bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinct predictive performance of Rac1 and Cdc42 in cell migration
Authors: Yamao Masataka , Naoki Honda , Kunida Katsuyuki , Aoki Kazuhiro , Matsuda Michiyuki , Ishii Shin 
Published: December 2015

AbstractWe propose a new computation-based approach for elucidating how signaling molecules are decoded in cell migration. In this approach, we performed FRET time-lapse imaging of Rac1 and Cdc42, members of Rho GTPases which are responsible for cell motility and quantitatively identified the response functions that describe the conversion from the molecular activities to the morphological changes. Based on the identified response functions, we clarified the profiles of how the morphology spatiotemporally changes in response to local and transient activation of Rac1 and Cdc42 and found that Rac1 and Cdc42 activation triggers laterally propagating membrane protrusion. The response functions were also endowed with property of differentiator, which is beneficial for maintaining sensitivity under adaptation to the mean level of input. Using the response function, we could predict the morphological change from molecular activity and its predictive performance provides a new quantitative measure of how much the Rho GTPases participate in the cell migration. Interestingly, we discovered distinct predictive performance of Rac1 and Cdc42 depending on the migration modes, indicating that Rac1 and Cdc42 contribute to persistent and random migration, respectively. Thus, our proposed predictive approach enabled us to uncover the hidden information processing rules of Rho GTPases in the cell migration.
Multifractal analysis of weighted networks by a modified sandbox algorithm
Authors: Song Yu-Qin , Liu Jin-Long , Yu Zu-Guo , Li Bao-Gen 
Published: December 2015

AbstractComplex networks have attracted growing attention in many fields. As a generalization of fractal analysis, multifractal analysis (MFA) is a useful way to systematically describe the spatial heterogeneity of both theoretical and experimental fractal patterns. Some algorithms for MFA of unweighted complex networks have been proposed in the past a few years, including the sandbox (SB) algorithm recently employed by our group. In this paper, a modified SB algorithm (we call it SBw algorithm) is proposed for MFA of weighted networks. First, we use the SBw algorithm to study the multifractal property of two families of weighted fractal networks (WFNs): “Sierpinski” WFNs and “Cantor dust” WFNs. We also discuss how the fractal dimension and generalized fractal dimensions change with the edge-weights of the WFN. From the comparison between the theoretical and numerical fractal dimensions of these networks, we can find that the proposed SBw algorithm is efficient and feasible for MFA of weighted networks. Then, we apply the SBw algorithm to study multifractal properties of some real weighted networks — collaboration networks. It is found that the multifractality exists in these weighted networks and is affected by their edge-weights.
Non-additive effects of litter diversity on greenhouse gas emissions from alpine steppe soil in Northern Tibet
Authors: Chen Youchao , Sun Jian , Xie Fangting , Yan Yan , Wang Xiaodan , Cheng Genwei , Lu Xuyang 
Published: December 2015

AbstractWhile litter decomposition is a fundamental ecological process, previous studies have mainly focused on the decay of single species. In this study, we conducted a litter-mixing experiment to investigate litter diversity effects on greenhouse gas (GHG) emissions from an alpine steppe soil in Northern Tibet. Significant non-additive effects of litter diversity on GHG dynamics can be detected; these non-additive effects were the result of species composition rather than species richness. Synergistic effects were frequent for CO2 and N2O emissions, as they were found to occur in 70.5% and 47.1% of total cases, respectively; antagonistic effects on CH4 uptake predominated in 60.3% of the cases examined. The degree of synergism and antagonism may be significantly impacted by litter chemical traits, such as lignin and N, lignin:N ratio and total phenols during decomposition (P < 0.05). In addition, the relationship between chemical traits and litter-mixing effects changed over incubation time. Our study provides an opportunity to gain insight into the relationship between litter diversity and soil ecological processes. The results indicate that higher plant diversity may generally enhance CO2 and N2O emissions while inhibiting CH4 uptake; meanwhile, the direction and strength of non-additive effects appear to be related to litter chemical traits.
SUMOylation of Syntaxin1A regulates presynaptic endocytosis
Authors: Craig Tim J. , Anderson Dina , Evans Ashley J. , Girach Fatima , Henley Jeremy M. 
Published: December 2015

