bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide analysis of alternative splicing during human heart development
Authors: Wang He , Chen Yanmei , Li Xinzhong , Chen Guojun , Zhong Lintao , Chen Gangbing , Liao Yulin , Liao Wangjun , Bin Jianping 
Published: October 2016

AbstractAlternative splicing (AS) drives determinative changes during mouse heart development. Recent high-throughput technological advancements have facilitated genome-wide AS, while its analysis in human foetal heart transition to the adult stage has not been reported. Here, we present a high-resolution global analysis of AS transitions between human foetal and adult hearts. RNA-sequencing data showed extensive AS transitions occurred between human foetal and adult hearts, and AS events occurred more frequently in protein-coding genes than in long non-coding RNA (lncRNA). A significant difference of AS patterns was found between foetal and adult hearts. The predicted difference in AS events was further confirmed using quantitative reverse transcription-polymerase chain reaction analysis of human heart samples. Functional foetal-specific AS event analysis showed enrichment associated with cell proliferation-related pathways including cell cycle, whereas adult-specific AS events were associated with protein synthesis. Furthermore, 42.6% of foetal-specific AS events showed significant changes in gene expression levels between foetal and adult hearts. Genes exhibiting both foetal-specific AS and differential expression were highly enriched in cell cycle-associated functions. In conclusion, we provided a genome-wide profiling of AS transitions between foetal and adult hearts and proposed that AS transitions and deferential gene expression may play determinative roles in human heart development.
High-Performance Metal/Carbide Composites with Far-From-Equilibrium Compositions and Controlled Microstructures
Authors: Hu Liangfa , O’Neil Morgan , Erturun Veysel , Benitez Rogelio , Proust Gwénaëlle , Karaman Ibrahim , Radovic Miladin 
Published: October 2016

AbstractThe prospect of extending existing metal-ceramic composites to those with the compositions that are far from thermodynamic equilibrium is examined. A current and pressure-assisted, rapid infiltration is proposed to fabricate composites, consisting of reactive metallic and ceramic phases with controlled microstructure and tunable properties. An aluminum (Al) alloy/Ti2AlC composite is selected as an example of the far-from-equilibrium systems to fabricate, because Ti2AlC exists only in a narrow region of the Ti-Al-C phase diagram and readily reacts with Al. This kind of reactive systems challenges conventional methods for successfully processing corresponding metal-ceramic composites. Al alloy/Ti2AlC composites with controlled microstructures, various volume ratios of constituents (40/60 and 27/73) and metallic phase sizes (42–83 μm, 77–276 μm, and 167–545 μm), are obtained using the Ti2AlC foams with different pore structures as preforms for molten metal (Al alloy) infiltration. The resulting composites are lightweight and display exceptional mechanical properties at both ambient and elevated temperatures. These structures achieve a compressive strength that is 10 times higher than the yield strength of the corresponding peak-aged Al alloy at ambient temperature and 14 times higher at 400 °C. Possible strengthening mechanisms are described, and further strategies for improving properties of those composites are proposed.
Viral fusion efficacy of specific H3N2 influenza virus reassortant combinations at single-particle level
Authors: Hsu Hung-Lun , Millet Jean K. , Costello Deirdre A. , Whittaker Gary R. , Daniel Susan 
Published: October 2016

AbstractVirus pseudotyping is a useful and safe technique for studying entry of emerging strains of influenza virus. However, few studies have compared different reassortant combinations in pseudoparticle systems, or compared entry kinetics of native viruses and their pseudotyped analogs. Here, vesicular stomatitis virus (VSV)-based pseudovirions displaying distinct influenza virus envelope proteins were tested for fusion activity. We produced VSV pseudotypes containing the prototypical X-31 (H3) HA, either alone or with strain-matched or mismatched N2 NAs. We performed single-particle fusion assays using total internal reflection fluorescence microscopy to compare hemifusion kinetics among these pairings. Results illustrate that matching pseudoparticles behaved very similarly to native virus. Pseudoparticles harboring mismatched HA-NA pairings fuse at significantly slower rates than native virus, and NA-lacking pseudoparticles exhibiting the slowest fusion rates. Relative viral membrane HA density of matching pseudoparticles was higher than in mismatching or NA-lacking pseudoparticles. An equivalent trend of HA expression level on cell membranes of HA/NA co-transfected cells was observed and intracellular trafficking of HA was affected by NA co-expression. Overall, we show that specific influenza HA-NA combinations can profoundly affect the critical role played by HA during entry, which may factor into viral fitness and the emergence of new pandemic influenza viruses.
Polysaccharide biosynthesis-related genes explain phenotype-genotype correlation of Microcystis colonies in Meiliang Bay of Lake Taihu, China
Authors: Xu Shutu , Sun Qianqian , Zhou Xiaohua , Tan Xiao , Xiao Man , Zhu Wei , Li Ming 
Published: October 2016

