bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene silencing in Tribolium castaneum as a tool for the targeted identification of candidate RNAi targets in crop pests
Authors: Knorr Eileen , Fishilevich Elane , Tenbusch Linda , Frey Meghan L. F. , Rangasamy Murugesan , Billion Andre , Worden Sarah E. , Gandra Premchand , Arora Kanika , Lo Wendy , Schulenberg Greg , Valverde-Garcia Pablo , Vilcinskas Andreas , Narva Kenneth E. 
Published: January 2018

AbstractRNAi shows potential as an agricultural technology for insect control, yet, a relatively low number of robust lethal RNAi targets have been demonstrated to control insects of agricultural interest. In the current study, a selection of lethal RNAi target genes from the iBeetle (Tribolium castaneum) screen were used to demonstrate efficacy of orthologous targets in the economically important coleopteran pests Diabrotica virgifera virgifera and Meligethes aeneus. Transcript orthologs of 50 selected genes were analyzed in D. v. virgifera diet-based RNAi bioassays; 21 of these RNAi targets showed mortality and 36 showed growth inhibition. Low dose injection- and diet-based dsRNA assays in T. castaneum and D. v. virgifera, respectively, enabled the identification of the four highly potent RNAi target genes: Rop, dre4, ncm, and RpII140. Maize was genetically engineered to express dsRNA directed against these prioritized candidate target genes. T0 plants expressing Rop, dre4, or RpII140 RNA hairpins showed protection from D. v. virgifera larval feeding damage. dsRNA targeting Rop, dre4, ncm, and RpII140 in M. aeneus also caused high levels of mortality both by injection and feeding. In summary, high throughput systems for model organisms can be successfully used to identify potent RNA targets for difficult-to-work with agricultural insect pests.
The effects of pressure on the energy landscape of proteins
Authors: Librizzi Fabio , Carrotta Rita , Peters Judith , Cupane Antonio 
Published: January 2018

AbstractProtein dynamics is characterized by fluctuations among different conformational substates, i.e. the different minima of their energy landscape. At temperatures above ~200 K, these fluctuations lead to a steep increase in the thermal dependence of all dynamical properties, phenomenon known as Protein Dynamical Transition. In spite of the intense studies, little is known about the effects of pressure on these processes, investigated mostly near room temperature. We studied by neutron scattering the dynamics of myoglobin in a wide temperature and pressure range. Our results show that high pressure reduces protein motions, but does not affect the onset temperature for the Protein Dynamical Transition, indicating that the energy differences and barriers among conformational substates do not change with pressure. Instead, high pressure values strongly reduce the average structural differences between the accessible conformational substates, thus increasing the roughness of the free energy landscape of the system.
Pattern recognition with machine learning on optical microscopy images of typical metallurgical microstructures
Authors: Bulgarevich Dmitry S. , Tsukamoto Susumu , Kasuya Tadashi , Demura Masahiko , Watanabe Makoto 
Published: January 2018

AbstractFor advanced materials characterization, a novel and extremely effective approach of pattern recognition in optical microscopic images of steels is demonstrated. It is based on fast Random Forest statistical algorithm of machine learning for reliable and automated segmentation of typical steel microstructures. Their percentage and location areas excellently agreed between machine learning and manual examination results. The accurate microstructure pattern recognition/segmentation technique in combination with other suitable mathematical methods of image processing and analysis can help to handle the large volumes of image data in a short time for quality control and for the quest of new steels with desirable properties.
The characterization, renoprotection and antioxidation of enzymatic and acidic exopolysaccharides from Hypsizigus marmoreus
Authors: Liu Min , Lan Yufei , Tian Chengye , Zhu Yongfa , Liu Hui , Wang Wenshuai , Liu Weiru , Zhang Jianjun , Jia Le 
Published: January 2018

