bluuebunny/crossref_metadata_2025_split huggingface dataset:
GenePANDA—a novel network-based gene prioritizing tool for complex diseases
Authors: Yin Tianshu , Chen Shu , Wu Xiaohui , Tian Weidong 
Published: March 2017

AbstractHere we describe GenePANDA, a novel network-based tool for prioritizing candidate disease genes. GenePANDA assesses whether a gene is likely a candidate disease gene based on its relative distance to known disease genes in a functional association network. A unique feature of GenePANDA is the introduction of adjusted network distance derived by normalizing the raw network distance between two genes with their respective mean raw network distance to all other genes in the network. The use of adjusted network distance significantly improves GenePANDA’s performance on prioritizing complex disease genes. GenePANDA achieves superior performance over five previously published algorithms for prioritizing disease genes. Finally, GenePANDA can assist in prioritizing functionally important SNPs identified by GWAS.
A high-performance liquid chromatography-electronic circular dichroism online method for assessing the absolute enantiomeric excess and conversion ratio of asymmetric reactions
Authors: Zhang Xiang , Wang Mingchao , Li Li , Yin Dali 
Published: March 2017

AbstractAsymmetric reactions often need to be evaluated during the synthesis of chiral compounds. However, traditional evaluation methods require the isolation of the individual enantiomer, which is tedious and time-consuming. Thus, it is desirable to develop simple, practical online detection methods. We developed a method based on high-performance liquid chromatography-electronic circular dichroism (HPLC-ECD) that simultaneously analyzes the material conversion ratio and absolute optical purity of each enantiomer. In particular, only a reverse-phase C18 column instead of a chiral column is required in our method because the ECD measurement provides a g-factor that describes the ratio of each enantiomer in the mixtures. We used our method to analyze the asymmetric hydrosilylation of β-enamino esters, and we discussed the advantage, feasibility, and effectiveness of this new methodology.
Inverse heat mimicking of given objects
Authors: Alwakil Ahmed , Zerrad Myriam , Bellieud Michel , Amra Claude 
Published: March 2017

AbstractWe address a general inverse mimicking problem in heat conduction. The objects to cloak and mimic are chosen beforehand; these objects identify a specific set of space transformations. The shapes that can be mimicked are derived from the conductivity matrices. Numerical calculation confirms all of the analytical predictions. The technique provides key advantages for applications and can be extended to the field of waves.
Traditional Chinese medicine xin-mai-jia recouples endothelial nitric oxide synthase to prevent atherosclerosis in vivo
Authors: Yin Ya-Ling , Zhu Mo-Li , Wan Jia , Zhang Chong , Pan Guo-Pin , Lu Jun-Xiu , Ping Song , Chen Yuan , Zhao Fan-Rong , Yu Hai-Ya , Guo Tao , Jian Xu , Liu Li-Ying , Zhang Jia-Ning , Wan Guang-Rui , Wang Shuang-Xi , Li Peng 
Published: March 2017

AbstractEndothelial dysfunction, which is caused by endothelial nitric oxide synthase (eNOS) uncoupling, is an initial step in atherosclerosis. This study was designed to explore whether Chinese medicine xin-mai-jia (XMJ) recouples eNOS to exert anti-atherosclerotic effects. Pretreatment of XMJ (25, 50, 100 μg/ml) for 30 minutes concentration-dependently activated eNOS, improved cell viabilities, increased NO generations, and reduced ROS productions in human umbilical vein endothelial cells incubated with H2O2 for 2 hours, accompanied with restoration of BH4. Importantly, these protective effects produced by XMJ were abolished by eNOS inhibitor L-NAME or specific eNOS siRNA in H2O2-treated cells. In ex vivo experiments, exposure of isolated aortic rings from rats to H2O2 for 6 hours dramatically impaired acetylcholine-induced vasorelaxation, reduced NO levels and increased ROS productions, which were ablated by XMJ in concentration-dependent manner. In vivo analysis indicated that administration of XMJ (0.6, 2.0, 6.0 g/kg/d) for 12 weeks remarkably recoupled eNOS and reduced the size of carotid atherosclerotic plaque in rats feeding with high fat diet plus balloon injury. In conclusion, XMJ recouples eNOS to prevent the growth of atherosclerosis in rats. Clinically, XMJ is potentially considered as a medicine to treat patients with atherosclerosis.
Serum snoRNAs as biomarkers for joint ageing and post traumatic osteoarthritis
Authors: Steinbusch Mandy M. F. , Fang Yongxiang , Milner Peter I. , Clegg Peter D. , Young David A. , Welting Tim J. M. , Peffers Mandy J. 
Published: March 2017