AbstractThe 16S rDNA, 16S-23S rDNA-ITS,cpcBA-IGS,mcygene and several polysaccharide biosynthesis-related genes (epsL andTagH) were analyzed along with the identification of the morphology ofMicrocystiscolonies collected in Lake Taihu in 2014.M. wesenbergiicolonies could be distinguished directly from other colonies usingespL.TagHdivided all of the samples into two clusters but failed to distinguish different phenotypes. Our results indicated that neither morphology nor molecular tools including 16S rDNA, 16S-23S ITS andcpcBA-IGS could distinguish toxic and non-toxic species among the identifiedMicrocystisspecies. No obvious relationship was detected between the phenotypes ofMicrocystisand their genotypes using 16S, 16S-23S andcpcBA-IGS, but polysaccharide biosynthesis-related genes may distinguish theMicrocystisphenotypes. Furthermore, the sequences of the polysaccharide biosynthesis-related genes (espLandTagH) extracted fromMicrocystisscums collected throughout 2015 was analyzed. Samples dominated byM. ichthyoblabe(60–100%) andM. wesenbergii(60–100%) were divided into different clade by bothespLandTagH, respectively. Therefore, it was confirmed thatM. wesenbergiiandM. ichthyoblabecould be distinguished by the polysaccharide biosynthesis-related genes (espLandTagH). This study is of great significance in filling the gap between classification of molecular biology and the morphological taxonomy ofMicrocystis.
Notch fatigue behavior: Metallic glass versus ultra-high strength steel
Authors: Wang X. D. , Qu R. T. , Wu S. J. , Duan Q. Q. , Liu Z. Q. , Zhu Z. W. , Zhang H. F. , Zhang Z. F. 
Published: October 2016

AbstractStudying the effect of notch on the fatigue behavior of structural materials is of significance for the reliability and safety designing of engineering structural components. In this work, we conducted notch fatigue experiments of two high-strength materials, i.e. a Ti32.8Zr30.2Ni5.3Cu9Be22.7 metallic glass (MG) and a 00Ni18Co15Mo8Ti ultra-high strength steel (CM400 UHSS), and compared their notch fatigue behavior. Experimental results showed that although both the strength and plasticity of the MG were much lower than those of the UHSS, the fatigue endurance limit of the notched MG approached to that of the notched UHSS, and the fatigue ratio of the notched MG was even higher. This interesting finding can be attributed to the unique shear banding mechanism of MG. It was found that during fatigue process abundant shear bands formed ahead of the notch root and in the vicinity of the crack in the notched MG, while limited plastic deformation was observed in the notched UHSS. The present results may improve the understanding on the fatigue mechanisms of high-strength materials and offer new strategies for structural design and engineering application of MG components with geometrical discontinuities.
Wolbachia endosymbionts induce neutrophil extracellular trap formation in human onchocerciasis
Authors: Tamarozzi Francesca , Turner Joseph D. , Pionnier Nicolas , Midgley Angela , Guimaraes Ana F. , Johnston Kelly L. , Edwards Steven W. , Taylor Mark J. 
Published: October 2016