AbstractNeurotransmitter release from the presynaptic terminal is under very precise spatial and temporal control. Following neurotransmitter release, synaptic vesicles are recycled by endocytosis and refilled with neurotransmitter. During the exocytosis event leading to release, SNARE proteins provide most of the mechanical force for membrane fusion. Here, we show one of these proteins, Syntaxin1A, is SUMOylated near its C-terminal transmembrane domain in an activity-dependent manner. Preventing SUMOylation of Syntaxin1A reduces its interaction with other SNARE proteins and disrupts the balance of synaptic vesicle endo/exocytosis, resulting in an increase in endocytosis. These results indicate that SUMOylation regulates the emerging role of Syntaxin1A in vesicle endocytosis, which in turn, modulates neurotransmitter release and synaptic function.
Two-dimensional imaging in hyperbolic media–the role of field components and ordinary waves
Authors: Tuniz Alessandro , Kuhlmey Boris T. 
Published: December 2015

AbstractWe study full vector imaging of two dimensional source fields through finite slabs of media with extreme anisotropy, such as hyperbolic media. For this, we adapt the exact transfer matrix method for uniaxial media to calculate the two dimensional transfer functions and point spread functions for arbitrary vector fields described in Cartesian coordinates. This is more convenient for imaging simulations than the use of the natural, propagation direction-dependent TE/TM basis and clarifies which field components contribute to sub-diffraction imaging. We study the effect of ordinary waves on image quality, which previous one-dimensional approaches could not consider. Perfect sub-diffraction imaging can be achieved if longitudinal fields are measured, but in the more common case where field intensities or transverse fields are measured, ordinary waves cause artefacts. These become more prevalent when attempting to image large objects with high resolution. We discuss implications for curved hyperbolic imaging geometries such as hyperlenses.
3D visualization of XFEL beam focusing properties using LiF crystal X-ray detector
Authors: Pikuz Tatiana , Faenov Anatoly , Matsuoka Takeshi , Matsuyama Satoshi , Yamauchi Kazuto , Ozaki Norimasa , Albertazzi Bruno , Inubushi Yuichi , Yabashi Makina , Tono Kensuke , Sato Yuya , Yumoto Hirokatsu , Ohashi Haruhiko , Pikuz Sergei , Grum-Grzhimailo Alexei N. , Nishikino Masaharu , Kawachi Tetsuya , Ishikawa Tetsuya , Kodama Ryosuke 
Published: December 2015

AbstractHere, we report, that by means of direct irradiation of lithium fluoride a (LiF) crystal, in situ 3D visualization of the SACLA XFEL focused beam profile along the propagation direction is realized, including propagation inside photoluminescence solid matter. High sensitivity and large dynamic range of the LiF crystal detector allowed measurements of the intensity distribution of the beam at distances far from the best focus as well as near the best focus and evaluation of XFEL source size and beam quality factor M2. Our measurements also support the theoretical prediction that for X-ray photons with energies ~10 keV the radius of the generated photoelectron cloud within the LiF crystal reaches about 600 nm before thermalization. The proposed method has a spatial resolution ~ 0.4–2.0 μm for photons with energies 6–14 keV and potentially could be used in a single shot mode for optimization of different focusing systems developed at XFEL and synchrotron facilities.
Body mass index and risk of subtypes of head-neck cancer: the Netherlands Cohort Study
Authors: Maasland Denise H. E. , Brandt Piet A. van den , Kremer Bernd , Schouten Leo J. 
Published: December 2015

