bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inflammasome components ASC and AIM2 modulate the acute phase of biomaterial implant-induced foreign body responses
Authors: Christo Susan N. , Diener Kerrilyn R. , Manavis Jim , Grimbaldeston Michele A. , Bachhuka Akash , Vasilev Krasimir , Hayball John D. 
Published: February 2016

AbstractDetailing the inflammatory mechanisms of biomaterial-implant induced foreign body responses (FBR) has implications for revealing targetable pathways that may reduce leukocyte activation and fibrotic encapsulation of the implant. We have adapted a model of poly(methylmethacrylate) (PMMA) bead injection to perform an assessment of the mechanistic role of the ASC-dependent inflammasome in this process. We first demonstrate that ASC−/−mice subjected to PMMA bead injections had reduced cell infiltration and altered collagen deposition, suggesting a role for the inflammasome in the FBR. We next investigated the NLRP3 and AIM2 sensors because of their known contributions in recognising damaged and apoptotic cells. We found that NLRP3 was dispensable for the fibrotic encapsulation; however AIM2 expression influenced leukocyte infiltration and controlled collagen deposition, suggesting a previously unexplored link between AIM2 and biomaterial-induced FBR.
Positron annihilation spectroscopy of vacancy-related defects in CdTe:Cl and CdZnTe:Ge at different stoichiometry deviations
Authors: Šedivý L. , Čížek J. , Belas E. , Grill R. , Melikhova O. 
Published: February 2016

AbstractPositron annihilation spectroscopy (PAS) was used to examine the effect of defined Cd-rich and Te-rich annealing on point defects in Cl-doped CdTe and Ge-doped CdZnTe semi-insulating single crystals. The as-grown crystals contain open-volume defects connected with Cd vacancies "Equation missing". It was found that the Cd vacancies agglomerate into clusters coupled with Cl in CdTe:Cl, and in CdZnTe:Ge they are coupled with Ge donors. While annealing in Cd pressure reduces of the "Equation missing" density, subsequent annealing in Te pressure restores "Equation missing". The CdTe:Cl contains negatively-charged shallow traps interpreted as Rydberg states of "Equation missing" A-centres and representing the major positron trapping sites at low temperature. Positrons confined in the shallow traps exhibit lifetime, which is shorter than the CdTe bulk lifetime. Interpretation of the PAS data was successfully combined with electrical resistivity, Hall effect measurements and chemical analysis, and allowed us to determine the principal point defect densities.
Excess Entropy Scaling Law for Diffusivity in Liquid Metals
Authors: Jakse N. , Pasturel A. 
Published: February 2016

AbstractUnderstanding how dynamic properties depend on the structure and thermodynamics in liquids is a long-standing open problem in condensed matter physics. A very simple approach is based on the Dzugutov contribution developed on model fluids in which a universal (i.e. species-independent) connection relates the pair excess entropy of a liquid to its reduced diffusion coefficient. However its application to “real” liquids still remains uncertain due to the ability of a hard sphere (HS) reference fluid used in reducing parameters to describe complex interactions that occur in these liquids. Here we use ab initio molecular dynamics simulations to calculate both structural and dynamic properties at different temperatures for a wide series of liquid metals including Al, Au, Cu, Li, Ni, Ta, Ti, Zn as well as liquid Si and B. From this analysis, we demonstrate that the Dzugutov scheme can be applied successfully if a self-consistent method to determine the packing fraction of the hard sphere reference fluid is used as well as the Carnahan-Starling approach to express the excess entropy.
On the reliability of powder diffraction Line Profile Analysis of plastically deformed nanocrystalline systems
Authors: Rebuffi Luca , Troian Andrea , Ciancio Regina , Carlino Elvio , Amimi Amine , Leonardi Alberto , Scardi Paolo 
Published: February 2016

AbstractAn iron-molybdenum alloy powder was extensively deformed by high energy milling, so to refine the bcc iron domain size to nanometer scale (~10 nm) and introduce a strong inhomogeneous strain. Both features contribute to comparable degree to the diffraction peak profile broadening, so that size and strain contributions can be easily separated by exploiting their different dependence on the diffraction angle. To assess the reliability of Line Profile Analysis, results were compared with evidence from other techniques, including scanning and transmission electron microscopy and X-ray small angle scattering. Results confirm the extent of the size broadening effect, whereas molecular dynamics simulations provide insight into the origin of the local atomic, inhomogeneous strain, pointing out the role of dislocations, domain boundaries and interactions among crystalline domains.
Few layer epitaxial germanene: a novel two-dimensional Dirac material
Authors: Dávila María Eugenia , Le Lay Guy 
Published: February 2016