AbstractThe endosymbiotic bacteria, Wolbachia, induce neutrophilic responses to the human helminth pathogen Onchocerca volvulus. The formation of Neutrophil Extracellular Traps (NETs), has been implicated in anti-microbial defence, but has not been identified in human helminth infection. Here, we demonstrate NETs formation in human onchocerciasis. Extracellular NETs and neutrophils were visualised around O. volvulus in nodules excised from untreated patients but not in nodules from patients treated with the anti-Wolbachia drug, doxycycline. Whole Wolbachia or microspheres coated with a synthetic Wolbachia lipopeptide (WoLP) of the major nematode Wolbachia TLR2/6 ligand, peptidoglycan associated lipoprotein, induced NETosis in human neutrophils in vitro. TLR6 dependency of Wolbachia and WoLP NETosis was demonstrated using purified neutrophils from TLR6 deficient mice. Thus, we demonstrate for the first time that NETosis occurs during natural human helminth infection and demonstrate a mechanism of NETosis induction via Wolbachia endobacteria and direct ligation of Wolbachia lipoprotein by neutrophil TLR2/6.
Activated Factor X Induces Endothelial Cell Senescence Through IGFBP-5
Authors: Sanada Fumihiro , Taniyama Yoshiaki , Muratsu Jun , Otsu Rei , Iwabayashi Masaaki , Carracedo Miguel , Rakugi Hiromi , Morishita Ryuichi 
Published: October 2016

AbstractUncontrolled coagulation contributes to the pathophysiology of several chronic inflammatory diseases. In these conditions, senescent cells are often observed and is involved in the generation of inflammation. The coincidence of hyper-coagulation, cell senescence, and inflammation suggests the existence of a common underlying mechanism. Recent evidence indicates that activated coagulation factor X (FXa) plays a role in the processes beyond blood coagulation. This non-hematologic function entails the mediation of inflammation and tissue remodeling. We therefore tested the hypothesis that FXa induces cell senescence resulting in tissue inflammation and impaired tissue regeneration. Human umbilical vein endothelial cells were stimulated with FXa for 14 days. The proliferation of cells treated with FXa was significantly smaller, and the fraction of senescence-associated β-galactosidase-positive cells was increased as compared to the control group. RT-qPCR array revealed that FXa increased the expression of IGFBP-5, EGR-1, p53, and p16INK4a. Inhibition of FXa by a direct FXa inhibitor, rivaroxaban, or IGFBP-5 by siRNA decreased FXa-induced cell senescence, restoring cell proliferation. Moreover, in an ischemic hind limb mouse model, FXa inhibited neovascularization by endothelial progenitor cell. However, rivaroxaban significantly restored FXa-induced impaired angiogenesis. In summary, FXa induced endothelial cell senescence through IGFBP-5, resulting in impaired angiogenesis.
Spin pumping in magnetic trilayer structures with an MgO barrier
Authors: Baker A. A. , Figueroa A. I. , Pingstone D. , Lazarov V. K. , van der Laan G. , Hesjedal T. 
Published: October 2016

AbstractWe present a study of the interaction mechanisms in magnetic trilayer structures with an MgO barrier grown by molecular beam epitaxy. The interlayer exchange coupling, Aex, is determined using SQUID magnetometry and ferromagnetic resonance (FMR), displaying an unexpected oscillatory behaviour as the thickness, tMgO, is increased from 1 to 4 nm. Transmission electron microscopy confirms the continuity and quality of the tunnelling barrier, eliminating the prospect of exchange arising from direct contact between the two ferromagnetic layers. The Gilbert damping is found to be almost independent of the MgO thickness, suggesting the suppression of spin pumping. The element-specific technique of x-ray detected FMR reveals a small dynamic exchange interaction, acting in concert with the static interaction to induce coupled precession across the multilayer stack. These results highlight the potential of spin pumping and spin transfer torque for device applications in magnetic tunnel junctions relying on commonly used MgO barriers.
The properties of nuclear matter with lattice NN potential in relativistic Brueckner-Hartree-Fock theory
Authors: Hu Jinniu , Toki Hiroshi , Shen Hong 
Published: October 2016

AbstractWe study the properties of nuclear matter with lattice nucleon-nucleon (NN) potential in the relativistic Brueckner-Hartree-Fock (RBHF) theory. To use this potential in such a microscopic many-body theory, we firstly have to construct a one-boson-exchange potential (OBEP) based on the latest lattice NN potential. Three mesons, pion, σ meson, and ω meson, are considered. Their coupling constants and cut-off momenta are determined by fitting the on-shell behaviors and phase shifts of the lattice force, respectively. Therefore, we obtain two parameter sets of the OBEP potential (named as LOBEP1 and LOBEP2) with these two fitting ways. We calculate the properties of symmetric and pure neutron matter with LOBEP1 and LOBEP2. In non-relativistic Brueckner-Hartree-Fock case, the binding energies of symmetric nuclear matter are around −3 and −5 MeV at saturation density, while it becomes −8 and −12 MeV in relativistic framework with 1S0, 3S1, and 3D1 channels using our two parameter sets. For the pure neutron matter, the equations of state in non-relativistic and relativistic cases are very similar due to only consideration 1S0 channel with isospin T = 1 case.
Attosecond streaking measurement of extreme ultraviolet pulses using a long-wavelength electric field
Authors: Saito Nariyuki , Ishii Nobuhisa , Kanai Teruto , Watanabe Shuntaro , Itatani Jiro 
Published: October 2016

