bluuebunny/crossref_metadata_2025_split huggingface dataset:
An ensemble framework for identifying essential proteins
Authors: Zhang Xue , Xiao Wangxin , Acencio Marcio Luis , Lemke Ney , Wang Xujing 
Published: August 2016

Abstract
Background
Many centrality measures have been proposed to mine and characterize the correlations between network topological properties and protein essentiality. However, most of them show limited prediction accuracy, and the number of common predicted essential proteins by different methods is very small.

Results
In this paper, an ensemble framework is proposed which integrates gene expression data and protein-protein interaction networks (PINs). It aims to improve the prediction accuracy of basic centrality measures. The idea behind this ensemble framework is that different protein-protein interactions (PPIs) may show different contributions to protein essentiality. Five standard centrality measures (degree centrality, betweenness centrality, closeness centrality, eigenvector centrality, and subgraph centrality) are integrated into the ensemble framework respectively. We evaluated the performance of the proposed ensemble framework using yeast PINs and gene expression data. The results show that it can considerably improve the prediction accuracy of the five centrality measures individually. It can also remarkably increase the number of common predicted essential proteins among those predicted by each centrality measure individually and enable each centrality measure to find more low-degree essential proteins.

Conclusions
This paper demonstrates that it is valuable to differentiate the contributions of different PPIs for identifying essential proteins based on network topological characteristics. The proposed ensemble framework is a successful paradigm to this end.
Exosomes bind to autotaxin and act as a physiological delivery mechanism to stimulate LPA receptor signalling in cells
Authors: Jethwa Susanna A. , Leah Emma J. , Zhang Qifeng , Bright Nicholas A. , Oxley David , Bootman Martin D. , Rudge Simon A. , Wakelam Michael J. O. 
Published: August 2016

ABSTRACT
Autotaxin (ATX; also known as ENPP2), the lysophospholipase responsible for generating the lipid receptor agonist lysophosphatidic acid (LPA), is a secreted enzyme. Here we show that, once secreted, ATX can bind to the surface of cell-secreted exosomes. Exosome-bound ATX is catalytically active and carries generated LPA. Once bound to a cell, through specific integrin interactions, ATX releases the LPA to activate cell surface G-protein-coupled receptors of LPA; inhibition of signalling by the receptor antagonist Ki1642 suggests that these receptors are LPAR1 and LPAR3. The binding stimulates downstream signalling, including phosphorylation of AKT and mitogen-activated protein kinases, the release of intracellular stored Ca2+ and cell migration. We propose that exosomal binding of LPA-loaded ATX provides a means of efficiently delivering the lipid agonist to cell surface receptors to promote signalling. We further propose that this is a means by which ATX–LPA signalling operates physiologically.
Invariant death
Authors: Frank Steven A. 
Published: August 2016

In nematodes, environmental or physiological perturbations alter death’s scaling of time. In human cancer, genetic perturbations alter death’s curvature of time. Those changes in scale and curvature follow the constraining contours of death’s invariant geometry. I show that the constraints arise from a fundamental extension to the theories of randomness, invariance and scale. A generalized Gompertz law follows. The constraints imposed by the invariant Gompertz geometry explain the tendency of perturbations to stretch or bend death’s scaling of time. Variability in death rate arises from a combination of constraining universal laws and particular biological processes.
Lingoing, language labels and metrolingual practices
Authors: Pennycook Alastair , Otsuji Emi 
Published: August 2016

Abstract
There is a potential tension between the descriptions of language use by contemporary sociolinguistic researchers keen to focus on metro- poly- or translanguaging – with a focus on repertoires of semiotic resources – and the terms used by language users themselves – which may accord much more with traditional linguistic labels. While we tried to account for this disparity in previous discussions by focusing on the push and pull between fluid and fixed language use and descriptions, we focus in this paper on the negotiations around the labels used by the participants themselves. While it is certainly the case that the tools for discussing language use and affiliation in everyday discourse are themselves linguistically constrained (using commonly accepted language labels) the terms people use to talk about their multilingual environments are not necessarily as normative as they first appear. Such apparently stable referents are themselves part of a more complex set of identity repertoires that are always being reworked. What is at stake, therefore, is not so much a polarisation between fluid language use and fixed language ascriptions as a constant reconfiguration of language meanings.
Monitoring nicotine intake from e-cigarettes: measurement of parent drug and metabolites in oral fluid and plasma
Authors: Papaseit Esther , Farré Magí , Graziano Silvia , Pacifici Roberta , Pérez-Mañá Clara , García-Algar Oscar , Pichini Simona 
Published: August 2016