AbstractThe present work was designed to investigate the characterization, as well as the antioxidation and renoprotection in streptozocin (STZ)-induced diabetic mice, of exopolysaccharides (EPS) and the enzymatic-EPS (EEPS) and acidic-EPS (AEPS) hydrolysates, which were separated from the fermentation liquor ofHypsizigus marmoreus. Animal results demonstrated that EPS, EEPS and AEPS had potential antioxidant and renoprotective effects, especially EEPS. Additionally, they were the most effective, reflecting increases in superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), catalase (CAT), total antioxidant capacity (T-AOC), and albumin (ALB) of 168.33%, 124.8%, 268.17% 179.49%, and 68.71%, respectively, and decreases in the contents of malondialdehyde (MDA), lipid peroxide (LPO) and levels of serum urea nitrogen (BUN) and creatinine (CRE) by 70.58%, 58.43%, 23.97% and 29.60%, respectively, at a dose of 800 mg/kg compared to those of model mice. Three polysaccharides ameliorated the histopathological alterations which were observed in the kidney of diabetic mice. Furthermore, the characterization of polysaccharides had been expressed. These findings indicated that the EEPS fromH.marmoreuspossesses more effective renoprotection and antioxidation effects and provided insight into its potential clinical values on preventing diabetes.
ATP12A promotes mucus dysfunction during Type 2 airway inflammation
Authors: Lennox Alison T. , Coburn Stefanie L. , Leech John A. , Heidrich Elisa M. , Kleyman Thomas R. , Wenzel Sally E. , Pilewski Joseph M. , Corcoran Timothy E. , Myerburg Mike M. 
Published: January 2018

AbstractAllergic airway disease is known to cause significant morbidity due to impaired mucociliary clearance, however the mechanism that leads to the mucus dysfunction is not entirely understood. Interleukin 13 (IL-13), a key mediator of Type 2 (T2) inflammation, profoundly alters the ion transport properties of airway epithelium. However, these electrophysiological changes cannot explain the thick, tenacious airway mucus that characterizes the clinical phenotype. Here we report that IL-13 dramatically increases the airway surface liquid (ASL) viscosity in cultured primary human bronchial epithelial cells and thereby inhibits mucus clearance. These detrimental rheological changes require ATP12A, a non-gastric H+/K+-ATPase that secretes protons into the ASL. ATP12A knockdown or inhibition prevented the IL-13 dependent increase in ASL viscosity but did not alter the ASL pH. We propose that ATP12A promotes airway mucus dysfunction in individuals with T2 inflammatory airway diseases and that ATP12A may be a novel therapeutic target to improve mucus clearance.
Development and performance of prototype serologic and molecular tests for hepatitis delta infection
Authors: Coller Kelly E. , Butler Emily K. , Luk Ka-Cheung , Rodgers Mary A. , Cassidy Michael , Gersch Jeffrey , McNamara Anne L. , Kuhns Mary C. , Dawson George J. , Kaptue Lazare , Bremer Birgit , Wedemeyer Heiner , Cloherty Gavin A. 
Published: January 2018

AbstractWorldwide, an estimated 5% of hepatitis B virus (HBV) infected people are coinfected with hepatitis delta virus (HDV). HDV infection leads to increased mortality over HBV mono-infection, yet HDV diagnostics are not widely available. Prototype molecular (RNA) and serologic (IgG) assays were developed for high-throughput testing on the Abbott m2000 and ARCHITECT systems, respectively. RNA detection was achieved through amplification of a ribozyme region target, with a limit of detection of 5 IU/ml. The prototype serology assay (IgG) was developed using peptides derived from HDV large antigen (HDAg), and linear epitopes were further identified by peptide scan. Specificity of an HBV negative population was 100% for both assays. A panel of 145 HBsAg positive samples from Cameroon with unknown HDV status was tested using both assays: 16 (11.0%) had detectable HDV RNA, and 23 (15.7%) were sero-positive including the 16 HDV RNA positive samples. Additionally, an archival serial bleed panel from an HDV superinfected chimpanzee was tested with both prototypes; data was consistent with historic testing data using a commercial total anti-Delta test. Overall, the two prototype assays provide sensitive and specific methods for HDV detection using high throughput automated platforms, allowing opportunity for improved diagnosis of HDV infected patients.
Polyoxygenated cyathane diterpenoids from the mushroom Cyathus africanus, and their neurotrophic and anti-neuroinflammatory activities
Authors: Wei Jing , Guo Wan-Hui , Cao Chen-Yu , Kou Rong-Wei , Xu Yuan-Zhen , Górecki Marcin , Di Bari Lorenzo , Pescitelli Gennaro , Gao Jin-Ming 
Published: January 2018