AbstractLong-wavelength lasers have great potential to become a new-generation drive laser for tabletop coherent light sources in the soft X-ray region. Because of the significantly low conversion efficiency from a long-wavelength light field to high-order harmonics, their pulse characterization has been carried out by measuring the carrier-envelope phase and/or spatial dependences of high harmonic spectra. However, these photon detection schemes, in general, have difficulty in obtaining information on the spectral phases, which is crucial to determine the temporal structures of high-order harmonics. Here, we report the first attosecond streaking measurement of high harmonics generated by few-cycle optical pulses at 1.7 μm from a BiB3O6–based optical parametric chirped-pulse amplifier. This is also the first demonstration of time-resolved photoelectron spectroscopy using high harmonics from a long-wavelength drive laser other than Ti:sapphire lasers, which paves the way towards ultrafast soft X-ray photoelectron spectroscopy.
Identification of reliable reference genes for qRT-PCR studies of the developing mouse mammary gland
Authors: van de Moosdijk Anoeska Agatha Alida , van Amerongen Renée 
Published: October 2016

AbstractCell growth and differentiation are often driven by subtle changes in gene expression. Many challenges still exist in detecting these changes, particularly in the context of a complex, developing tissue. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) allows relatively high-throughput evaluation of multiple genes and developmental time points. Proper quantification of gene expression levels by qRT-PCR requires normalization to one or more reference genes. Traditionally, these genes have been selected based on their presumed “housekeeping” function, with the implicit assumption that they are stably expressed over the entire experimental set. However, this is rarely tested empirically. Here we describe the identification of novel reference genes for the mouse mammary gland based on their stable expression in published microarray datasets. We compared eight novel candidate reference genes (Arpc3, Clock, Ctbp1, Phf7, Prdx1, Sugp2, Taf11 and Usp7) to eight traditional ones (18S, Actb, Gapdh, Hmbs, Hprt, Rpl13a, Sdha and Tbp) and analysed all genes for stable expression in the mouse mammary gland from pre-puberty to adulthood using four different algorithms (GeNorm, DeltaCt, BestKeeper and NormFinder). Prdx1, Phf7 and Ctbp1 were validated as novel and reliable, tissue-specific reference genes that outperform traditional reference genes in qRT-PCR studies of postnatal mammary gland development.
LPS-TLR4 Pathway Mediates Ductular Cell Expansion in Alcoholic Hepatitis
Authors: Odena Gemma , Chen Jiegen , Lozano Juan Jose , Altamirano Jose , Rodrigo-Torres Daniel , Affo Silvia , Morales-Ibanez Oriol , Matsushita Hiroshi , Zou Jian , Dumitru Raluca , Caballeria Juan , Gines Pere , Arroyo Vicente , You Min , Rautou Pierre-Emmanuel , Valla Dominique , Crews Fulton , Seki Ekihiro , Sancho-Bru Pau , Bataller Ramon 
Published: October 2016

AbstractAlcoholic hepatitis (AH) is the most severe form of alcoholic liver disease for which there are no effective therapies. Patients with AH show impaired hepatocyte proliferation, expansion of inefficient ductular cells and high lipopolysaccharide (LPS) levels. It is unknown whether LPS mediates ductular cell expansion. We performed transcriptome studies and identified keratin 23 (KRT23) as a new ductular cell marker. KRT23 expression correlated with mortality and LPS serum levels. LPS-TLR4 pathway role in ductular cell expansion was assessed in human and mouse progenitor cells, liver slices and liver injured TLR4 KO mice. In AH patients, ductular cell expansion correlated with portal hypertension and collagen expression. Functional studies in ductular cells showed that KRT23 regulates collagen expression. These results support a role for LPS-TLR4 pathway in promoting ductular reaction in AH. Maneuvers aimed at decreasing LPS serum levels in AH patients could have beneficial effects by preventing ductular reaction development.
Folylpolyglutamate synthase is a major determinant of intracellular methotrexate polyglutamates in patients with rheumatoid arthritis
Authors: Yamamoto Tatsuhiro , Shikano Kotaro , Nanki Toshihiro , Kawai Shinichi 
Published: October 2016