AbstractLow body mass index (BMI) has been associated with risk of head-neck cancer (HNC), but prospective data are scarce. We investigated the association between BMI, BMI at age 20 years and change in BMI during adulthood with risk of HNC and HNC subtypes. 120,852 participants completed a questionnaire on diet and other cancer risk factors, including anthropometric measurements, at baseline in 1986. After 20.3 years of follow-up, 411 HNC (127 oral cavity cancer (OCC), 84 oro-/hypopharyngeal cancer (OHPC) and 197 laryngeal cancer (LC)) cases and 3,980 subcohort members were available for case-cohort analysis using Cox proportional hazards models. BMI at baseline was inversely associated with risk of HNC overall, with a multivariate rate ratio of 3.31 (95% CI 1.40–7.82) for subjects with a BMI < 18.5 kg/m2, compared to participants with a BMI of 18.5 to 25 kg/m2. Among HNC subtypes, this association was strongest for OCC and OHPC. The association between BMI at age 20 and HNC risk appeared to be positive. In this large prospective cohort study, we found an inverse association between BMI at baseline and HNC risk. For BMI at age 20, however, a positive rather than inverse association was found.
Characterization of Pseudooxynicotine Amine Oxidase of Pseudomonas putida S16 that Is Crucial for Nicotine Degradation
Authors: Hu Haiyang , Wang Weiwei , Tang Hongzhi , Xu Ping 
Published: December 2015

AbstractPseudooxynicotine amine oxidase (Pnao) is essential to the pyrrolidine pathway of nicotine degradation of Pseudomonas putida strain S16, which is significant for the detoxification of nicotine, through removing the CH3NH2 group. However, little is known about biochemical mechanism of this enzyme. Here, we characterized its properties and biochemical mechanism. Isotope labeling experiments provided direct evidence that the newly introduced oxygen atom in 3-succinoylsemialdehyde-pyridine is derived from H2O, but not from O2. Pnao was very stable at temperatures below 50 °C; below this temperature, the enzyme activity increased as temperature rose. Site-directed mutagenesis studies showed that residue 180 is important for its thermal stability. In addition, tungstate may enhance the enzyme activity, which has rarely been reported before. Our findings make a further understanding of the crucial Pnao in nicotine degradation.
Low-temperature synthesis of high-ordered anatase TiO2 nanotube array films coated with exposed {001} nanofacets
Authors: Ding Jie , Huang Zhennan , Zhu Jihao , Kou Shengzhong , Zhang Xiaobin , Yang Hangsheng 
Published: December 2015

AbstractHigh-ordered anatase TiO2 nanotube array films coated with exposed high-reactive {001} nanofacets were fabricated by a modified hydrothermal method using amorphous anodic TiO2 nanotube arrays (ATONAs) as starting materials. It was found that the reaction between gas phase HF and solid ATONAs played a key role in the transformation process from amorphous to anatase TiO2 and the TiO2 tubular structure kept unchanged during the surface modification with an exposed {001} facets up to 76.5%, which could be attributed to the low reaction temperature of 130 °C. Our study provided a novel route for the facile preparation of {001} facets exposed anatase TiO2.
Comparing photosynthetic characteristics of Isoetes sinensis Palmer under submerged and terrestrial conditions
Authors: Yang Tao , Liu Xing 
Published: December 2015

AbstractCrassulacean acid metabolism (CAM) is widespread in terrestrial and aquatic species, plastic in response to environmental changes.IsoetesL. is one of the earliest basal vascular plants and CAM is popular in this genus.Isoetes sinensisPalmer is an amphibious species, alternating frequently between terrestrial and aquatic environments. Given this, we investigated and compared photosynthetic characteristics over a diurnal cycle under submerged condition (SC) and terrestrial condition (TC). The results suggest thatI. sinensispossesses a stronger CAM capacity under SC. Compared with under TC, titratable acidity levels and organic acid concentrations were more enriched under SC, whereas soluble sugar or starch and protein levels were lower under SC. Transcript analyses for nine photosynthetic genes revealed that CAM-associated genes possessed high transcripts under SC, but C3-related transcripts were highly expressed under TC. In addition, the enzyme activity measurements demonstrated that PEPC activity over a diurnal cycle was slightly higher under SC, whereas Rubisco activity during the daytime was greater under TC. This comprehensive study probably facilitates general understandings about the CAM photosynthetic characteristics ofIsoetesin response to the environmental changes.
Learning-induced synaptic potentiation in implanted neural precursor cell-derived neurons
Authors: Park Kyungjoon , Heo Hwon , Han Ma Eum , Choi Kyuhyun , Yi Jee Hyun , Kang Shin Jung , Kwon Yunhee Kim , Shin Ki Soon 
Published: December 2015