AbstractThe development of effective treatments for the age-related disease osteoarthritis and the ability to predict disease progression has been hampered by the lack of biomarkers able to demonstrate the course of the disease. Profiling the expression patterns of small nucleolar RNAs (snoRNAs) in joint ageing and OA may provide diagnostic biomarkers and therapeutic targets. This study determined expression patterns of snoRNAs in joint ageing and OA and examined them as potential biomarkers. Using SnoRNASeq and real-time quantitative PCR (qRT-PCR) we demonstrate snoRNA expression levels in murine ageing and OA joints and serum for the first time. SnoRNASeq identified differential expression (DE) of 6 snoRNAs in young versus old joints and 5 snoRNAs in old sham versus old experimental osteoarthritic joints. In serum we found differential presence of 27 snoRNAs in young versus old serum and 18 snoRNAs in old sham versus old experimental osteoarthritic serum. Confirmatory qRT-PCR analysis demonstrated good correlation with SnoRNASeq findings. Profiling the expression patterns of snoRNAs is the initial step in determining their functional significance in ageing and osteoarthritis, and provides potential diagnostic biomarkers and therapeutic targets. Our results establish snoRNAs as novel markers of musculoskeletal ageing and osteoarthritis.
Direct evidence of flat band voltage shift for TiN/LaO or ZrO/SiO2 stack structure via work function depth profiling
Authors: Heo Sung , Park Hyoungsun , Ko Dong-Su , Kim Yong Su , Kyoung Yong Koo , Lee Hyung-Ik , Cho Eunae , Lee Hyo Sug , Park Gyung-Su , Shin Jai Kwang , Lee Dongjin , Lee Jieun , Jung Kyoungho , Jeong Moonyoung , Yamada Satoru , Kang Hee Jae , Choi Byoung-Deog 
Published: March 2017

AbstractWe demonstrated that a flat band voltage (VFB) shift could be controlled in TiN/(LaO or ZrO)/SiO2 stack structures. The VFB shift described in term of metal diffusion into the TiN film and silicate formation in the inserted (LaO or ZrO)/SiO2 interface layer. The metal doping and silicate formation confirmed by using transmission electron microscopy (TEM) and energy dispersive spectroscopy (EDS) line profiling, respectively. The direct work function measurement technique allowed us to make direct estimate of a variety of flat band voltages (VFB). As a function of composition ratio of La or Zr to Ti in the region of a TiN/(LaO or ZrO)/SiO2/Si stack, direct work function modulation driven by La and Zr doping was confirmed with the work functions obtained from the cutoff value of secondary electron emission by auger electron spectroscopy (AES). We also suggested an analytical method to determine the interface dipole via work function depth profiling.
Aggretin Venom Polypeptide as a Novel Anti-angiogenesis Agent by Targeting Integrin alpha2beta1
Authors: Chung Ching Hu , Chang Chien Hsin , Hsu Chun Chieh , Lin Kung Tin , Peng Hui Chin , Huang Tur Fu 
Published: March 2017

AbstractVEGF and VEGFR antibodies have been used as a therapeutic strategy to inhibit angiogenesis in many diseases; however, frequent and repeated administration of these antibodies to patients induces immunogenicity. In previous studies, we demonstrated that aggretin, a heterodimeric snake venom C-type lectin, exhibits pro-angiogenic activities via integrin α2β1 ligation. We hypothesised that small-mass aggretin fragments may bind integrin α2β1 and act as antagonists of angiogenesis. In this study, the anti-angiogenic efficacy of a synthesised aggretin α-chain C-terminus (AACT, residue 106–136) was evaluated in both in vitro and in vivo angiogenesis models. The AACT demonstrated inhibitory effects on collagen-induced platelet aggregation and HUVEC adhesion to immobilised collagen. These results indicated that AACT may block integrin α2β1−collagen interaction. AACT also inhibited HUVEC migration and tube formation. Aortic ring sprouting and Matrigel implant models demonstrated that AACT markedly inhibited VEGF-induced neovascularisation. In addition, induction of FAK/PI3K/ERK1/2 tyrosine phosphorylation and talin 1/2 associated with integrin β1 which are induced by VEGF were blocked by AACT. Similarly, tyrosine phosphorylation of VEFGR2 and ERK1/2 induced by VEGF was diminished in integrin α2-silenced endothelial cells. Our results demonstrate that AACT is a potential therapeutic candidate for angiogenesis related-diseases via integrin α2β1 blockade.
Chromatin states shape insertion profiles of the piggyBac, Tol2 and Sleeping Beauty transposons and murine leukemia virus
Authors: Yoshida Junko , Akagi Keiko , Misawa Ryo , Kokubu Chikara , Takeda Junji , Horie Kyoji 
Published: March 2017

