bluuebunny/crossref_metadata_2025_split huggingface dataset:
Activity in the fronto-parietal network indicates numerical inductive reasoning beyond calculation: An fMRI study combined with a cognitive model
Authors: Liang Peipeng , Jia Xiuqin , Taatgen Niels A. , Borst Jelmer P. , Li Kuncheng 
Published: May 2016

AbstractNumerical inductive reasoning refers to the process of identifying and extrapolating the rule involved in numeric materials. It is associated with calculation and shares the common activation of the fronto-parietal regions with calculation, which suggests that numerical inductive reasoning may correspond to a general calculation process. However, compared with calculation, rule identification is critical and unique to reasoning. Previous studies have established the central role of the fronto-parietal network for relational integration during rule identification in numerical inductive reasoning. The current question of interest is whether numerical inductive reasoning exclusively corresponds to calculation or operates beyond calculation and whether it is possible to distinguish between them based on the activity pattern in the fronto-parietal network. To directly address this issue, three types of problems were created: numerical inductive reasoning, calculation and perceptual judgment. Our results showed that the fronto-parietal network was more active in numerical inductive reasoning which requires more exchanges between intermediate representations and long-term declarative knowledge during rule identification. These results survived even after controlling for the covariates of response time and error rate. A computational cognitive model was developed using the cognitive architecture ACT-R to account for the behavioral results and brain activity in the fronto-parietal network.
Competing covalent and ionic bonding in Ge-Sb-Te phase change materials
Authors: Mukhopadhyay Saikat , Sun Jifeng , Subedi Alaska , Siegrist Theo , Singh David J. 
Published: May 2016

AbstractGe2Sb2Te5 and related phase change materials are highly unusual in that they can be readily transformed between amorphous and crystalline states using very fast melt, quench, anneal cycles, although the resulting states are extremely long lived at ambient temperature. These states have remarkably different physical properties including very different optical constants in the visible in strong contrast to common glass formers such as silicates or phosphates. This behavior has been described in terms of resonant bonding, but puzzles remain, particularly regarding different physical properties of crystalline and amorphous phases. Here we show that there is a strong competition between ionic and covalent bonding in cubic phase providing a link between the chemical basis of phase change memory property and origins of giant responses of piezoelectric materials (PbTiO3, BiFeO3). This has important consequences for dynamical behavior in particular leading to a simultaneous hardening of acoustic modes and softening of high frequency optic modes in crystalline phase relative to amorphous. This different bonding in amorphous and crystalline phases provides a direct explanation for different physical properties and understanding of the combination of long time stability and rapid switching and may be useful in finding new phase change compositions with superior properties.
Coaxial Dual-wavelength Interferometric Method for a Thermal Infrared Focal-plane-array with Integrated Gratings
Authors: Shang Yuanfang , Ye Xiongying , Cao Liangcai , Song Pengfei , Feng Jinyang 
Published: May 2016

AbstractUncooled infrared (IR) focal-plane-array (FPA) with both large sensing range and high sensitivity is a great challenge due to the limited dynamic range of the detected signals. A coaxial dual-wavelength interferometric system was proposed here to detect thermal-induced displacements of an ultrasensitive FPA based on polyvinyl-chloride(PVC)/gold bimorph cantilevers and carbon nanotube (CNT)-based IR absorbing films. By alternately selecting the two displacement measurements performed by λ1 (=640 nm) and λ2 (=660 nm), the temperature measuring range with greater than 50% maximum sensitivity can be extended by eight-fold in comparison with the traditional single-wavelength mode. Meanwhile, the relative measurement error over the full measuring range is below 0.4%. In addition, it offers a feasible approach for on-line and on-wafer FPA characterization with great convenience and high efficiency.
A significant causal association between C-reactive protein levels and schizophrenia
Authors: Inoshita Masatoshi , Numata Shusuke , Tajima Atsushi , Kinoshita Makoto , Umehara Hidehiro , Nakataki Masahito , Ikeda Masashi , Maruyama Souichiro , Yamamori Hidenaga , Kanazawa Tetsufumi , Shimodera Shinji , Hashimoto Ryota , Imoto Issei , Yoneda Hiroshi , Iwata Nakao , Ohmori Tetsuro 
Published: May 2016

