bluuebunny/crossref_metadata_2025_split huggingface dataset:
Broken rotational symmetry on the Fermi surface of a high-Tc superconductor
Authors: Ramshaw B. J. , Harrison N. , Sebastian S. E. , Ghannadzadeh S. , Modic K. A. , Bonn D. A. , Hardy W. N. , Liang Ruixing , Goddard P. A. 
Published: February 2017

AbstractBroken fourfold rotational (C4) symmetry is observed in the experimental properties of several classes of unconventional superconductors. It has been proposed that this symmetry breaking is important for superconducting pairing in these materials, but in the high-Tc cuprates this broken symmetry has never been observed on the Fermi surface. Here we report a pronounced anisotropy in the angle dependence of the interlayer magnetoresistance of the underdoped high transition temperature (high-Tc) superconductor YBa2Cu3O6.58, directly revealing broken C4 symmetry on the Fermi surface. Moreover, we demonstrate that this Fermi surface has C2 symmetry of the type produced by a uniaxial or anisotropic density-wave phase. This establishes the central role of C4 symmetry breaking in the Fermi surface reconstruction of YBa2Cu3O6+δ
, and suggests a striking degree of universality among unconventional superconductors.
Meta-analysis of host response networks identifies a common core in tuberculosis
Authors: Sambarey Awanti , Devaprasad Abhinandan , Baloni Priyanka , Mishra Madhulika , Mohan Abhilash , Tyagi Priyanka , Singh Amit , Akshata JS , Sultana Razia , Buggi Shashidhar , Chandra Nagasuma 
Published: February 2017

AbstractTuberculosis remains a major global health challenge worldwide, causing more than a million deaths annually. To determine newer methods for detecting and combating the disease, it is necessary to characterise global host responses to infection. Several high throughput omics studies have provided a rich resource including a list of several genes differentially regulated in tuberculosis. An integrated analysis of these studies is necessary to identify a unified response to the infection. Such data integration is met with several challenges owing to platform dependency, patient heterogeneity, and variability in the extent of infection, resulting in little overlap among different datasets. Network-based approaches offer newer alternatives to integrate and compare diverse data. In this study, we describe a meta-analysis of host’s whole blood transcriptomic profiles that were integrated into a genome-scale protein–protein interaction network to generate response networks in active tuberculosis, and monitor their behaviour over treatment. We report the emergence of a highly active common core in disease, showing partial reversals upon treatment. The core comprises 380 genes in which STAT1, phospholipid scramblase 1 (PLSCR1), C1QB, OAS1, GBP2 and PSMB9 are prominent hubs. This network captures the interplay between several biological processes including pro-inflammatory responses, apoptosis, complement signalling, cytoskeletal rearrangement, and enhanced cytokine and chemokine signalling. The common core is specific to tuberculosis, and was validated on an independent dataset from an Indian cohort. A network-based approach thus enables the identification of common regulators that characterise the molecular response to infection, providing a platform-independent foundation to leverage maximum insights from available clinical data.
Butyrate induces apoptosis by activating PDC and inhibiting complex I through SIRT3 inactivation
Authors: Xu Sha , Liu Cai-Xia , Xu Wei , Huang Lei , Zhao Jian-Yuan , Zhao Shi-Min 
Published: February 2017

AbstractThe underlying anticancer effects of butyrate, an end-product of the intestinal microbial fermentation of dietary fiber, remain elusive. Here, we report that butyrate promotes cancer cell apoptosis by acting as a SIRT3 inhibitor. Butyrate inhibits SIRT3 both in cultured cells and in vitro. Butyrate-induced PDHA1 hyperacetylation relieves the inhibitory phosphorylation of PDHA1 at serine 293, thereby activating an influx of glycolytic intermediates into the tricarboxylic acid (TCA) cycle and reversing the Warburg effect. Meanwhile, butyrate-induced hyperacetylation inactivates complex I of the electron transfer chain and prevents the utilization of TCA cycle intermediates. These metabolic stresses promote apoptosis in hyperglycolytic cancer cells, such as HCT116p53−/− cells. SIRT3 deacetylates both PDHA1 and complex I. Genetic ablation of Sirt3 in mouse hepatocytes abrogated the ability of butyrate to induce apoptosis. Our results identify a butyrate-mediated anti-tumor mechanism and indicate that the combined activation of PDC and inhibition of complex I is a novel tumor treatment strategy.
Algal Cell Response to Pulsed Waved Stimulation and Its Application to Increase Algal Lipid Production
Authors: Savchenko Oleksandra , Xing Jida , Yang Xiaoyan , Gu Quanrong , Shaheen Mohamed , Huang Min , Yu Xiaojian , Burrell Robert , Patra Prabir , Chen Jie 
Published: February 2017