AbstractDNA transposons and retroviruses are versatile tools in functional genomics and gene therapy. To facilitate their application, we conducted a genome-wide insertion site profiling of the piggyBac (PB), Tol2 and Sleeping Beauty (SB) transposons and the murine leukemia virus (MLV) in mouse embryonic stem cells (ESCs). PB and MLV preferred highly expressed genes, whereas Tol2 and SB preferred weakly expressed genes. However, correlations with DNase I hypersensitive sites were different for all vectors, indicating that chromatin accessibility is not the sole determinant. Therefore, we analysed various chromatin states. PB and MLV highly correlated with Cohesin, Mediator and ESC-specific transcription factors. Notably, CTCF sites were correlated with PB but not with MLV, suggesting MLV prefers smaller promoter–enhancer loops, whereas PB insertion encompasses larger chromatin loops termed topologically associating domains. Tol2 also correlated with Cohesin and CTCF. However, correlations with ESC-specific transcription factors were weaker, suggesting that Tol2 prefers transcriptionally weak chromatin loops. Consistently, Tol2 insertions were associated with bivalent histone modifications characteristic of silent and inducible loci. SB showed minimum preference to all chromatin states, suggesting the least adverse effect on adjacent genes. These results will be useful for vector selection for various applications.
Automated sub-5 nm image registration in integrated correlative fluorescence and electron microscopy using cathodoluminescence pointers
Authors: Haring Martijn T. , Liv Nalan , Zonnevylle A. Christiaan , Narvaez Angela C. , Voortman Lenard M. , Kruit Pieter , Hoogenboom Jacob P. 
Published: March 2017

AbstractIn the biological sciences, data from fluorescence and electron microscopy is correlated to allow fluorescence biomolecule identification within the cellular ultrastructure and/or ultrastructural analysis following live-cell imaging. High-accuracy (sub-100 nm) image overlay requires the addition of fiducial markers, which makes overlay accuracy dependent on the number of fiducials present in the region of interest. Here, we report an automated method for light-electron image overlay at high accuracy, i.e. below 5 nm. Our method relies on direct visualization of the electron beam position in the fluorescence detection channel using cathodoluminescence pointers. We show that image overlay using cathodoluminescence pointers corrects for image distortions, is independent of user interpretation, and does not require fiducials, allowing image correlation with molecular precision anywhere on a sample.
Holophyllane A: A Triterpenoid Possessing an Unprecedented B-nor-3,4-seco-17,14-friedo-lanostane Architecture from Abies holophylla
Authors: Kim Chung Sub , Oh Joonseok , Subedi Lalita , Kim Sun Yeou , Choi Sang Un , Lee Kang Ro 
Published: March 2017

AbstractA novel triterpenoid, holophyllane A (1), featuring a B-nor-3,4-seco-17,14-friedo-lanostane, along with its putative precursor, compound2were isolated from the methanol extract of the trunks ofAbies holophylla. The 2D structure and relative configuration of1were initially determined via analysis of 1D and 2D NMR spectroscopic data and the assignment was confirmed by quantum mechanics-based NMR chemical shift calculations. The absolute configuration was established by comparison of the experimental and simulated ECD data generated at different theory levels. Compounds1and2exhibited moderate to weak cytotoxicity and significant inhibitory activity against nitric oxide (NO) production.
Acute podocyte injury is not a stimulus for podocytes to migrate along the glomerular basement membrane in zebrafish larvae
Authors: Siegerist Florian , Blumenthal Antje , Zhou Weibin , Endlich Karlhans , Endlich Nicole 
Published: March 2017