AbstractMany observational studies have shown elevated blood CRP levels in schizophrenia compared with controls and one population-based prospective study has reported that elevated plasma CRP levels were associated with late- and very-late-onset schizophrenia. Furthermore, several clinical studies have reported the efficacy of anti-inflammatory drugs on the symptoms in patients with schizophrenia. However, whether elevated CRP levels are causally related to schizophrenia is not still established because of confounding factors and reverse causality. In the present study, we demonstrated that serum CRP levels were significantly higher in patients with schizophrenia than in the controls by conducting a case-control study and a meta-analysis of case-control studies between schizophrenia and serum CRP levels. Furthermore, we provided evidence for a causal association between elevated CRP levels and increased schizophrenia risk by conducting a Mendelian randomization analysis. Our findings suggest that elevated CRP itself may be a causal risk factor for schizophrenia.
GRK5 Deficiency Leads to Selective Basal Forebrain Cholinergic Neuronal Vulnerability
Authors: He Minchao , Singh Prabhakar , Cheng Shaowu , Zhang Qiang , Peng Wei , Ding XueFeng , Li Longxuan , Liu Jun , Premont Richard T. , Morgan Dave , Burns Jeffery M. , Swerdlow Russell H. , Suo William Z. 
Published: May 2016

AbstractWhy certain diseases primarily affect one specific neuronal subtype rather than another is a puzzle whose solution underlies the development of specific therapies. Selective basal forebrain cholinergic (BFC) neurodegeneration participates in cognitive impairment in Alzheimer’s disease (AD), yet the underlying mechanism remains elusive. Here, we report the first recapitulation of the selective BFC neuronal loss that is typical of human AD in a mouse model termed GAP. We created GAP mice by crossing Tg2576 mice that over-express the Swedish mutant human β-amyloid precursor protein gene with G protein-coupled receptor kinase-5 (GRK5) knockout mice. This doubly defective mouse displayed significant BFC neuronal loss at 18 months of age, which was not observed in either of the singly defective parent strains or in the wild type. Along with other supporting evidence, we propose that GRK5 deficiency selectively renders BFC neurons more vulnerable to degeneration.
Proteome-wide drug screening using mass spectrometric imaging of bead-arrays
Authors: Zhou Ying , Liu Ziying , Rothschild Kenneth J. , Lim Mark J. 
Published: May 2016

AbstractA fundamental challenge in the drug discovery process is to develop compounds with high efficacy and minimal side-effects. We describe a new approach to proteome-wide drug screening for detection of on- and off-target binding which combines the advantages of mass spectrometry with microarray technology. The method involves matrix-assisted laser desorption/ionization mass spectrometric imaging (MALDI-MSI) of agarose micro-beads randomly arrayed at high-density in custom micro-well plates. Each bead carries a unique protein target and a corresponding photocleavable mass-tag for coding (PC-Mass-Tag). Compounds bound to specific protein beads and a photo-released coding PC-Mass-Tag are detected simultaneously using MALDI-MSI. As an initial demonstration of this approach, two kinase-targeted drugs, Dasatinib and Brigatinib (AP26113), were simultaneously screened against a model 50-member kinase-bead library. A MALDI-MSI scan performed at the equivalent density of 495,000 beads in the footprint of a microscope slide yielded 100% sensitivity for detecting known strong interactions with no false positives.
Triclosan-induced genes Rv1686c-Rv1687c and Rv3161c are not involved in triclosan resistance in Mycobacterium tuberculosis
Authors: Gomez Andromeda , Andreu Núria , Ferrer-Navarro Mario , Yero Daniel , Gibert Isidre 
Published: May 2016

AbstractA key issue towards developing new chemotherapeutic approaches to fight Mycobacterium tuberculosis is to understand the mechanisms underlying drug resistance. Previous studies have shown that genes Rv1686c-Rv1687c and Rv3161c, predicted to encode an ATP-binding cassette transporter and a dioxygenase respectively, are induced in the presence of triclosan and other antimicrobial compounds. Therefore a possible role in drug resistance has been suggested for the products of these genes although no functional studies have been done. The aim of the present study was to clarify the role of Rv1686c-Rv1687c and Rv3161c in M. tuberculosis resistance to triclosan and other drugs. To this end, deficient mutants and overproducing strains for both systems were constructed and their minimal inhibitory concentration (MIC) against over 20 compounds, including triclosan, was evaluated. Unexpectedly, no differences between the MIC of these strains and the wild-type H37Rv were observed for any of the compounds tested. Moreover the MIC of triclosan was not affected by efflux pump inhibitors that inhibit the activity of transporters similar to the one encoded by Rv1686c-Rv1687c. These results suggest that none of the two systems is directly involved in M. tuberculosis resistance to triclosan or to any of the antimicrobials tested.
Uniform electric field generation in circular multi-well culture plates using polymeric inserts
Authors: Tsai Hsieh-Fu , Cheng Ji-Yen , Chang Hui-Fang , Yamamoto Tadashi , Shen Amy Q. 
Published: May 2016