AbstractGenerating renewable energy while sequestering CO2 using algae has recently attracted significant research attention, mostly directing towards biological methods such as systems biology, genetic engineering and bio-refining for optimizing algae strains. Other approaches focus on chemical screening to adjust culture conditions or culture media. We report for the first time the physiological changes of algal cells in response to a novel form of mechanical stimulation, or a pulsed wave at the frequency of 1.5 MHz and the duty cycle of 20%. We studied how the pulsed wave can further increase algal lipid production on top of existing biological and chemical methods. Two commonly used algal strains, fresh-water Chlorella vulgaris and seawater Tetraselmis chuii, were selected. We have performed the tests in shake flasks and 1 L spinner-flask bioreactors. Conventional Gravimetric measurements show that up to 20% increase for algal lipid could be achieved after 8 days of stimulation. The total electricity cost needed for the stimulations in a one-liter bioreactor is only one-tenth of a US penny. Gas liquid chromatography shows that the fatty acid composition remains unchanged after pulsed-wave stimulation. Scanning electron microscope results also suggest that pulsed wave stimulation induces shear stress and thus increases algal lipid production.
Spatial variations in the molecular diversity of dissolved organic matter in water moving through a boreal forest in eastern Finland
Authors: Ide Jun’ichiro , Ohashi Mizue , Takahashi Katsutoshi , Sugiyama Yuko , Piirainen Sirpa , Kortelainen Pirkko , Fujitake Nobuhide , Yamase Keitaro , Ohte Nobuhito , Moritani Mina , Hara Miyako , Finér Leena 
Published: February 2017

AbstractDissolved organic matter (DOM) strongly affects water quality within boreal forest ecosystems. However, how the quality of DOM itself changes spatially is not well understood. In this study, to examine how the diversity of DOM molecules varies in water moving through a boreal forest, the number of DOM molecules in different water samples, i.e., rainwater, throughfall, soil water, groundwater, and stream water was determined using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) in Norway spruce and Scots pine stands in eastern Finland during May and June 2010. The number of molecular compounds identified by FT-ICR MS (molecular diversity) ranged from 865 to 2,194, revealing large DOM molecular diversity in the water samples. Additionally, some of the molecular compounds were shared between different water samples. The DOM molecular diversity linearly correlated with the number of low-biodegradable molecules, such as, lignin-like molecules (lignins), but not with dissolved organic carbon concentration. The number of lignins shared between different sampling locations was larger than that of any other biomolecular class. Our results suggest that low-biodegradable molecules, especially lignins, regulate spatial variations in DOM molecular diversity in boreal forests.
Engineering the residual side chains of HAP phytases to improve their pepsin resistance and catalytic efficiency
Authors: Niu Canfang , Yang Peilong , Luo Huiying , Huang Huoqing , Wang Yaru , Yao Bin 
Published: February 2017

AbstractStrong resistance to proteolytic attack is important for feed enzymes. Here, we selected three predicted pepsin cleavage sites, L99, L162, and E230 (numbering from the initiator M of premature proteins), in pepsin-sensitive HAP phytases YkAPPA from Yersinia kristensenii and YeAPPA from Y. enterocolitica, which corresponded to L99, V162, and D230 in pepsin-resistant YrAPPA from Y. rohdei. We constructed mutants with different side chain structures at these sites using site-directed mutagenesis and produced all enzymes in Escherichia coli for catalytic and biochemical characterization. The substitutions E230G/A/P/R/S/T/D, L162G/A/V, L99A, L99A/L162G, and L99A/L162G/E230G improved the pepsin resistance. Moreover, E230G/A and L162G/V conferred enhanced pepsin resistance on YkAPPA and YeAPPA, increased their catalytic efficiency 1.3–2.4-fold, improved their stability at 60 °C and pH 1.0–2.0 and alleviated inhibition by metal ions. In addition, E230G increased the ability of YkAPPA and YeAPPA to hydrolyze phytate from corn meal at a high pepsin concentration and low pH, which indicated that optimization of the pepsin cleavage site side chains may enhance the pepsin resistance, improve the stability at acidic pH, and increase the catalytic activity. This study proposes an efficient approach to improve enzyme performance in monogastric animals fed feed with a high phytate content.
Association of polygenic risk for major psychiatric illness with subcortical volumes and white matter integrity in UK Biobank
Authors: Reus L. M. , Shen X. , Gibson J. , Wigmore E. , Ligthart L. , Adams M. J. , Davies G. , Cox S. R. , Hagenaars S. P. , Bastin M. E. , Deary I. J. , Whalley H. C. , McIntosh A. M. 
Published: February 2017