AbstractBackground:Electronic cigarettes (e-cig) known as electronic nicotine devices recently gained popularity among smokers. Despite many studies investigating their safety and toxicity, few examined the delivery of e-cig-derived nicotine and its metabolites in alternative biological fluids.Methods:We performed a randomized, crossover, and controlled clinical trial in nine healthy smokers. Nicotine (NIC), cotinine (COT), and trans-3′-hydroxycotinine (3-HCOT) were measured in plasma and oral fluid by liquid chromatography-tandem mass spectrometry after consumption of two consecutive e-cig administrations or two consecutive tobacco cigarettes.Results:NIC and its metabolites were detected both in oral fluid and plasma following both administration conditions. Concentrations in oral fluid resulted various orders of magnitude higher than those observed in plasma. Oral fluid concentration of tobacco cigarette and e-cig-derived NIC peaked at 15 min after each administration and ranged between 1.0 and 1396 μg/L and from 0.3 to 860 μg/L; those of COT between 52.8 and 110 μg/L and from 33.8 to 94.7 μg/L; and those of 3-HCOT between 12.4 and 23.5 μg/L and from 8.5 to 24.4 μg/L. The oral fluid to plasma concentration ratio of both e-cig- and tobacco cigarette-derived NIC peaked at 15 min after both administrations and correlated with oral fluid NIC concentration.Conclusions:The obtained results support the measurement of NIC and metabolites in oral fluid in the assessment of intake after e-cig use and appear to be a suitable alternative to plasma when monitoring nicotine delivery from e-cig for clinical and toxicological studies.
Microbiological Analysis of Dried Goose Carcasses
Authors: Kamber Ufuk , Yaman Hilmi 
Published: August 2016

Abstract
Microbiological studies on chicken meat and carcasses are well documented, but very few studies exist on goose meat and carcasses. Therefore, in this study, dried goose carcass samples were collected from the local households in Kars/Turkey and microbiologically analyzed in terms of public health risks. The total mesophilic viable count was found to be 6.58 (mean log10 CFU g−1) (100%). The number of Enterobacteriaceae was 4.85 (92.8%). Coliform bacteria was counted at the numbers of 2.98 (67.8%), while it was 3.95 (91.1%) for the enterococci, 0.42 (26.7%) for the clostridia, 0.04 (3.5%) for the Clostridium perfringens, and 0.41 (12.5%) for the coagulase positive staphylococci. The numbers of mould and yeast were 0.93 (25%) and 4.81 (94.6%), respectively. Salmonellae and Bacillus cereus could not be isolated in the samples. The results indicate that the dried goose meat samples had poor hygienic quality, contained some of the pathogen microorganisms that are likely to pose a potential health risk.
The Methanol Seed Extract of Garcinia kola Attenuated Angiotensin II- and Lipopolyssacharide-Induced Vascular Smooth Muscle Cell Proliferation and Nitric Oxide Production
Authors: Adedapo Adeolu A. , Omobowale Temidayo O. , Oyagbemi Ademola A. , Yakubu Momoh A. 
Published: August 2016