AbstractApplying uniform electric field (EF) in vitro in the physiological range has been achieved in rectangular shaped microchannels. However, in a circular-shaped device, it is difficult to create uniform EF from two electric potentials due to different electrical resistances originated from the length difference between the diameter of the circle and the length of any parallel chord of the bottom circular chamber where cells are cultured. To address this challenge, we develop a three-dimensional (3D) computer-aided designed (CAD) polymeric insert to create uniform EF in circular shaped multi-well culture plates. A uniform EF with a coefficient of variation (CV) of 1.2% in the 6-well plate can be generated with an effective stimulation area percentage of 69.5%. In particular, NIH/3T3 mouse embryonic fibroblast cells are used to validate the performance of the 3D designed Poly(methyl methacrylate) (PMMA) inserts in a circular-shaped 6-well plate. The CAD based inserts can be easily scaled up (i.e., 100 mm dishes) to further increase effective stimulation area percentages, and also be implemented in commercially available cultureware for a wide variety of EF-related research such as EF-cell interaction and tissue regeneration studies.
Polymyxin Resistance in Acinetobacter baumannii: Genetic Mutations and Transcriptomic Changes in Response to Clinically Relevant Dosage Regimens
Authors: Cheah Soon-Ee , Johnson Matthew D. , Zhu Yan , Tsuji Brian T. , Forrest Alan , Bulitta Jurgen B. , Boyce John D. , Nation Roger L. , Li Jian 
Published: May 2016

AbstractPolymyxins are often last-line therapeutic agents used to treat infections caused by multidrug-resistantA. baumannii. Recent reports of polymyxin-resistantA. baumanniihighlight the urgent need for research into mechanisms of polymyxin resistance. This study employed genomic and transcriptomic analyses to investigate the mechanisms of polymyxin resistance inA. baumanniiAB307-0294 using anin vitrodynamic model to mimic four different clinically relevant dosage regimens of polymyxin B and colistin over 96 h. Polymyxin B dosage regimens that achieved peak concentrations above 1 mg/L within 1 h caused significant bacterial killing (~5 log10CFU/mL), while the gradual accumulation of colistin resulted in no bacterial killing. Polymyxin resistance was observed across all dosage regimens; partial reversion to susceptibility was observed in 6 of 8 bacterial samples during drug-free passaging. Stable polymyxin-resistant samples contained a mutation inpmrB. The transcriptomes of stable and non-stable polymyxin-resistant samples were not substantially different and featured altered expression of genes associated with outer membrane structure and biogenesis. These findings were further supportedviaintegrated analysis of previously published transcriptomics data from strain ATCC19606. Our results provide a foundation for understanding the mechanisms of polymyxin resistance following exposure to polymyxins and the need to explore effective combination therapies.
Changes in hydration structure are necessary for collective motions of a multi-domain protein
Authors: Oroguchi Tomotaka , Nakasako Masayoshi 
Published: May 2016

AbstractConformational motions of proteins are necessary for their functions. To date, experimental studies measuring conformational fluctuations of a whole protein structure have revealed that water molecules hydrating proteins are necessary to induce protein functional motions. However, the underlying microscopic mechanism behind such regulation remains unsolved. To clarify the mechanism, multi-domain proteins are good targets because it is obvious that water molecules between domains play an important role in domain motions. Here, we show how changes in hydration structure microscopically correlate with large-amplitude motions of a multi-domain protein, through molecular dynamics simulation supported by structural analyses and biochemical experiments. We first identified collective domain motions of the protein, which open/close an active-site cleft between domains. The analyses on changes in hydration structure revealed that changes in local hydration in the depth of the cleft are necessary for the domain motion and vice versa. In particular, ‘wetting’/‘drying’ at a hydrophobic pocket and ‘adsorption’/‘dissociation’ of a few water molecules at a hydrophilic crevice in the cleft were induced by dynamic rearrangements of hydrogen-bond networks, and worked as a switch for the domain motions. Our results microscopically demonstrated the importance of hydrogen-bond networks of water molecules in understanding energy landscapes of protein motions.
A rationally engineered yeast pyruvyltransferase Pvg1p introduces sialylation-like properties in neo-human-type complex oligosaccharide
Authors: Higuchi Yujiro , Yoshinaga Sho , Yoritsune Ken-ichi , Tateno Hiroaki , Hirabayashi Jun , Nakakita Shin-ichi , Kanekiyo Miho , Kakuta Yoshimitsu , Takegawa Kaoru 
Published: May 2016

