlations were found between the elasticity score and testicular volume and the percentage of normal forms (P = .029; P = .005). The varicocele grade showed significant positive correlations with both the strain ratio and elasticity score (P < .001).ConclusionsStrong correlations were found between real‐time strain elastography and the testicular volume, varicocele grade, and sperm morphologic characteristics. Real‐time strain elastography is a simple, noninvasive investigative modality that can potentially be used to study the structure and function of the testicular tissue in varicocele.
A Hybrid Multilayer Filtering Approach for Thyroid Nodule Segmentation on Ultrasound Images
Authors: Abbasian Ardakani Ali , Bitarafan‐Rajabi Ahmad , Mohammadzadeh Ali , Mohammadi Afshin , Riazi Reza , Abolghasemi Jamileh , Homayoun Jafari Amir , Bagher Shiran Mohammad 
Published: September 2018

ObjectivesSpeckle noise is the main factor that degrades ultrasound image contrast and segmentation failure. Determining an effective filter can reduce speckle noise and improve segmentation performances. The aim of this study was to define a useful filter to improve the segmentation outcome.MethodsTwelve filters, including median, hybrid median (Hmed), Fourier Butterworth, Fourier ideal, wavelet (Wlet), homomorphic Fourier Butterworth, homomorphic Fourier ideal, homomorphic wavelet (Hmp_Wlet), frost, anisotropic diffusion, probabilistic patch‐based (PPB), and homogeneous area filters, were used to find the best filter(s) to prepare thyroid nodule segmentation. A receiver operating characteristic (ROC) analysis was used for filter evaluation in the nodule segmentation process. Accordingly, 10 morphologic parameters were measured from segmented regions to find the best parameters that predict the segmentation performance.ResultsThe best segmentation performance was reached by using 4 hybrid filters that mainly contain contrast‐limited adaptive histogram equalization, Wlet, Hmed, Hmp_Wlet, and PPB filters. The area under the ROC curve for these filters ranged from 0.900 to 0.943 in comparison with the original image, with an area under the curve of 0.685. From 10 morphologic parameters, the area, convex area, equivalent diameter, solidity, and extent can evaluate segmentation performance.ConclusionsHybrid filters that contain contrast‐limited adaptive histogram equalization, Wlet, Hmed, Hmp_Wlet, and PPB filters have a high potential to provide good conditions for thyroid nodule segmentation in ultrasound images. In addition to an ROC analysis, morphometry of a segmented region can be used to evaluate segmentation performances.
Atmospheric chemistry ofn‐CH3(CH2)xCN (x = 0–3): Kinetics and mechanisms
Authors: Andersen Simone Thirstrup , Kyte Mildrid , Andersen Lene Løffler , Nielsen Ole John , Sulbaek Andersen Mads P. 
Published: September 2018

AbstractSmog chamber/Fourier transform infrared (FTIR) techniques were used to measure the kinetics of the reaction ofn‐CH3(CH2)xCN (x = 0–3) with Cl atoms and OH radicals:k(CH3CN + Cl) = (1.04 ± 0.25) × 10−14,k(CH3CH2CN + Cl) = (9.20 ± 3.95) × 10−13,k(CH3(CH2)2CN + Cl) = (2.03 ± 0.23) × 10−11,k(CH3(CH2)3CN + Cl) = (6.70 ± 0.67) × 10−11,k(CH3CN + OH) = (4.07 ± 1.21) × 10−14,k(CH3CH2CN + OH) = (1.24 ± 0.27) × 10−13,k(CH3(CH2)2CN + OH) = (4.63 ± 0.99) × 10−13, andk(CH3(CH2)3CN + OH) = (1.58 ± 0.38) × 10−12cm3molecule−1s−1at a total pressure of 700 Torr of air or N2diluents at 296 ± 2 K. The atmospheric oxidation of alkyl nitriles proceeds through hydrogen abstraction leading to several carbonyl containing primary oxidation products. HC(O)CN, NCC(O)OONO2, ClC(O)OONO2, and HCN were identified as the main oxidation products from CH3CN, whereas CH3CH2CN gives the products HC(O)CN, CH3C(O)CN, NCC(O)OONO2, and HCN. The oxidation ofn‐CH3(CH2)xCN (x = 2–3) leads to a range of oxygenated primary products. Based on the measured OH radical rate constants, the atmospheric lifetimes ofn‐CH3(CH2)xCN (x = 0–3) were estimated to be 284, 93, 25, and 7 days forx = 0,1, 2, and 3, respectively.
Response of Riparian Vegetation, Instream Habitat, and Aquatic Biota to Riparian Grazing Exclosures
Authors: Dauwalter Daniel C. , Fesenmyer Kurt A. , Miller Scott W. , Porter Tucker 
Published: September 2018