Abstract
All over the world, cardiovascular diseases are a risk factor for poor health and early death with predisposing factors to include age, gender, tobacco use, physical inactivity, excessive alcohol consumption, unhealthy diet, obesity, family history of cardiovascular disease, hypertension, diabetes mellitus, hyperlipidemia, psychosocial factors, poverty and low educational status, and air pollution. It is envisaged that herbal products that can stem this trend would be of great benefit. Garcinia kola (GK), also known as bitter kola is one of such plants. Generally used as a social snack and offered to guests in some cultural settings, bitter kola has been indicated in the treatment of laryngitis, general inflammation, bronchitis, viral infections and diabetes. In this study, the effects of methanol seed extract of Garcinia kola on the proliferation of Vascular Smooth Muscle Cells (VSMCs) in cell culture by Angiotensin II (Ang II) and LPS-induced NO production were carried out. Confluent VSMCs were exposed to GK (25, 50 and 100 μg/ml) before or after treatment with lipopolyssacharide (100μg/ml), and Angiotensin II (10−8-10−6M). Cellular proliferation was determined by MTT assay and NO production by Griess assay. Treatment with Angiotensin II (10−8, 10−6) or LPS significantly enhanced proliferation of VSM cells while LPS significantly increased nitric oxide (NO) production. Treatment with GK (25, 50 & 100 μg/ml) attenuated VSM cell proliferation. The results indicate that GK has potential to inhibit mitogen activated vascular cell growth and possibly inhibit inflammatory responses to LPS. Thus GK may be useful in condition that is characterized by cellular proliferation and inflammatory responses.
Photoreduction of Pu(V,VI) by TiO2
Authors: Romanchuk Anna Yu. , Kalmykov Stepan N. , Egorov Alexander V. , Zubavichus Yan V. , Shiryaev Andrei A. , Smirnov Eugene A. , Garshev Alexey V. 
Published: August 2016

Abstract
In this study, the effect of light on the kinetics and speciation of plutonium at its interaction with particles of TiO2 under different light conditions is shown for the first time. It was found that sorption was followed by reduction of the plutonium to Pu(IV). In this, the reduction reaction and sorption in conditions of the presence of light proceed significantly more rapidly due to the photocatalytic activity of titanium dioxide, providing a source of electrons for the reaction. Spectral methods (XAFS and TEM) showed that plutonium forms nanoclusters with the structure of PuO2, which decorate the surface of the solid phase.
Nitrate quantification: recent insights into enzyme-based methods
Authors: Hooda Vinita , Sachdeva Veena , Chauhan Nidhi 
Published: August 2016

Abstract
Nitrate monitoring of environmental samples is essential to safeguard human and environmental health. Various non-enzymatic methods such as Griess reaction-based chemical method; Fourier transform infrared spectroscopy; chromatographic, electrochemical and optical sensors yield reproducible results but suffer from drawbacks such as use of hazardous chemicals, interference from coexistent anions, and bulky and expensive instrumentation and hence are not favored for routine analysis. On the other hand, nitrate reductase (NR)-based methods are simple, sensitive, specific, environment friendly, easy to carry out, and, therefore, suitable for routine analysis. NR in these methods is employed in both free (in commercially available kits) and immobilized form. In comparison to the native NR, immobilized NR shows better activity and stability accompanied by overall reduction in the cost of the method. The review gives a brief account of non-enzymatic nitrate quantification, whereas recent advances in enzyme-based determination have been explored in more detail.
Neuroprotective properties of mitochondria-targeted antioxidants of the SkQ-type
Authors: Isaev Nickolay K. , Stelmashook Elena V. , Genrikhs Elisaveta E. , Korshunova Galina A. , Sumbatyan Natalya V. , Kapkaeva Marina R. , Skulachev Vladimir P. 
Published: August 2016

Abstract
In 2008, using a model of compression brain ischemia, we presented the first evidence that mitochondria-targeted antioxidants of the SkQ family, i.e. SkQR1 [10-(6′-plastoquinonyl)decylrhodamine], have a neuroprotective action. It was shown that intraperitoneal injections of SkQR1 (0.5–1 μmol/kg) 1 day before ischemia significantly decreased the damaged brain area. Later, we studied in more detail the anti-ischemic action of this antioxidant in a model of experimental focal ischemia provoked by unilateral intravascular occlusion of the middle cerebral artery. The neuroprotective action of SkQ family compounds (SkQR1, SkQ1, SkQTR1, SkQT1) was manifested through the decrease in trauma-induced neurological deficit in animals and prevention of amyloid-β-induced impairment of long-term potentiation in rat hippocampal slices. At present, most neurophysiologists suppose that long-term potentiation underlies cellular mechanisms of memory and learning. They consider inhibition of this process by amyloid-β1-42 as an in vitro model of memory disturbance in Alzheimer’s disease. Further development of the above studies revealed that mitochondria-targeted antioxidants could retard accumulation of hyperphosphorylated τ-protein, as well as amyloid-β1-42, and its precursor APP in the brain, which are involved in developing neurodegenerative processes in Alzheimer’s disease.
Multimode Characteristics of Space-Charge Waves in a Plasma Waveguide
Authors: Hong Woo-Pyo , Jung Young-Dae 
Published: August 2016