AbstractNeuronal loss caused by neurodegenerative diseases, traumatic brain injury and stroke results in cognitive dysfunctioning. Implantation of neural stem/precursor cells (NPCs) can improve the brain function by replacing lost neurons. Proper synaptic integration following neuronal differentiation of implanted cells is believed to be a prerequisite for the functional recovery. In the present study, we characterized the functional properties of immortalized neural progenitor HiB5 cells implanted into the rat hippocampus with chemically induced lesion. The implanted HiB5 cells migrated toward CA1 pyramidal layer and differentiated into vGluT1-positive glutamatergic neurons with morphological and electrophysiological properties of endogenous CA1 pyramidal cells. Functional synaptic integration of HiB5 cell-derived neurons was also evidenced by immunohistochemical and electrophysiological data. Lesion-caused memory deficit was significantly recovered after the implantation when assessed by inhibitory avoidance (IA) learning. Remarkably, IA learning preferentially produced long-term potentiation (LTP) at the synapses onto HiB5 cell-derived neurons, which occluded paring protocol-induced LTPex vivo. We conclude that the implanted HiB5 cell-derived neurons actively participate in learning process through LTP formation, thereby counteracting lesion-mediated memory impairment.
Innate Immune Molecule Surfactant Protein D Attenuates Sepsis-induced Acute Pancreatic Injury through Modulating Apoptosis and NF-κB-mediated Inflammation
Authors: Liu Zhiyong , Shi Qiao , Liu Jiao , Abdel-Razek Osama , Xu Yongan , Cooney Robert N , Wang Guirong 
Published: December 2015

AbstractSepsis causes multiple-organ dysfunction including pancreatic injury, thus resulting in high mortality. Innate immune molecule surfactant protein D (SP-D) plays a critical role in host defense and regulating inflammation of infectious diseases. In this study we investigated SP-D functions in the acute pancreatic injury (API) with C57BL/6 Wild-type (WT) and SP-D knockout (KO) mice in cecal ligation and puncture (CLP) model. Our results confirm SP-D expression in pancreatic islets and intercalated ducts and are the first to explore the role of pancreatic SP-D in sepsis. CLP decreased pancreatic SP-D levels and caused severe pancreatic injury with higher serum amylase 24 h after CLP. Apoptosis and neutrophil infiltration were increased in the pancreas of septic KO mice (p < 0.05, vs septic WT mice), with lower Bcl-2 and higher caspase-3 levels in septic KO mice (p < 0.05). Molecular analysis revealed increased NF-κB-p65 and phosphorylated IκB-α levels along with higher serum levels of TNF-α and IL-6 in septic KO mice compared to septic WT mice (p < 0.01). Furthermore, in vitro islet cultures stimulated with LPS produced higher TNF-α and IL-6 (p < 0.05) from KO mice compared to WT mice. Collectively, these results demonstrate SP-D plays protective roles by inhibiting apoptosis and modulating NF-κB-mediated inflammation in CLP-induced API.
Silicon etching using only Oxygen at high temperature: An alternative approach to Si micro-machining on 150 mm Si wafers
Authors: Chai Jessica , Walker Glenn , Wang Li , Massoubre David , Tan Say Hwa , Chaik Kien , Hold Leonie , Iacopi Alan 
Published: December 2015

AbstractUsing a combination of low-pressure oxygen and high temperatures, isotropic and anisotropic silicon (Si) etch rates can be controlled up to ten micron per minute. By varying the process conditions, we show that the vertical-to-lateral etch rate ratio can be controlled from 1:1 isotropic etch to 1.8:1 anisotropic. This simple Si etching technique combines the main respective advantages of both wet and dry Si etching techniques such as fast Si etch rate, stiction-free and high etch rate uniformity across a wafer. In addition, this alternative O2-based Si etching technique has additional advantages not commonly associated with dry etchants such as avoiding the use of halogens and has no toxic by-products, which improves safety and simplifies waste disposal. Furthermore, this process also exhibits very high selectivity (>1000:1) with conventional hard masks such as silicon carbide, silicon dioxide and silicon nitride, enabling deep Si etching. In these initial studies, etch rates as high as 9.2 μm/min could be achieved at 1150 °C. Empirical estimation for the calculation of the etch rate as a function of the feature size and oxygen flow rate are presented and used as proof of concepts.
Evolution of crystal and electronic structures of magnesium dicarbide at high pressure
Authors: Wang Dashuai , Yan Yan , Zhou Dan , Liu Yanhui 
Published: December 2015