AbstractWe investigated major determinants of the intracellular concentrations of methotrexate polyglutamates (MTXPGs) in patients with rheumatoid arthritis (RA). In 271 RA patients on stable oral low dose weekly pulse MTX therapy, the concentrations of MTXPGs in red blood cells (RBCs) were measured by liquid chromatography-electrospray ionization-tandem mass spectrometry. Polymerase chain reaction-restriction fragment length polymorphism analysis was performed to determine the genotypes of solute carrier family 19 member 1 (SLC19A1), folylpolyglutamate synthase (FPGS), and gamma-glutamyl hydrolase (GGH). The mean total MTXPG concentration and the concentrations of individual MTXPGs increased dose-dependently, but reached a plateau at MTX doses >10 mg weekly. The MTXPG3-5/1-2 ratio was lower in patients with adverse events related to MTX than in patients without adverse events. Three polymorphisms of FPGS significantly influenced the MTXPG3-5/1-2 ratio in RBCs, while polymorphisms of SLC19A1 and GGH had no impact. The minor allele frequencies of 2 FPGS genotypes were significantly increased in our patients compared with a Caucasian population. FPGS may have a major role in regulating intracellular polyglutamation of MTX in RA patients receiving low-dose weekly MTX therapy.
αTAT1 controls longitudinal spreading of acetylation marks from open microtubules extremities
Authors: Ly Nathalie , Elkhatib Nadia , Bresteau Enzo , Piétrement Olivier , Khaled Mehdi , Magiera Maria M. , Janke Carsten , Le Cam Eric , Rutenberg Andrew D. , Montagnac Guillaume 
Published: October 2016

AbstractAcetylation of the lysine 40 of α-tubulin (K40) is a post-translational modification occurring in the lumen of microtubules (MTs) and is controlled by the α-tubulin acetyl-transferase αTAT1. How αTAT1 accesses the lumen and acetylates α-tubulin there has been an open question. Here, we report that acetylation starts at open ends of MTs and progressively spreads longitudinally from there. We observed acetylation marks at the open ends of in vivo MTs re-growing after a Nocodazole block, and acetylated segments growing in length with time. Bias for MTs extremities was even more pronounced when using non-dynamic MTs extracted from HeLa cells. In contrast, K40 acetylation was mostly uniform along the length of MTs reconstituted from purified tubulin in vitro. Quantitative modelling of luminal diffusion of αTAT1 suggested that the uniform acetylation pattern observed in vitro is consistent with defects in the MT lattice providing lateral access to the lumen. Indeed, we observed that in vitro MTs are permeable to macromolecules along their shaft while cellular MTs are not. Our results demonstrate αTAT1 enters the lumen from open extremities and spreads K40 acetylation marks longitudinally along cellular MTs. This mode of tip-directed microtubule acetylation may allow for selective acetylation of subsets of microtubules.
Highly Efficient Perovskite Solar Cells with Substantial Reduction of Lead Content
Authors: Liu Chong , Fan Jiandong , Li Hongliang , Zhang Cuiling , Mai Yaohua 
Published: October 2016

AbstractDespite organometal halide perovskite solar cells have recently exhibited a significant leap in efficiency, the Sn-based perovskite solar cells still suffer from low efficiency. Here, a series homogeneous CH3NH3Pb(1−x)SnxI3 (0 ≤ x ≤ 1) perovskite thin films with full coverage were obtained via solvent engineering. In particular, the intermediate complexes of PbI2/(SnI2)∙(DMSO)x were proved to retard the crystallization of CH3NH3SnI3, thus allowing the realization of high quality Sn-introduced perovskite thin films. The external quantum efficiency (EQE) of as-prepared solar cells were demonstrated to extend a broad absorption minimum over 50% in the wavelength range from 350 to 950 nm accompanied by a noteworthy absorption onset up to 1050 nm. The CH3NH3Pb0.75Sn0.25I3 perovskite solar cells with inverted structure were consequently realized with maximum power conversion efficiency (PCE) of 14.12%.