Abstract
The multimode characteristics of the space-charge wave are investigated in a cylindrical waveguide complex plasma. The dispersion relation of the space-charge wave is derived in a waveguide, including two-temperature electrons. The results show that the wave frequencies in a plasma with a high population of high-temperature electrons are always smaller those in a plasma with a low population of high-temperature electrons. It is also found that the population of high-temperature electrons suppresses the group velocity of the space-charge wave. In addition, it is found that the frequency increases with an increase in the radius of the cylindrical wave guide. The variations of the frequency and the group velocity due to the density, temperature, and geometric effects are also discussed.
A Genome-Wide Association Study Identifies Multiple Regions Associated with Head Size in Catfish
Authors: Geng Xin , Liu Shikai , Yao Jun , Bao Lisui , Zhang Jiaren , Li Chao , Wang Ruijia , Sha Jin , Zeng Peng , Zhi Degui , Liu Zhanjiang 
Published: August 2016

AbstractSkull morphology is fundamental to evolution and the biological adaptation of species to their environments. With aquaculture fish species, head size is also important for economic reasons because it has a direct impact on fillet yield. However, little is known about the underlying genetic basis of head size. Catfish is the primary aquaculture species in the United States. In this study, we performed a genome-wide association study using the catfish 250K SNP array with backcross hybrid catfish to map the QTL for head size (head length, head width, and head depth). One significantly associated region on linkage group (LG) 7 was identified for head length. In addition, LGs 7, 9, and 16 contain suggestively associated regions for head length. For head width, significantly associated regions were found on LG9, and additional suggestively associated regions were identified on LGs 5 and 7. No region was found associated with head depth. Head size genetic loci were mapped in catfish to genomic regions with candidate genes involved in bone development. Comparative analysis indicated that homologs of several candidate genes are also involved in skull morphology in various other species ranging from amphibian to mammalian species, suggesting possible evolutionary conservation of those genes in the control of skull morphologies.
Potential Direct Regulators of theDrosophila yellowGene Identified by Yeast One-Hybrid and RNAi Screens
Authors: Kalay Gizem , Lusk Richard , Dome Mackenzie , Hens Korneel , Deplancke Bart , Wittkopp Patricia J 
Published: August 2016

AbstractThe regulation of gene expression controls development, and changes in this regulation often contribute to phenotypic evolution. Drosophila pigmentation is a model system for studying evolutionary changes in gene regulation, with differences in expression of pigmentation genes such as yellow that correlate with divergent pigment patterns among species shown to be caused by changes in cis- and trans-regulation. Currently, much more is known about the cis-regulatory component of divergent yellow expression than the trans-regulatory component, in part because very few trans-acting regulators of yellow expression have been identified. This study aims to improve our understanding of the trans-acting control of yellow expression by combining yeast-one-hybrid and RNAi screens for transcription factors binding to yellow cis-regulatory sequences and affecting abdominal pigmentation in adults, respectively. Of the 670 transcription factors included in the yeast-one-hybrid screen, 45 showed evidence of binding to one or more sequence fragments tested from the 5′ intergenic and intronic yellow sequences from D. melanogaster, D. pseudoobscura, and D. willistoni, suggesting that they might be direct regulators of yellow expression. Of the 670 transcription factors included in the yeast-one-hybrid screen, plus another TF previously shown to be genetically upstream of yellow, 125 were also tested using RNAi, and 32 showed altered abdominal pigmentation. Nine transcription factors were identified in both screens, including four nuclear receptors related to ecdysone signaling (Hr78, Hr38, Hr46, and Eip78C). This finding suggests that yellow expression might be directly controlled by nuclear receptors influenced by ecdysone during early pupal development when adult pigmentation is forming.
Obp56hModulates Mating Behavior inDrosophila melanogaster
Authors: Shorter John R , Dembeck Lauren M , Everett Logan J , Morozova Tatiana V , Arya Gunjan H , Turlapati Lavanya , St. Armour Genevieve E , Schal Coby , Mackay Trudy F C , Anholt Robert R H 
Published: August 2016