Abstract
Improper riparian grazing can alter riparian vegetation and reduce streambank stability, negatively impacting aquatic habitat and biota. We evaluated differences in riparian and instream habitat, benthic macroinvertebrates, and fish inside versus outside seven riparian exclosures constructed from 1982 to 2005 in Idaho. The normalized difference vegetation index from Landsat imagery (1985 to 2015) showed significant increases in riparian vegetation productivity after some but not all exclosures were constructed. Field data collected in 2015 showed woody riparian vegetation to be more abundant, streambanks less altered, and stream channels narrower inside versus outside exclosures, as we expected. However, instream habitat, a benthic macroinvertebrate index, fish species richness, and adult salmonid density showed no response. Higher age-0 salmonid densities were the only aquatic organism response observed. Broader watershed-scale factors likely limited strong and consistent responses by aquatic biota to exclosures. We conclude that riparian exclosures have localized effects on stream systems, such as increased riparian vegetation, reduced streambank alteration, and improved channel stability, but may not always influence aquatic biota that commonly reflect larger watershed-scale processes and conditions. Therefore, well-maintained riparian exclosures should be used to eliminate livestock use in localized areas of stream corridors that are sensitive to disturbance. To improve stream health at the larger watershed scale that is relevant to most aquatic biota, exclosures should only be one of several grazing management tools implemented simultaneously to reduce the impacts of improper livestock grazing.
Hybridization and Genetic Structure of Neosho Smallmouth Bass in the Ozark Highlands
Authors: Taylor Andrew T. , Long James M. , Schwemm Michael R. , Brewer Shannon K. 
Published: September 2018

Abstract
The Neosho Smallmouth Bass Micropterus dolomieu velox is endemic to Arkansas River tributaries originating in the Ozark Highlands and Boston Mountains. Although morphologically and genetically distinct from other populations of Smallmouth Bass M. dolomieu, the conservation-genetic status of Neosho Smallmouth Bass is largely unknown. To assist in filling this data gap, we quantified introgressive hybridization, genetic diversity, and population structure of Neosho Smallmouth Bass in two major river basins (Grand River and Illinois River) using seven polymorphic microsatellite markers. Introgressive hybridization with stocked Tennessee lake-strain Smallmouth Bass was most prevalent in the Illinois River, wherein the overall genomic proportion of Neosho Smallmouth Bass alleles was only 0.422. After accounting for hybrid individuals, genetic diversity of Neosho Smallmouth Bass was generally higher in larger rivers and lower in smaller, isolated streams. Three distinct population clusters were identified at the uppermost level of genetic structure—one from the Illinois River basin and two from the Grand River basin. These three population boundaries accounted for approximately 7% of the hierarchical genetic variation within our data set, and substructure below the uppermost level accounted for an additional 2% of genetic variation. The population structure we discovered can provide a blueprint for management that conserves diversity within and among populations; for example, population boundaries can be used to determine brood source locations for supplemental stocking efforts to counter nonnative introgression. Introgressive hybridization with nonnative Smallmouth Bass appears to be the most pertinent threat to the Neosho Smallmouth Bass subspecies, which is of conservation value to the overall adaptability of Smallmouth Bass as a species.
Chromatin Remodeling Factor BRG1 Regulates Stemness and Chemosensitivity of Glioma Initiating Cells
Authors: Ganguly Debolina , Sims Michelle , Cai Chun , Fan Meiyun , Pfeffer Lawrence M. 
Published: September 2018