AbstractPyruvylation onto the terminus of oligosaccharide, widely seen from prokaryote to eukaryote, confers negative charges on the cell surface and seems to be functionally similar to sialylation, which is found at the end of human-type complex oligosaccharide. However, detailed molecular mechanisms underlying pyruvylation have not been clarified well. Here, we first determined the crystal structure of fission yeast pyruvyltransferase Pvg1p at a resolution of 2.46 Å. Subsequently, by combining molecular modeling with mutational analysis of active site residues, we obtained a Pvg1p mutant (Pvg1pH168C) that efficiently transferred pyruvyl moiety onto a human-type complex glycopeptide. The resultant pyruvylated human-type complex glycopeptide recognized similar lectins on lectin arrays as the α2,6-sialyl glycopeptides. This newly-generated pyruvylation of human-type complex oligosaccharides would provide a novel method for glyco-bioengineering.
Phenotypic dynamics of microglial and monocyte-derived cells in glioblastoma-bearing mice
Authors: Ricard Clément , Tchoghandjian Aurélie , Luche Hervé , Grenot Pierre , Figarella-Branger Dominique , Rougon Geneviève , Malissen Marie , Debarbieux Franck 
Published: May 2016

AbstractInflammatory cells, an integral component of tumor evolution, are present in Glioblastomas multiforme (GBM). To address the cellular basis and dynamics of the inflammatory microenvironment in GBM, we established an orthotopic syngenic model by grafting GL261-DsRed cells in immunocompetent transgenic LysM-EGFP//CD11c-EYFP reporter mice. We combined dynamic spectral two-photon imaging with multiparametric cytometry and multicolor immunostaining to characterize spatio-temporal distribution, morphology and activity of microglia and blood-derived infiltrating myeloid cells in live mice. Early stages of tumor development were dominated by microglial EYFP+ cells invading the tumor, followed by massive recruitment of circulating LysM-EGFP+ cells. Fluorescent invading cells were conventional XCR1+ and monocyte-derived dendritic cells distributed in subpopulations of different maturation stages, located in different areas relative to the tumor core. The lethal stage of the disease was characterized by the progressive accumulation of EGFP+/EYFP+ monocyte-derived dendritic cells. This local phenotypic regulation of monocyte subtypes marked a transition in the immune response.
The simple neuroendocrine-immune regulatory network in oyster Crassostrea gigas mediates complex functions
Authors: Liu Zhaoqun , Wang Lingling , Zhou Zhi , Sun Ying , Wang Mengqiang , Wang Hao , Hou Zhanhui , Gao Dahai , Gao Qiang , Song Linsheng 
Published: May 2016

AbstractThe neuroendocrine-immune (NEI) regulatory network is a complex system, which plays an indispensable role in the immunity of the host. In the present study, the bioinformatical analysis of the transcriptomic data from oyster Crassostrea gigas and further biological validation revealed that oyster TNF (CgTNF-1 CGI_10018786) could activate the transcription factors NF-κB and HSF (heat shock transcription factor) through MAPK signaling pathway, and then regulate apoptosis, redox reaction, neuro-regulation and protein folding in oyster haemocytes. The activated immune cells then released neurotransmitters including acetylcholine, norepinephrine and [Met5]-enkephalin to regulate the immune response by arising the expression of three TNF (CGI_10005109, CGI_10005110 and CGI_10006440) and translocating two NF-κB (Cgp65, CGI_10018142 and CgRel, CGI_10021567) between the cytoplasm and nuclei of haemocytes. Neurotransmitters exhibited the immunomodulation effects by influencing apoptosis and phagocytosis of oyster haemocytes. Acetylcholine and norepinephrine could down-regulate the immune response, while [Met5]-enkephalin up-regulate the immune response. These results suggested that the simple neuroendocrine-immune regulatory network in oyster might be activated by oyster TNF and then regulate the immune response by virtue of neurotransmitters, cytokines and transcription factors.
Identification and Characterization of miRNAs in Chondrus crispus by High-Throughput Sequencing and Bioinformatics Analysis
Authors: Gao Fan , Nan FangRu , Song Wei , Feng Jia , Lv JunPing , Xie ShuLian 
Published: May 2016