AbstractPodocytes have a unique 3D structure of major and interdigitating foot processes which is the prerequisite for renal blood filtration. Loss of podocytes leads to chronic kidney disease ending in end stage renal disease. Until now, the question if podocytes can be replaced by immigration of cells along the glomerular basement membrane (GBM) is under debate. We recently showed that in contrast to former theories, podocytes are stationary in the zebrafish pronephros and neither migrate nor change their branching pattern of major processes over 23 hours. However, it was still unclear whether podocytes are able to migrate during acute injury. To investigate this, we applied the nitroreductase/metronidazole zebrafish model of podocyte injury to in vivo two-photon microscopy. The application of metronidazole led to retractions of major processes associated with a reduced expression of podocyte-specific proteins and a formation of subpodocyte pseudocyst. Electron microscopy showed that broad areas of the capillaries became denuded. By 4D in vivo observation of single podocytes, we could show that the remaining podocytes did not walk along GBM during 24 h. This in vivo study reveals that podocytes are very stationary cells making regenerative processes by podocyte walking along the GBM very unlikely.
Radiotherapy for cancer using X-ray fluorescence emitted from iodine
Authors: Tamura Masato , Ito Hiromu , Matsui Hirofumi 
Published: March 2017

AbstractRadiation treatment is popular and the apparatus is already available in many hospitals. Conventional radiation treatment by itself is not sufficient to achieve complete cure. Therefore, radiosensitizers have been developed to enhance the therapeutic effects of the treatment. The concept of radiosensitization with high-Z-elements was first considered many decades ago. However, radiosensitizers are not commonly used in the clinical setting. Here, we propose a radiotherapy method that utilizes fluorescent X-ray emissions from iodine. This approach should achieve a greater therapeutic effect than that of conventional radiotherapy treatments. In our radiotherapy, iomeprol was used as the iodine-donor. The X-ray apparatus with copper and aluminum filters could be used for the X-ray irradiation, the apparatus is not needed for exclusive use. The X-ray apparatus is only required to prepare the copper and aluminum filters. As proof-of-concept, we show that tumor growth was attenuated using this treatment with iomeprol.
Double-bond-containing polyallene-based triblock copolymers via phenoxyallene and (meth)acrylate
Authors: Ding Aishun , Lu Guolin , Guo Hao , Huang Xiaoyu 
Published: March 2017

AbstractA series of ABA triblock copolymers, consisting of double-bond-containing poly(phenoxyallene) (PPOA), poly(methyl methacrylate) (PMMA), or poly(butyl acrylate) (PBA) segments, were synthesized by sequential free radical polymerization and atom transfer radical polymerization (ATRP). A new bifunctional initiator bearing azo and halogen-containing ATRP initiating groups was first prepared followed by initiating conventional free radical homopolymerization of phenoxyallene with cumulated double bond to give a PPOA-based macroinitiator with ATRP initiating groups at both ends. Next, PMMA-b-PPOA-b-PMMA and PBA-b-PPOA-b-PBA triblock copolymers were synthesized by ATRP of methyl methacrylate and n-butyl acrylate initiated by the PPOA-based macroinitiator through the site transformation strategy. These double-bond-containing triblock copolymers are stable under UV irradiation and free radical circumstances.
Inhibition of Proliferation and Epithelial Mesenchymal Transition in Retinal Pigment Epithelial Cells by Heavy Chain-Hyaluronan/Pentraxin 3
Authors: He Hua , Kuriyan Ajay E. , Su Chen-Wei , Mahabole Megha , Zhang Yuan , Zhu Ying-Ting , Flynn Harry W. , Parel Jean-Marie , Tseng Scheffer C. G. 
Published: March 2017

AbstractProliferative vitreoretinopathy (PVR) is mediated by proliferation and epithelial mesenchymal transition (EMT) of retinal pigment epithelium (RPE). Because heavy chain-hyaluronic acid/pentraxin 3 (HC-HA/PTX3) purified from human amniotic membrane exerts anti-inflammatory and anti-scarring actions, we hypothesized that HC-HA/PTX3 could inhibit these PVR-related processes in vitro. In this study, we first optimized an ARPE-19 cell culture model to mimic PVR by defining cell density, growth factors, and cultivation time. Using this low cell density culture model and HA as a control, we tested effects of HC-HA/PTX3 on the cell viability (cytotoxicity), proliferation (EGF + FGF-2) and EMT (TGF-β1). Furthermore, we determined effects of HC-HA/PTX3 on cell migration (EGF + FGF-2 + TGF-β1) and collagen gel contraction (TGF-β1). We found both HA and HC-HA/PTX3 were not toxic to unstimulated RPE cells. Only HC-HA/PTX3 dose-dependently inhibited proliferation and EMT of stimulated RPE cells by down-regulating Wnt (β-catenin, LEF1) and TGF-β (Smad2/3, collagen type I, α-SMA) signaling, respectively. Additionally, HA and HC-HA/PTX3 inhibited migration but only HC-HA/PTX3 inhibited collagen gel contraction. These results suggest HC-HA/PTX3 is a non-toxic, potent inhibitor of proliferation and EMT of RPE in vitro, and HC-HA/PTX3’s ability to inhibit PVR formation warrants evaluation in an animal model.
Determination of the pKa of the N-terminal amino group of ubiquitin by NMR
Authors: Oregioni Alain , Stieglitz Benjamin , Kelly Geoffrey , Rittinger Katrin , Frenkiel Tom 
Published: March 2017