AbstractIn a previous study, we reported ten new polyoxygenated cyathane diterpenoids, neocyathins A–J, and their anti-neuroinflammatory effects from the liquid culture of the medicinal BasidiomyceteCyathus africanus. In the present study, eight new highly polyoxygenated cyathane diterpenoids, named neocyathins K–R (1–8), were isolated from the solid culture ofC. africanuscultivated on cooked rice, together with three known congeners (9–11). The structures and the absolute configurations of the new compounds were elucidated through comprehensive NMR and HRESIMS spectroscopic data, electronic circular dichroism (ECD) data, and chemical conversion. Compounds1and2represent the first reported naturally occurring compounds with 4,9-seco-cyathane carbon skeleton incorporating an unprecedented medium-sized 9/7 fused ring system, while the 3,4-seco-cyathane derivative (3) was isolated fromCyathusspecies for the first time. All compounds were evaluated for their neurotrophic and anti-neuroinflammatory activity. All the isolates at 1–25 μM displayed differential nerve growth factor (NGF)-induced neurite outgrowth-promoting activity in PC-12 cells, while one of the compounds, allocyathin B2(11), inhibited NO production in lipopolysaccharide (LPS)-stimulated microglia BV-2 cells. In addition, molecular docking studies showed that compound11generated interactions with the inducible nitric oxide synthase (iNOS) protein.
Unravelling genetic variation underlying de novo-synthesis of bovine milk fatty acids
Authors: Knutsen Tim Martin , Olsen Hanne Gro , Tafintseva Valeria , Svendsen Morten , Kohler Achim , Kent Matthew Peter , Lien Sigbjørn 
Published: January 2018

AbstractThe relative abundance of specific fatty acids in milk can be important for consumer health and manufacturing properties of dairy products. Understanding of genes controlling milk fat synthesis may contribute to the development of dairy products with high quality and nutritional value. This study aims to identify key genes and genetic variants affecting de novo synthesis of the short- and medium-chained fatty acids C4:0 to C14:0. A genome-wide association study using 609,361 SNP markers and 1,811 animals was performed to detect genomic regions affecting fatty acid levels. These regions were further refined using sequencing data to impute millions of additional genetic variants. Results suggest associations of PAEP with the content of C4:0, AACS with the content of fatty acids C4:0-C6:0, NCOA6 or ACSS2 with the longer chain fatty acids C6:0-C14:0, and FASN mainly associated with content of C14:0. None of the top-ranking markers caused amino acid shifts but were mostly situated in putatively regulating regions and suggested a regulatory role of the QTLs. Sequencing mRNA from bovine milk confirmed the expression of all candidate genes which, combined with knowledge of their roles in fat biosynthesis, supports their potential role in de novo synthesis of bovine milk fatty acids.
Deep vein thrombosis in mice is regulated by platelet HMGB1 through release of neutrophil-extracellular traps and DNA
Authors: Dyer Mitchell R. , Chen Qiwei , Haldeman Shannon , Yazdani Hamza , Hoffman Rosemary , Loughran Patricia , Tsung Allan , Zuckerbraun Brian S. , Simmons Richard L. , Neal Matthew D. 
Published: January 2018

AbstractVenous thromboembolic (VTE) disease, consisting of deep venous thrombosis (DVT) and pulmonary embolism (PE) is a leading cause of morbidity and mortality. Current prophylactic measures are insufficient to prevent all occurrence in part due to an incomplete understanding of the underlying pathophysiology. Mounting evidence describes interplay between activation of the innate immune system and thrombus development. Recent work has demonstrated that platelet release of HMGB1 leads to increased microvascular complications following injury. Additionally, platelet HMGB1 was found to enhance DVT and increase the formation of neutrophil extracellular traps (NETs), although the role of HMGB1 induced NET release in thrombosis remains unexplored. Utilizing a transgenic mouse lacking HMGB1 specifically from platelets and megakaryocytes we now demonstrate the specific role of platelet-derived HMGB1 in acute and subacute/chronic venous thrombosis. Platelets account for the majority of circulating HMGB1 and HMGB1 deposition within the developing clot. The pro-thrombotic effect of platelet-derived HMGB1 is mediated through enhanced neutrophil recruitment, NET formation and specifically release of extracellular DNA during NET formation. Taken together, these data suggest that platelet HMGB1 mediated NET release is a primary regulator of DVT formation in mice.
Kaempferol mitigates Endoplasmic Reticulum Stress Induced Cell Death by targeting caspase 3/7
Authors: Abdullah Ahmad , Ravanan Palaniyandi 
Published: January 2018