AbstractMonolayer germanene, a novel graphene-like germanium allotrope akin to silicene has been recently grown on metallic substrates. Lying directly on the metal surfaces the reconstructed atom-thin sheets are prone to lose the massless Dirac fermion character and unique associated physical properties of free standing germanene. Here, we show that few layer germanene, which we create by dry epitaxy on a gold template, possesses Dirac cones thanks to a reduced interaction. This finding established on synchrotron-radiation-based photoemission, scanning tunneling microscopy imaging and surface electron diffraction places few layer germanene among the rare two-dimensional Dirac materials. Since germanium is currently used in the mainstream Si-based electronics, perspectives of using germanene for scaling down beyond the 5 nm node appear very promising. Other fascinating properties seem at hand, typically the robust quantum spin Hall effect for applications in spintronics and the engineering of Floquet Majorana fermions by light for quantum computing.
Functional analysis of long intergenic non-coding RNAs in phosphate-starved rice using competing endogenous RNA network
Authors: Xu Xi-Wen , Zhou Xiong-Hui , Wang Rui-Ru , Peng Wen-Lei , An Yue , Chen Ling-Ling 
Published: February 2016

AbstractLong intergenic non-coding RNAs (lincRNAs) may play widespread roles in gene regulation and other biological processes, however, a systematic examination of the functions of lincRNAs in the biological responses of rice to phosphate (Pi) starvation has not been performed. Here, we used a computational method to predict the functions of lincRNAs in Pi-starved rice. Overall, 3,170 lincRNA loci were identified using RNA sequencing data from the roots and shoots of control and Pi-starved rice. A competing endogenous RNA (ceRNA) network was constructed for each tissue by considering the competing relationships between lincRNAs and genes, and the correlations between the expression levels of RNAs in ceRNA pairs. Enrichment analyses showed that most of the communities in the networks were related to the biological processes of Pi starvation. The lincRNAs in the two tissues were individually functionally annotated based on the ceRNA networks, and the differentially expressed lincRNAs were biologically meaningful. For example, XLOC_026030 was upregulated from 3 days after Pi starvation, and its functional annotation was ‘cellular response to Pi starvation’. In conclusion, we systematically annotated lincRNAs in rice and identified those involved in the biological response to Pi starvation.
Comparative transcriptome analysis of peripheral blood mononuclear cells in hepatitis B-related acute-on-chronic liver failure
Authors: Zhou Qian , Ding Wenchao , Jiang Longyan , Xin Jiaojiao , Wu Tianzhou , Shi Dongyan , Jiang Jing , Cao Hongcui , Li Lanjuan , Li Jun 
Published: February 2016

AbstractAnalysis of the transcriptome of peripheral blood mononuclear cells (PBMCs) from patients with hepatitis B-related acute-on-chronic liver failure (HBV-ACLF) is essential to elucidate the pathogenesis of HBV-ACLF and identify HBV-ACLF-specific biomarkers. In this study, high-throughput sequencing was performed to characterize the transcriptome of PMBCs from patients with HBV-ACLF. Specifically, 2381 differentially expressed genes (DEGs) and 776 differentially expressed transcripts were identified through comparisons with patients with chronic hepatitis B (CHB) and healthy controls. Gene Ontology (GO) analysis identified 114 GO terms that were clustered into 12 groups. We merged 10 dysregulated genes selected from these grouped GO terms and non-clustered terms with four significant genes with a specificity of >0.8 in the HBV-ACLF patients to obtain a set of 13 unique genes. The quantitative real-time polymerase chain reaction (qRT-PCR) validation of the top six genes (CYP19A1, SEMA6B, INHBA, DEFT1P, AZU1 and DEFA4) was consistent with the results of messenger ribonucleic acid (mRNA) sequencing. A further receiver operating characteristic (ROC) analysis revealed that the areas under the ROC curves of the six genes were all >0.8, which indicated their significant diagnostic potentials for HBV-ACLF. Conclusion: The transcriptome characteristics of PBMCs are altered in patients with HBV-ACLF, and six genes may serve as biomarkers of HBV-ACLF.
A comprehensive framework for functional diversity patterns of marine chromophytic phytoplankton using rbcL phylogeny
Authors: Samanta Brajogopal , Bhadury Punyasloke 
Published: February 2016