AbstractUbiquitination regulates nearly every aspect of cellular life. It is catalysed by a cascade of three enzymes and results in the attachment of the C-terminal carboxylate of ubiquitin to a lysine side chain in the protein substrate. Chain extension occurs via addition of subsequent ubiquitin molecules to either one of the seven lysine residues of ubiquitin, or via its N-terminal α-amino group to build linear ubiquitin chains. The pKa of lysine side chains is around 10.5 and hence E3 ligases require a mechanism to deprotonate the amino group at physiological pH to produce an effective nucleophile. In contrast, the pKa of N-terminal α-amino groups of proteins can vary significantly, with reported values between 6.8 and 9.1, raising the possibility that linear chain synthesis may not require a general base. In this study we use NMR spectroscopy to determine the pKa for the N-terminal α-amino group of methionine1 of ubiquitin for the first time. We show that it is 9.14, one of the highest pKa values ever reported for this amino group, providing a rational for the observed need for a general base in the E3 ligase HOIP, which synthesizes linear ubiquitin chains.
Gene Deletion in Barley Mediated by LTR-retrotransposon BARE
Authors: Shang Yi , Yang Fei , Schulman Alan H. , Zhu Jinghuan , Jia Yong , Wang Junmei , Zhang Xiao-Qi , Jia Qiaojun , Hua Wei , Yang Jianming , Li Chengdao 
Published: March 2017

AbstractA poly-row branched spike (prbs) barley mutant was obtained from soaking a two-rowed barley inflorescence in a solution of maize genomic DNA. Positional cloning and sequencing demonstrated that the prbs mutant resulted from a 28 kb deletion including the inflorescence architecture gene HvRA2. Sequence annotation revealed that the HvRA2 gene is flanked by two LTR (long terminal repeat) retrotransposons (BARE) sharing 89% sequence identity. A recombination between the integrase (IN) gene regions of the two BARE copies resulted in the formation of an intact BARE and loss of HvRA2. No maize DNA was detected in the recombination region although the flanking sequences of HvRA2 gene showed over 73% of sequence identity with repetitive sequences on 10 maize chromosomes. It is still unknown whether the interaction of retrotransposons between barley and maize has resulted in the recombination observed in the present study.
Altered gene expression and repressed markers of autophagy in skeletal muscle of insulin resistant patients with type 2 diabetes
Authors: Møller Andreas Buch , Kampmann Ulla , Hedegaard Jakob , Thorsen Kasper , Nordentoft Iver , Vendelbo Mikkel Holm , Møller Niels , Jessen Niels 
Published: March 2017

AbstractThis case-control study was designed to investigate the gene expression profile in skeletal muscle from severely insulin resistant patients with long-standing type 2 diabetes (T2D), and to determine associated signaling pathways. Gene expression profiles were examined by whole transcriptome, strand-specific RNA-sequencing and associated signaling was determined by western blot. We identified 117 differentially expressed gene transcripts. Ingenuity Pathway Analysis related these differences to abnormal muscle morphology and mitochondrial dysfunction. Despite a ~5-fold difference in plasma insulin, we did not observe any difference in phosphorylation of AKT or AS160, although other insulin-sensitive cascades, as mTOR/4EBP1, had retained their sensitivity. Autophagy-related gene (ATG14, RB1CC1/FIP200, GABARAPL1, SQSTM1/p62, and WIPI1) and protein (LC3BII, SQSTM1/p62 and ATG5) expression were decreased in skeletal muscle from the patients, and this was associated with a trend to increased phosphorylation of the insulin-sensitive regulatory transcription factor FOXO3a. These data show that gene expression is highly altered and related to mitochondrial dysfunction and abnormal morphology in skeletal muscle from severely insulin resistant patients with T2D, and that this is associated with decreased expression of autophagy-related genes and proteins. We speculate that prolonged treatment with high doses of insulin may suppress autophagy thereby generating a vicious cycle maintaining insulin resistance.