AbstractSocial interactions in insects are driven by conspecific chemical signals that are detected via olfactory and gustatory neurons. Odorant binding proteins (Obps) transport volatile odorants to chemosensory receptors, but their effects on behaviors remain poorly characterized. Here, we report that RNAi knockdown of Obp56h gene expression in Drosophila melanogaster enhances mating behavior by reducing courtship latency. The change in mating behavior that results from inhibition of Obp56h expression is accompanied by significant alterations in cuticular hydrocarbon (CHC) composition, including reduction in 5-tricosene (5-T), an inhibitory sex pheromone produced by males that increases copulation latency during courtship. Whole genome RNA sequencing confirms that expression of Obp56h is virtually abolished in Drosophila heads. Inhibition of Obp56h expression also affects expression of other chemoreception genes, including upregulation of lush in both sexes and Obp83ef in females, and reduction in expression of Obp19b and Or19b in males. In addition, several genes associated with lipid metabolism, which underlies the production of cuticular hydrocarbons, show altered transcript abundances. Our data show that modulation of mating behavior through reduction of Obp56h is accompanied by altered cuticular hydrocarbon profiles and implicate 5-T as a possible ligand for Obp56h.
Mitochondrial-Nuclear Interactions Mediate Sex-Specific Transcriptional Profiles inDrosophila
Authors: Mossman Jim A , Tross Jennifer G , Li Nan , Wu Zhijin , Rand David M 
Published: August 2016

AbstractThe assembly and function of mitochondria require coordinated expression from two distinct genomes, the mitochondrial DNA (mtDNA) and nuclear DNA (nDNA). Mutations in either genome can be a source of phenotypic variation, yet their coexpression has been largely overlooked as a source of variation, particularly in the emerging paradigm of mitochondrial replacement therapy. Here we tested how the transcriptome responds to mtDNA and nDNA variation, along with mitonuclear interactions (mtDNA × nDNA) in Drosophila melanogaster. We used two mtDNA haplotypes that differ in a substantial number of single nucleotide polymorphisms, with &gt;100 amino acid differences. We placed each haplotype on each of two D. melanogaster nuclear backgrounds and tested for transcription differences in both sexes. We found that large numbers of transcripts were differentially expressed between nuclear backgrounds, and that mtDNA type altered the expression of nDNA genes, suggesting a retrograde, trans effect of mitochondrial genotype. Females were generally more sensitive to genetic perturbation than males, and males demonstrated an asymmetrical effect of mtDNA in each nuclear background; mtDNA effects were nuclear-background specific. mtDNA-sensitive genes were not enriched in male- or female-limited expression space in either sex. Using a variety of differential expression analyses, we show the responses to mitonuclear covariation to be substantially different between the sexes, yet the mtDNA genes were consistently differentially expressed across nuclear backgrounds and sexes. Our results provide evidence that the main mtDNA effects can be consistent across nuclear backgrounds, but the interactions between mtDNA and nDNA can lead to sex-specific global transcript responses.
Insights into Interspecific Hybridization Events in Allotetraploid Cotton Formation from Characterization of a Gene-Regulating Leaf Shape
Authors: Chang Lijing , Fang Lei , Zhu Yajuan , Wu Huaitong , Zhang Zhiyuan , Liu Chunxiao , Li Xinghe , Zhang Tianzhen 
Published: August 2016

Abstract
The morphology of cotton leaves varies considerably. Phenotypes, including okra, sea-island, super-okra, and broad leaf, are controlled by a multiple allele locus, L2. Okra leaf (L2°) is an incomplete mutation that alters leaf shape by increasing the length of lobes with deeper sinuses. Using a map-based cloning strategy, we cloned the L2 locus gene, which encodes a LATE MERISTEM IDENTITY 1 (LMI1)-like transcription factor (GhOKRA). Silencing GhOKRA leads to a change in phenotype from okra to broad leaf. Overexpression of GhOKRA in Arabidopsis thaliana greatly increases the degree of the leaf lobes and changes the leaf shape. Premature termination of translation in GhOKRA results in the production of broad leaves. The sequences of OKRA from diploid progenitor D-genome species, and wild races and domesticated allotetraploid cottons in Gossypium hirsutum show that a premature termination mutation occurred before and after the formation of tetraploid cotton, respectively. This study provides genomic insights into the two interspecific hybridization events: one produced the present broad leaf and another formed okra leaf phenotype with complete OKRA, that occurred during allotetraploid cotton formation.