AbstractThe Endoplasmic Reticulum (ER) plays a fundamental role in executing multiple cellular processes required for normal cellular function. Accumulation of misfolded/unfolded proteins in the ER triggers ER stress which contributes to progression of multiple diseases including neurodegenerative disorders. Recent reports have shown that ER stress inhibition could provide positive response against neuronal injury, ischemia and obesity inin vivomodels. Our search towards finding an ER stress inhibitor has led to the functional discovery of kaempferol, a phytoestrogen possessing ER stress inhibitory activity in cultured mammalian cells. We have shown that kaempferol pre-incubation significantly inhibits the expression ofGRP78(a chaperone) andCHOP(ER stress associated pro-apoptotic transcription factor) under stressed condition. Also, our investigation in the inhibitory specificity of kaempferol has revealed that it inhibits cell death induced by diverse stimuli. Further study on exploring the molecular mechanism implied that kaempferol renders protection by targeting caspases. Both thein silicodocking andin vitroassay using recombinant caspase-3 enzyme confirmed the binding of kaempferol to caspases, through an allosteric mode of competitive inhibition. Altogether, we have demonstrated the ability of kaempferol to alleviate ER stress inin vitromodel.
Duplicated RGS (Regulator of G-protein signaling) proteins exhibit conserved biochemical but differential transcriptional regulation of heterotrimeric G-protein signaling in Brassica species
Authors: Kumar Roshan , Bisht Naveen C. 
Published: January 2018

AbstractG-alpha (Gα) and ‘Regulator of G-protein Signaling (RGS)’ proteins are the two key components primarily involved in regulation of heterotrimeric G-proteins signaling across phyla. Unlike Arabidopsis thaliana, our knowledge about G-protein regulation in polyploid Brassica species is sparse. In this study, we identified one Gα and two RGS genes each from three species of Brassica ‘U’ triangle and assessed the effects of whole genome triplication on the divergence of gene sequence and structure, protein-protein interaction, biochemical activities, and gene expression. Sequence and phylogenetic analysis revealed that the deduced Gα and RGS proteins are evolutionarily conserved across Brassica species. The duplicated RGS proteins of each Brassica species interacted with their cognate Gα but displayed varying levels of interaction strength. The Gα and the duplicated RGS proteins of Brassica species exhibited highly conserved G-protein activities when tested under in-vitro conditions. Expression analysis of the B. rapa RGS genes revealed a high degree of transcriptional differentiation across the tested tissue types and in response to various elicitors, particularly under D-glucose, salt and phytohormone treatments. Taken together, our results suggest that the RGS-mediated regulation of G-protein signaling in Brassica species is predominantly governed by stage and condition-specific expression differentiation of the duplicated RGS genes.
COMSOL-Based Modeling and Simulation of SnO2/rGO Gas Sensor for Detection of NO2
Authors: Yaghouti Niyat Farshad , Shahrokh Abadi M. H. 
Published: January 2018

AbstractDespite SIESTA and COMSOL being increasingly used for the simulation of the sensing mechanism in the gas sensors, there are no modeling and simulation reports in literature for detection of NO2 based rGO/SnO2 sensors. In the present study, we model, simulate, and characterize an NO2 based rGO/SnO2 gas sensor using COMSOL by solving the Poisson’s equations under associated boundary conditions of mass, heat and electrical transitions. To perform the simulation, we use an exposure model for presenting the required NO2, a heat transfer model to obtain a reaction temperature, and an electrical model to characterize the sensor’s response in the presence of the gas. We characterize the sensor’s response in the presence of different concentrations of NO2 at different working temperatures and compare the results with the experimental data, reported by Zhang et al. The results from the simulated sensor show a good agreement with the real sensor with some inconsistencies due to differences between the practical conditions in the real chamber and applied conditions to the analytical equations. The results also show that the method can be used to define and predict the behavior of the rGO-based gas sensors before undergoing the fabrication process.
5-HT1A receptor-dependent modulation of emotional and neurogenic deficits elicited by prolonged consumption of alcohol
Authors: Belmer Arnauld , Patkar Omkar L. , Lanoue Vanessa , Bartlett Selena E. 
Published: January 2018