Abstract
Glioblastoma multiforme (GBM) is a highly aggressive and malignant brain tumor that is refractory to existing therapeutic regimens, which reflects the presence of stem-like cells, termed glioma-initiating cells (GICs). The complex interactions between different signaling pathways and epigenetic regulation of key genes may be critical in the maintaining GICs in their stem-like state. Although several signaling pathways have been identified as being dysregulated in GBM, the prognosis of GBM patients remains miserable despite improvements in targeted therapies. In this report, we identified that BRG1, the catalytic subunit of the SWI/SNF chromatin remodeling complex, plays a fundamental role in maintaining GICs in their stem-like state. In addition, we identified a novel mechanism by which BRG1 regulates glycolysis genes critical for GICs. BRG1 downregulates the expression of TXNIP, a negative regulator of glycolysis. BRG1 knockdown also triggered the STAT3 pathway, which led to TXNIP activation. We further identified that TXNIP is an STAT3-regulated gene. Moreover, BRG1 suppressed the expression of interferon-stimulated genes, which are negatively regulated by STAT3 and regulate tumorigenesis. We further demonstrate that BRG1 plays a critical role in the drug resistance of GICs and in GIC-induced tumorigenesis. By genetic and pharmacological means, we found that inhibiting BRG1 can sensitize GICs to chemotherapeutic drugs, temozolomide and carmustine. Our studies suggest that BRG1 may be a novel therapeutic target in GBM. The identification of the critical role that BRG1 plays in GIC stemness and chemosensitivity will inform the development of better targeted therapies in GBM and possibly other cancers.
Concise Review: Heart-Derived Cell Therapy 2.0: Paracrine Strategies to Increase Therapeutic Repair of Injured Myocardium
Authors: Rafatian Ghazaleh , Davis Darryl R. 
Published: September 2018

Abstract
Despite progress in cardiovascular medicine, the incidence of heart failure is rising and represents a growing challenge. To address this, ex vivo proliferated heart-derived cell products have emerged as a promising investigational cell-treatment option. Despite being originally proposed as a straightforward myocyte replacement strategy, emerging evidence has shown that cell-mediated gains in cardiac function are leveraged on paracrine stimulation of endogenous repair and tissue salvage. In this concise review, we focus on the paracrine repertoire of heart-derived cells and outline strategies used to boost cell potency by targeting cytokines, metabolic preconditioning and supportive biomaterials. Mechanistic insights from these studies will shape future efforts to use defined factors and/or synthetic cell approaches to help the millions of patients worldwide suffering from heart failure.
NLO QCD corrections to SM-EFT dilepton and electroweak Higgs boson production, matched to parton shower in POWHEG
Authors: Alioli Simone , Dekens Wouter , Girard Michael , Mereghetti Emanuele 
Published: September 2018

AbstractWe discuss the Standard Model — Effective Field Theory (SM-EFT) contributions to neutral- and charge-current Drell-Yan production, associated production of the Higgs and a vector boson, and Higgs boson production via vector boson fusion. We consider all the dimension-six SM-EFT operators that contribute to these processes at leading order, include next-to-leading order QCD corrections, and interface them with parton showering and hadronization in Pythia8 according to the POWHEG method. We discuss existing constraints on the coefficients of dimension-six operators and identify differential and angular distributions that can differentiate between different effective operators, pointing to specific features of Beyond-the-Standard-Model physics.
Ultraluminous X-ray sources as magnetically powered sub-Eddington advective accretion flows around stellar mass black holes
Authors: Mondal Tushar , Mukhopadhyay Banibrata 
Published: September 2018

ABSTRACT
In order to explain unusually high luminosity and spectral nature of ultraluminous X-ray sources (ULXs), some of the underlying black holes are argued to be of intermediate mass, between several tens to million solar masses. Indeed, there is a long standing question of missing mass of intermediate range of black holes. However, as some ULXs are argued to be neutron stars too, often their unusual high luminosity is argued by super-Eddington accretions. Nevertheless, all the models are based on non-magnetized or weakly magnetized accretion. There are, however, pieces of evidence that magnetic fields in accretion discs/flows around a stellar mass black hole could be million Gauss. Such a magnetically arrested accretion flow plausibly plays a key role to power many combined disc-jet/outflow systems. Here we show that flow energetics of a 2.5-dimensional advective magnetized accretion disc/outflow system around a stellar mass black hole are sufficient to explain power of ULXs in their hard states. Hence, they are neither expected to have intermediate mass black holes nor super-Eddington accretors. We suggest that at least some ULXs are magnetically powered sub-Eddington accretors around a stellar mass black hole.
Structuralist Neologicism†
Authors: Boccuni Francesca , Woods Jack 
Published: September 2018

ABSTRACTNeofregeanism and structuralism are among the most promising recent approaches to the philosophy of mathematics. Yet both have serious costs. We develop a view, structuralist neologicism, which retains the central advantages of each while avoiding their more serious costs. The key to our approach is using arbitrary reference to explicate how mathematical terms, introduced by abstraction principles, refer. Focusing on numerical terms, this allows us to treat abstraction principles as implicit definitions determining all (known) properties of the numbers, achieving a key neofregean advantage, while preserving the key structuralist advantage, which objects play the number role does not matter.