AbstractMarine chromophytes are taxonomically diverse group of algae and contribute approximately half of the total oceanic primary production. To understand the global patterns of functional diversity of chromophytic phytoplankton, robust bioinformatics and statistical analyses including deep phylogeny based on 2476 form ID rbcL gene sequences representing seven ecologically significant oceanographic ecoregions were undertaken. In addition, 12 form ID rbcL clone libraries were generated and analyzed (148 sequences) from Sundarbans Biosphere Reserve representing the world’s largest mangrove ecosystem as part of this study. Global phylogenetic analyses recovered 11 major clades of chromophytic phytoplankton in varying proportions with several novel rbcL sequences in each of the seven targeted ecoregions. Majority of OTUs was found to be exclusive to each ecoregion, whereas some were shared by two or more ecoregions based on beta-diversity analysis. Present phylogenetic and bioinformatics analyses provide a strong statistical support for the hypothesis that different oceanographic regimes harbor distinct and coherent groups of chromophytic phytoplankton. It has been also shown as part of this study that varying natural selection pressure on form ID rbcL gene under different environmental conditions could lead to functional differences and overall fitness of chromophytic phytoplankton populations.
Experimental realization of the Yang-Baxter Equation via NMR interferometry
Authors: Vind F. Anvari , Foerster A. , Oliveira I. S. , Sarthour R. S. , Soares-Pinto D. O. , Souza A. M. , Roditi I. 
Published: February 2016

AbstractThe Yang-Baxter equation is an important tool in theoretical physics, with many applications in different domains that span from condensed matter to string theory. Recently, the interest on the equation has increased due to its connection to quantum information processing. It has been shown that the Yang-Baxter equation is closely related to quantum entanglement and quantum computation. Therefore, owing to the broad relevance of this equation, besides theoretical studies, it also became significant to pursue its experimental implementation. Here, we show an experimental realization of the Yang-Baxter equation and verify its validity through a Nuclear Magnetic Resonance (NMR) interferometric setup. Our experiment was performed on a liquid state Iodotrifluoroethylene sample which contains molecules with three qubits. We use Controlled-transfer gates that allow us to build a pseudo-pure state from which we are able to apply a quantum information protocol that implements the Yang-Baxter equation.
Genome-wide identification and characterization of long intergenic noncoding RNAs and their potential association with larval development in the Pacific oyster
Authors: Yu Hong , Zhao Xuelin , Li Qi 
Published: February 2016

AbstractAn increasing amount of evidence suggests that long intergenic noncoding RNAs (lincRNAs) may play diverse roles in many cellular processes. However, little is known about lincRNAs in marine invertebrates. Here, we presented the first identification and characterization of lincRNAs in the Pacific oyster (Crassostrea gigas). We developed a pipeline and identified 11,668 lincRNAs in C. gigas based on RNA-Seq resources available. These lincRNAs exhibited many common characteristics with vertebrate lincRNAs: relatively short length, low exon numbers, low expression and low sequence conservation. 1,175 lincRNAs were expressed in a tissue-specific manner, with 35.2% preferentially expressed in male gonad. 776 lincRNAs were specifically expressed in juvenile during different developmental stages. In addition, 47 lincRNAs were found to be potentially related to oyster settlement and metamorphosis. Such diverse temporal and spatial patterns of expression suggest that these lincRNAs might function in cell differentiation during early development, as well as sex differentiation and reproduction. Based on a co-expression network analysis, five lincRNAs were detected that have an expression correlation with key hub genes in four modules significantly correlated with larval development. Our study provides the first large-scale identification of lincRNAs in molluscs and offers new insights into potential functions of lincRNAs in marine invertebrates.
Taxonomic status and molecular phylogeography of two sibling species of Polytremis (Lepidoptera: Hesperiidae)
Authors: Jiang Weibin , He Haiyan , Li Yingdong , Ren Mengyi , Ma Yazhong , Zheng Lingli , Zhu Jianqing , Yu Weidong 
Published: February 2016

AbstractThe skipperPolytremis thecaspecies complex is widely distributed in the south of the Qinling Mountains in China. A recent study of thePolytremisgenus suggested that this species might encompass two differentiated lineages. We tested this hypothesis, by carrying out a phylogenetic study of this agricultural pest based on nationwide sampling and the evaluation of mitochondrial and nuclear DNA markers. We show that this species is actually an amalgamation of two sibling taxa (P. t. thecaandP. t. fukia), which displayed levels of genetic divergence as great as those generally found between sister species in thePolytremisgenus, suggesting that they actually correspond to two distinct species. The Divergence time estimates suggest that an active period of speciation withinPolytremisoccurred within the Pleistocene eras. Based on its distinct phylogenetic placement and geographical isolation, we suggest that the subspecies should be elevated to full species status under the phylogenetic species concept, which has significant management implications.
Direct Band Gap Gallium Antimony Phosphide (GaSbxP1−x) Alloys
Authors: Russell H. B. , Andriotis A. N. , Menon M. , Jasinski J. B. , Martinez-Garcia A. , Sunkara M. K. 
Published: February 2016