AbstractMajor depressive disorder (MDD), schizophrenia (SCZ) and bipolar disorder (BP) are common, disabling and heritable psychiatric diseases with a complex overlapping polygenic architecture. Individuals with these disorders, as well as their unaffected relatives, show widespread structural differences in corticostriatal and limbic networks. Structural variation in many of these brain regions is also heritable and polygenic but whether their genetic architecture overlaps with that of major psychiatric disorders is unknown. We sought to address this issue by examining the impact of polygenic risk of MDD, SCZ, and BP on subcortical brain volumes and white matter (WM) microstructure in a large single sample of neuroimaging data; the UK Biobank Imaging study. The first release of UK Biobank imaging data comprised participants with overlapping genetic data and subcortical volumes (N = 978) and WM measures (N = 816). The calculation of polygenic risk scores was based on genome-wide association study results generated by the Psychiatric Genomics Consortium. Our findings indicated no statistically significant associations between either subcortical volumes or WM microstructure, and polygenic risk for MDD, SCZ or BP. These findings suggest that subcortical brain volumes and WM microstructure may not be closely linked to the genetic mechanisms of major psychiatric disorders.
Dissipation and resonance frequency shift of a resonator magnetically coupled to a semiclassical spin
Authors: de Voogd J. M. , Wagenaar J. J. T. , Oosterkamp T. H. 
Published: February 2017

AbstractWe calculate the change of the properties of a resonator, when coupled to a semiclassical spin by means of the magnetic field. Starting with the Lagrangian of the complete system, we provide an analytical expression for the linear response function for the motion in the case of a mechanical resonator and the current for the case of an electromagnetic resonator, thereby considering the influence of the resonator on the spin and vice versa. This analysis shows that the resonance frequency and effective dissipation factor can change significantly due to the relaxation times of the spin. We first derive this for a system consisting of a spin and mechanical resonator and thereafter apply the same calculations to an electromagnetic resonator. Moreover, the applicability of the method is generalized to a resonator coupled to two-level systems and more, providing a key to understand some of the problems of two-level systems in quantum devices.
Identification of Symmetrical RNA Editing Events in the Mitochondria of Salvia miltiorrhiza by Strand-specific RNA Sequencing
Authors: Wu Bin , Chen Haimei , Shao Junjie , Zhang Hui , Wu Kai , Liu Chang 
Published: February 2017

AbstractSalvia miltiorrhiza is one of the most widely-used medicinal plants. Here, we systematically analyzed the RNA editing events in its mitochondria. We developed a pipeline using REDItools to predict RNA editing events from stand-specific RNA-Seq data. The predictions were validated using reverse transcription, RT-PCR amplification and Sanger sequencing experiments. Putative sequences motifs were characterized. Comparative analyses were carried out between S. miltiorrhiza, Arabidopsis thaliana and Oryza sativa. We discovered 1123 editing sites, including 225 “C to U” sites in the protein-coding regions. Fourteen of sixteen (87.5%) sites were validated. Three putative DNA motifs were identified around the predicted sites. The nucleotides on both strands at 115 of the 225 sites had undergone RNA editing, which we called symmetrical RNA editing (SRE). Four of six these SRE sites (66.7%) were experimentally confirmed. Re-examination of strand-specific RNA-Seq data from A. thaliana and O. sativa identified 327 and 369 SRE sites respectively. 78, 20 and 13 SRE sites were found to be conserved among A. thaliana, O. sativa and S. miltiorrhiza respectively. This study provides a comprehensive picture of RNA editing events in the mitochondrial genome of S. miltiorrhiza. We identified SREs for the first time, which may represent a universal phenomenon.
GlcNAc6ST-1 regulates sulfation of N-glycans and myelination in the peripheral nervous system
Authors: Yoshimura Takeshi , Hayashi Akiko , Handa-Narumi Mai , Yagi Hirokazu , Ohno Nobuhiko , Koike Takako , Yamaguchi Yoshihide , Uchimura Kenji , Kadomatsu Kenji , Sedzik Jan , Kitamura Kunio , Kato Koichi , Trapp Bruce D. , Baba Hiroko , Ikenaka Kazuhiro 
Published: February 2017