AbstractChondrus crispus, an economically and medicinally important red alga, is a medicinally active substance and important for anti-tumor research. In this study, 117C. crispusmiRNAs (108 conserved and 9 novel) were identified from 2,416,181 small-RNA reads using high-throughput sequencing and bioinformatics methods. According to the BLAST search against the miRBase database, these miRNAs belonged to 110 miRNA families. Sequence alignment combined with homology searching revealed both the conservation and diversity of predicted potential miRNA families in different plant species. Four and 19 randomly selected miRNAs were validated by northern blotting and stem-loop quantitative real-time reverse transcription polymerase chain reaction detection, respectively. The validation rates (75% and 94.7%) demonstrated that most of the identified miRNAs could be credible. A total of 160 potential target genes were predicted and functionally annotated by Gene Ontology analysis and Kyoto Encyclopedia of Genes and Genomes analysis. We also analyzed the interrelationship of miRNAs, miRNA-target genes and target genes inC. crispusby constructing a Cytoscape network. The 117 miRNAs identified in our study should supply large quantities of information that will be important for red algae small RNA research.
Design of α-Fe2O3 nanorods functionalized tubular NiO nanostructure for discriminating toluene molecules
Authors: Wang Chen , Wang Tianshuang , Wang Boqun , Zhou Xin , Cheng Xiaoyang , Sun Peng , Zheng Jie , Lu Geyu 
Published: May 2016

AbstractA novel tubular NiO nanostructure was synthesized by a facile and low-cost hydrothermal strategy and then further functionalized by decorating α-Fe2O3 nanorods. The images of electron microscopy indicated that the α-Fe2O3 nanorods were assembled epitaxially on the surfaces of NiO nanotubes to form α-Fe2O3/NiO nanotubes. As a proof-of-concept demonstration of the function, gas sensing devices were fabricated from as-prepared α-Fe2O3/NiO nanotubes and showed enhanced gas response and excellent selectivity toward toluene, giving a response of 8.8 to 5 ppm target gas, which was about 7.8 times higher than that of pure NiO nanotubes at 275 °C. The improved gas sensing performance of α-Fe2O3/NiO nanotubes could be attributed to the unique tubular morphology features, p-n heterojunctions and the synergetic behavior of α-Fe2O3 and NiO.
Structural and functional insights into the E3 ligase, RNF126
Authors: Krysztofinska Ewelina M. , Martínez-Lumbreras Santiago , Thapaliya Arjun , Evans Nicola J. , High Stephen , Isaacson Rivka L. 
Published: May 2016

AbstractRNF126 is an E3 ubiquitin ligase that collaborates with the BAG6 sortase complex to ubiquitinate hydrophobic substrates in the cytoplasm that are destined for proteasomal recycling. Composed of a trimeric complex of BAG6, TRC35 and UBL4A the BAG6 sortase is also associated with SGTA, a co-chaperone from which it can obtain hydrophobic substrates. Here we solve the solution structure of the RNF126 zinc finger domain in complex with the BAG6 UBL domain. We also characterise an interaction between RNF126 and UBL4A and analyse the competition between SGTA and RNF126 for the N-terminal BAG6 binding site. This work sheds light on the sorting mechanism of the BAG6 complex and its accessory proteins which, together, decide the fate of stray hydrophobic proteins in the aqueous cytoplasm.
Synthesis of advanced aluminide intermetallic coatings by low-energy Al-ion radiation
Authors: Shen Mingli , Gu Yan , Zhao Panpan , Zhu Shenglong , Wang Fuhui 
Published: May 2016

AbstractMetals that work at high temperatures (for instance, superalloys in gas-turbines) depend on thermally grown oxide (TGO, commonly alumina) to withstand corrosion attack. Nickel Aluminide (NiAl) as one superior alumina TGO former plays an important role in protective coatings for turbine blades in gas-turbine engines used for aircraft propulsion and power generation. Lowering TGO growth rate is essentially favored for offering sustainable protection, especially in thermal barrier coatings (TBC). However, it can only be achieved currently by a strategy of adding the third element (Pt or reactive elements) into NiAl during traditional diffusion- or deposition-based synthesis of the coating. Here we present a highly flexible Al-ion radiation-based synthesis of advanced NiAl coatings, achieving low TGO growth rate without relying on the third element addition. Our results expand the strategy for lowering TGO growth rate and demonstrate potentials for ion radiation in advancing materials synthesis.