AbstractRepeated episodes of binge-like alcohol consumption produce anxiety, depression and various deleterious effects including alterations in neurogenesis. While the involvement of the serotonin receptor 1 A (5-HT1A) in the regulation of anxiety-like behavior and neurogenesis is well documented, its contribution to alcohol withdrawal-induced anxiety and alcohol-induced deficits in neurogenesis is less documented. Using the Drinking-In-the-Dark (DID) paradigm to model chronic long-term (12 weeks) binge-like voluntary alcohol consumption in mice, we show that the selective partial activation of 5-HT1A receptors by tandospirone (3 mg/kg) prevents alcohol withdrawal-induced anxiety in a battery of behavioral tests (marble burying, elevated-plus-maze, open-field), which is accompanied by a robust decrease in binge-like ethanol intake (1 and 3 mg/kg). Furthermore, using triple immunolabelling of proliferation and neuronal differentiation markers, we show that long-term DID elicits profound deficits in neurogenesis and neuronal fate specification in the dorsal hippocampus that are entirely reversed by a 2-week chronic treatment with the 5-HT1A partial agonist tandospirone (3 mg/kg/day). Together, our results confirm previous observations that 5-HT1A receptors play a pivotal role in alcohol drinking behavior and the associated emotional and neurogenic impairments, and suggest that 5-HT1A partial agonists represent a promising treatment strategy for alcohol abuse.
High Energy electron and proton acceleration by circularly polarized laser pulse from near critical density hydrogen gas target
Authors: Sharma Ashutosh 
Published: January 2018

AbstractRelativistic electron rings hold the possibility of very high accelerating rates, and hopefully a relatively cheap and compact accelerator/collimator for ultrahigh energy proton source. In this work, we investigate the generation of helical shaped quasi-monoenergetic relativistic electron beam and high-energy proton beam from near critical density plasmas driven by petawatt-circularly polarized-short laser pulses. We numerically observe the efficient proton acceleration from magnetic vortex acceleration mechanism by using the three dimensional particle-in-cell simulations; proton beam with peak energy 350 MeV, charge ~10nC and conversion efficiency more than 6% (which implies 2.4 J proton beam out of the 40 J incident laser energy) is reported. We detailed the microphysics involved in the ion acceleration mechanism, which requires investigating the role of self-generated plasma electric and magnetic fields. The concept of efficient generation of quasi-monoenergetic electron and proton beam from near critical density gas targets may be verified experimentally at advanced high power – high repetition rate laser facilities e.g. ELI-ALPS. Such study should be an important step towards the development of high quality electron and proton beam.
Cholesterol-like effects of a fluorotelomer alcohol incorporated in phospholipid membranes
Authors: Jbeily Mark , Bärenwald Ruth , Kressler Jörg , Saalwächter Kay , Ferreira Tiago Mendes 
Published: January 2018

AbstractFluorocarbon amphiphiles are anthropogenic substances widely used in diverse applications such as food packaging, clothing or cookware. Due to their widespread use and non-biodegradability, these chemicals are now ubiquitous in the natural world with high propensity to bioaccumulate in biological membranes, wherein they may affect microscopic properties. Here, we test the hypothesis that a typical fluorocarbon amphiphile can affect lipid membranes similarly to cholesterol by investigating the effect of 1H,1H,2H,2H-perfluoro-1-decanol (8:2 FTOH) on 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) membranes. Using solid-state nuclear magnetic resonance spectroscopy, differential scanning calorimetry and confocal microscopy, we present a consistent set of independent experimental evidences supporting this hypothesis, namely that upon incorporation of 8:2 FTOH, (i) a condensing effect on the acyl chains occurs in the fluid phase, (ii) coexistence of two membrane phases is observed below melting, and (iii) the melting temperature of DPPC varies no more than approximately ±1 °C up to a concentration of 40 mol% of 8:2 FTOH. The condensing effect is quantified by means of advanced dipolar recoupling solid-state NMR experiments and is found to be of approximately half the magnitude of the cholesterol effect at the same concentration.