AbstractHighly specialized glial cells wrap axons with a multilayered myelin membrane in vertebrates. Myelin serves essential roles in the functioning of the nervous system. Axonal degeneration is the major cause of permanent neurological disability in primary myelin diseases. Many glycoproteins have been identified in myelin, and a lack of one myelin glycoprotein results in abnormal myelin structures in many cases. However, the roles of glycans on myelin glycoproteins remain poorly understood. Here, we report that sulfatedN-glycans are involved in peripheral nervous system (PNS) myelination. PNS myelin glycoproteins contain highly abundant sulfatedN-glycans. Major sulfatedN-glycans were identified in both porcine and mouse PNS myelin, demonstrating that the 6-O-sulfation ofN-acetylglucosamine (GlcNAc-6-O-sulfation) is highly conserved in PNS myelin between these species. P0protein, the most abundant glycoprotein in PNS myelin and mutations in which at the glycosylation site cause Charcot-Marie-Tooth neuropathy, has abundant GlcNAc-6-O-sulfatedN-glycans. Mice deficient inN-acetylglucosamine-6-O-sulfotransferase-1 (GlcNAc6ST-1) failed to synthesize sulfatedN-glycans and exhibited abnormal myelination and axonal degeneration in the PNS. Taken together, this study demonstrates that GlcNAc6ST-1 modulates PNS myelination and myelinated axonal survival through the GlcNAc-6-O-sulfation ofN-glycans on glycoproteins. These findings may provide novel insights into the pathogenesis of peripheral neuropathy.
Functionalized Graphene Oxide with Chitosan for Protein Nanocarriers to Protect against Enzymatic Cleavage and Retain Collagenase Activity
Authors: Emadi Fatemeh , Amini Abbas , Gholami Ahmad , Ghasemi Younes 
Published: February 2017

AbstractProteins have short half-life because of enzymatic cleavage. Here, a new protein nanocarrier made of graphene oxide (GO) + Chitosan (CS) is proposed to successfully prevent proteolysis in protein and simultaneously retain its activity. Bovine serum albumin (BSA) and collagenase were loaded on GO and GO-CS to explore the stability and activity of proteins. SEM, AFM, TEM, DSC, UV-Vis, FT-IR, RBS, Raman, SDS-PAGE and zymography were utilized as characterization techniques. The protecting role of GO and GO-CS against enzymatic cleavage was probed by protease digestion analysis on BSA, where the protease solution was introduced to GO-BSA and GO-CS-BSA at 37 °C for 0.5-1-3-6 hours. Characterizations showed the successful synthesis of few layers of GO and the coverage by CS. According to gelatin zymographic analysis, the loaded collagenase on GO and GO-CS lysed the gelatin and created non-staining bands which confirmed the activity of loaded collagenase. SDS-PAGE analysis revealed no significant change in the intact protein in the GO-BSA and GO-CS-BSA solution after 30-minute and 1-hour exposure to protease; however, free BSA was completely digested after 1 hour. After 6 hours, intact proteins were detected in GO-BSA and GO-CS-BSA solutions, while no intact protein was detected in the free BSA solution.
Triplet p-wave pairing correlation in low-doped zigzag graphene nanoribbons
Authors: Ma Tianxing , Yang Fan , Huang Zhongbing , Lin Hai-Qing 
Published: February 2017