AbstractHere, we report direct band gap transition for Gallium Phosphide (GaP) when alloyed with just 1–2 at% antimony (Sb) utilizing both density functional theory based computations and experiments. First principles density functional theory calculations of GaSbxP1−x alloys in a 216 atom supercell configuration indicate that an indirect to direct band gap transition occurs at x = 0.0092 or higher Sb incorporation into GaSbxP1−x. Furthermore, these calculations indicate band edge straddling of the hydrogen evolution and oxygen evolution reactions for compositions ranging from x = 0.0092 Sb up to at least x = 0.065 Sb making it a candidate for use in a Schottky type photoelectrochemical water splitting device. GaSbxP1−x nanowires were synthesized by reactive transport utilizing a microwave plasma discharge with average compositions ranging from x = 0.06 to x = 0.12 Sb and direct band gaps between 2.21 eV and 1.33 eV. Photoelectrochemical experiments show that the material is photoactive with p-type conductivity. This study brings attention to a relatively uninvestigated, tunable band gap semiconductor system with tremendous potential in many fields.
Uniform Nickel Vanadate (Ni3V2O8) Nanowire Arrays Organized by Ultrathin Nanosheets with Enhanced Lithium Storage Properties
Authors: Wang Chang , Fang Dong , Wang Hong’en , Cao Yunhe , Xu Weilin , Liu Xiaoqing , Luo Zhiping , Li Guangzhong , Jiang Ming , Xiong Chuanxi 
Published: February 2016

AbstractDevelopment of three-dimensional nano-architectures on current collectors has emerged as an effective strategy for enhancing rate capability and cycling stability of the electrodes. Herein, a novel type of Ni3V2O8 nanowires, organized by ultrathin hierarchical nanosheets (less than 5 nm) on Ti foil, has been obtained by a two-step hydrothermal synthesis method. Studies on structural and thermal properties of the as-prepared Ni3V2O8 nanowire arrays are carried out and their morphology has changed obviously in the following heat treatment at 300 and 500 °C. As an electrode material for lithium ion batteries, the unique configuration of Ni3V2O8 nanowires presents enhanced capacitance, satisfying rate capability and good cycling stability. The reversible capacity of the as-prepared Ni3V2O8 nanowire arrays reaches 969.72 mAh·g−1 with a coulombic efficiency over 99% at 500 mA·g−1 after 500 cycles.
Yttrium Iron Garnet Thin Films with Very Low Damping Obtained by Recrystallization of Amorphous Material
Authors: Hauser Christoph , Richter Tim , Homonnay Nico , Eisenschmidt Christian , Qaid Mohammad , Deniz Hakan , Hesse Dietrich , Sawicki Maciej , Ebbinghaus Stefan G. , Schmidt Georg 
Published: February 2016

AbstractWe have investigated recrystallization of amorphous Yttrium Iron Garnet (YIG) by annealing in oxygen atmosphere. Our findings show that well below the melting temperature the material transforms into a fully epitaxial layer with exceptional quality, both structural and magnetic. In ferromagnetic resonance (FMR) ultra low damping and extremely narrow linewidth can be observed. For a 56 nm thick layer a damping constant of α = (6.15 ± 1.50) · 10−5 is found and the linewidth at 9.6 GHz is as small as 1.30 ± 0.05 Oe which are the lowest values for PLD grown thin films reported so far. Even for a 20 nm thick layer a damping constant of α = (7.35 ± 1.40) · 10−5 is found which is the lowest value for ultrathin films published so far. The FMR linewidth in this case is 3.49 ± 0.10 Oe at 9.6 GHz. Our results not only present a method of depositing thin film YIG of unprecedented quality but also open up new options for the fabrication of thin film complex oxides or even other crystalline materials.
Effects of Heterogeneous Diffuse Fibrosis on Arrhythmia Dynamics and Mechanism
Authors: Kazbanov Ivan V. , ten Tusscher Kirsten H. W. J. , Panfilov Alexander V. 
Published: February 2016