AbstractWe reveal an edge spin triplet p–wave superconducting pairing correlation in slightly doped zigzag graphene nanoribbons. By employing a method that combines random-phase approximation, the finite-temperature determinant quantum Monte Carlo approach, and the ground-state constrained-path quantum Monte Carlo method, it is shown that such a spin-triplet pairing is mediated by the ferromagnetic fluctuations caused by the flat band at the edge. The spin susceptibility and effective pairing interactions at the edge strongly increase as the on-site Coulomb interaction increases, indicating the importance of electron-electron correlations. It is also found that the doping-dependent ground-state p-wave pairing correlation bears some similarity to the famous superconducting dome in the phase diagram of a high-temperature superconductor, while the spin correlation at the edge is weakened as the system is doped away from half filling.
Activated niacin receptor HCA2 inhibits chemoattractant-mediated macrophage migration via Gβγ/PKC/ERK1/2 pathway and heterologous receptor desensitization
Authors: Shi Ying , Lai Xiangru , Ye Lingyan , Chen Keqiang , Cao Zheng , Gong Wanghua , Jin Lili , Wang Chunyan , Liu Mingyong , Liao Yuan , Wang Ji Ming , Zhou Naiming 
Published: February 2017

AbstractThe niacin receptor HCA2 is implicated in controlling inflammatory host responses with yet poorly understood mechanistic basis. We previously reported that HCA2 in A431 epithelial cells transduced Gβγ-protein kinase C- and Gβγ-metalloproteinase/EGFR-dependent MAPK/ERK signaling cascades. Here, we investigated the role of HCA2 in macrophage-mediated inflammation and the underlying mechanisms. We found that proinflammatory stimulants LPS, IL-6 and IL-1β up-regulated the expression of HCA2 on macrophages. Niacin significantly inhibited macrophage chemotaxis in response to chemoattractants fMLF and CCL2 by disrupting polarized distribution of F-actin and Gβ protein. Niacin showed a selected additive effect on chemoattractant-induced activation of ERK1/2, JNK and PI3K pathways, but only the MEK inhibitor UO126 reduced niacin-mediated inhibition of macrophage chemotaxis, while activation of ERK1/2 by EGF alone did not inhibit fMLF-mediated migration of HEK293T cells co-expressing HCA2 and fMLF receptor FPR1. In addition, niacin induced heterologous desensitization and internalization of FPR1. Furthermore, niacin rescued mice from septic shock by diminishing inflammatory symptoms and the effect was abrogated in HCA2−/− mice. These results suggest that Gβγ/PKC-dependent ERK1/2 activation and heterologous desensitization of chemoattractant receptors are involved in the inhibition of chemoattractant-induced migration of macrophages by niacin. Thus, HCA2 plays a critical role in host protection against pro-inflammatory insults.
Velocity mode transition of dynamic crack propagation in hyperviscoelastic materials: A continuum model study
Authors: Kubo Atsushi , Umeno Yoshitaka 
Published: February 2017

AbstractExperiments of crack propagation in rubbers have shown that a discontinuous jump of crack propagation velocity can occur as energy release rate increases, which is known as the “mode transition” phenomenon. Although it is believed that the mode transition is strongly related to the mechanical properties, the nature of the mode transition had not been revealed. In this study, dynamic crack propagation on an elastomer was investigated using the finite element method (FEM) with a hyperviscoelastic material model. A series of pure shear test was carried out numerically with FEM simulations and crack velocities were measured under various values of tensile strain. As a result, our FEM simulations successfully reproduced the mode transition. The success of realising the mode transition phenomenon by a simple FEM model, which was achieved for the first time ever, helped to explain that the phenomenon occurs owing to a characteristic non-monotonic temporal development of principal stress near the crack tip.
Web malware spread modelling and optimal control strategies
Authors: Liu Wanping , Zhong Shouming 
Published: February 2017

AbstractThe popularity of the Web improves the growth of web threats. Formulating mathematical models for accurate prediction of malicious propagation over networks is of great importance. The aim of this paper is to understand the propagation mechanisms of web malware and the impact of human intervention on the spread of malicious hyperlinks. Considering the characteristics of web malware, a new differential epidemic model which extends the traditional SIR model by adding another delitescent compartment is proposed to address the spreading behavior of malicious links over networks. The spreading threshold of the model system is calculated, and the dynamics of the model is theoretically analyzed. Moreover, the optimal control theory is employed to study malware immunization strategies, aiming to keep the total economic loss of security investment and infection loss as low as possible. The existence and uniqueness of the results concerning the optimality system are confirmed. Finally, numerical simulations show that the spread of malware links can be controlled effectively with proper control strategy of specific parameter choice.