AbstractMyocardial fibrosis is an important risk factor for cardiac arrhythmias. Previous experimental and numerical studies have shown that the texture and spatial distribution of fibrosis may play an important role in arrhythmia onset. Here, we investigate how spatial heterogeneity of fibrosis affects arrhythmia onset using numerical methods. We generate various tissue textures that differ by the mean amount of fibrosis, the degree of heterogeneity and the characteristic size of heterogeneity. We study the onset of arrhythmias using a burst pacing protocol. We confirm that spatial heterogeneity of fibrosis increases the probability of arrhythmia induction. This effect is more pronounced with the increase of both the spatial size and the degree of heterogeneity. The induced arrhythmias have a regular structure with the period being mostly determined by the maximal local fibrosis level. We perform ablations of the induced fibrillatory patterns to classify their type. We show that in fibrotic tissue fibrillation is usually of the mother rotor type but becomes of the multiple wavelet type with increase in tissue size. Overall, we conclude that the most important factor determining the formation and dynamics of arrhythmia in heterogeneous fibrotic tissue is the value of maximal local fibrosis.
Identification of a nucleotide in 5′ untranslated region contributing to virus replication and virulence of Coxsackievirus A16
Authors: Li Zhaolong , Liu Xin , Wang Shaohua , Li Jingliang , Hou Min , Liu Guanchen , Zhang Wenyan , Yu Xiao-Fang 
Published: February 2016

AbstractCoxsackievirus A16 (CA16) and enterovirus 71 (EV71) are two main causative pathogens of hand, foot and mouth disease (HFMD). Unlike EV71, virulence determinants of CA16, particularly within 5′ untranslated region (5′UTR), have not been investigated until now. Here, a series of nucleotides present in 5′UTR of lethal but not in non-lethal CA16 strains were screened by aligning nucleotide sequences of lethal circulating Changchun CA16 and the prototype G10 as well as non-lethal SHZH05 strains. A representative infectious clone based on a lethal Changchun024 sequence and infectious mutants with various nucleotide alterations in 5′UTR were constructed and further investigated by assessing virus replication in vitro and virulence in neonatal mice. Compared to the lethal infectious clone, the M2 mutant with a change from cytosine to uracil at nucleotide 104 showed weaker virulence and lower replication capacity. The predicted secondary structure of the 5′UTR of CA16 RNA showed that M2 mutant located between the cloverleaf and stem-loop II, affected interactions between the 5′UTR and the heterogeneous nuclear ribonucleoprotein K (hnRNP K) and A1 (hnRNP A1) that are important for translational activity. Thus, our research determined a virulence-associated site in the 5′UTR of CA16, providing a crucial molecular target for antiviral drug development.
Maternal-foetal transfer of Plasmodium falciparum and Plasmodium vivax antibodies in a low transmission setting
Authors: Charnaud Sarah C. , McGready Rose , Herten-Crabb Asha , Powell Rosanna , Guy Andrew , Langer Christine , Richards Jack S. , Gilson Paul R. , Chotivanich Kesinee , Tsuboi Takafumi , Narum David L. , Pimanpanarak Mupawjay , Simpson Julie A. , Beeson James G. , Nosten François , Fowkes Freya J. I. 
Published: February 2016

AbstractDuring pregnancy immunolglobulin G (IgG) antibodies are transferred from mother to neonate across the placenta. Studies in high transmission areas have shown transfer of P. falciparum-specific IgG, but the extent and factors influencing maternal-foetal transfer in low transmission areas co-endemic for both P. falciparum and P. vivax are unknown. Pregnant women were screened weekly for Plasmodium infection. Mother-neonate paired serum samples at delivery were tested for IgG to antigens from P. falciparum, P. vivax and other infectious diseases. Antibodies to malarial and non-malarial antigens were highly correlated between maternal and neonatal samples (median [range] spearman ρ = 0.78 [0.57–0.93]), although Plasmodium spp. antibodies tended to be lower in neonates than mothers. Estimated gestational age at last P. falciparum infection, but not P. vivax infection, was positively associated with antibody levels in the neonate (P. falciparum merozoite, spearman ρ median [range] 0.42 [0.33–0.66], PfVAR2CSA 0.69; P. vivax ρ = 0.19 [0.09–0.3]). Maternal-foetal transfer of anti-malarial IgG to Plasmodium spp. antigens occurs in low transmission settings. P. vivax IgG acquisition is not associated with recent exposure unlike P. falciparum IgG, suggesting a difference in acquisition of antibodies. IgG transfer is greatest in the final weeks of pregnancy which has implications for the timing of future malaria vaccination strategies in pregnant women.