AbstractCarbon-based compounds exhibit unexpected structures and electronic behavior at high pressure arising from various bonding features of carbon (e.g., sp, sp2 and sp3 C-C bonds). Here we report evolution of crystal structures of MgC2 in a wide pressure range of 0–200 GPa as predicted through ab-initio calculations in combination with an unbiased swarm structure search. Three pressure-induced structural transformations are unraveled, following the phase sequence of ambient-pressure P42/mnm (α-phase) → Cmcm (β-phase) → C2m (γ-phase) → EuGe2-type P-3m1 (δ-phase), where significant C-C bonding modifications from C-C dimer to quasi 1-dimensionzigzag chain, to polymerized ribbon and then to winkled quasi 2- dimension graphite sheet are evident. The predicted β- and γ-phases with sp2 C-C hybridization are metals, while the δ- phase characterized by a sp3C-C hybridization is a narrow-gap semiconductor with a band gap of 0.667 eV. Strong electron-phonon couplings in the compressed β- and γ- phases arepredicted with β-phase showing a high superconducting critical temperature of 11.2 K. The current results indicate that pressure is effective in tuning the crystal and electronic structures of MgC2, which is expected to have impact on physical properties for potential applications.
Prevention of Dielectric Breakdown of Nanopore Membranes by Charge Neutralization
Authors: Matsui Kazuma , Yanagi Itaru , Goto Yusuke , Takeda Ken-ichi 
Published: December 2015

AbstractTo achieve DNA sequencing using a solid-state nanopore, it is necessary to reduce the electric noise current. The noise current can be decreased by reducing the capacitance (C) of the nanopore device. However, we found that an electric-charge difference (ΔQ) between the electrolyte in one chamber and the electrolyte in another chamber occurred. For low capacitance devices, this electric-charge imbalance can lead to unexpectedly high voltage (ΔV = ΔQ/C) which disrupted the membrane when the two electrolytes were independently poured into the chambers. We elucidated the mechanism for the generation of initial defects and established new procedures for preventing the generation of defects by connecting an electric bypass between the chambers.
Variance-corrected Michaelis-Menten equation predicts transient rates of single-enzyme reactions and response times in bacterial gene-regulation
Authors: Pulkkinen Otto , Metzler Ralf 
Published: December 2015

AbstractMany chemical reactions in biological cells occur at very low concentrations of constituent molecules. Thus, transcriptional gene-regulation is often controlled by poorly expressed transcription-factors, such as E.coli lac repressor with few tens of copies. Here we study the effects of inherent concentration fluctuations of substrate-molecules on the seminal Michaelis-Menten scheme of biochemical reactions. We present a universal correction to the Michaelis-Menten equation for the reaction-rates. The relevance and validity of this correction for enzymatic reactions and intracellular gene-regulation is demonstrated. Our analytical theory and simulation results confirm that the proposed variance-corrected Michaelis-Menten equation predicts the rate of reactions with remarkable accuracy even in the presence of large non-equilibrium concentration fluctuations. The major advantage of our approach is that it involves only the mean and variance of the substrate-molecule concentration. Our theory is therefore accessible to experiments and not specific to the exact source of the concentration fluctuations.
Busulfan and cyclosphamide induce liver inflammation through NLRP3 activation in mice after hematopoietic stem cell transplantation
Authors: Qiao Jianlin , Huang Yujin , Xia Yuan , Chu Peipei , Yao Haina , Xu Linyan , Qi Kunming , Liu Yun , Xu Kailin , Zeng Lingyu 
Published: December 2015

AbstractThe aim of this study was to evaluate the role of NLRP3 inflammasome on BU/CY-induced liver inflammation in mice after HSCT. HSCT mice model was established through infusion of 5 × 106 bone marrow mononuclear cells after conditioned with BU/CY. On day 7, 14, 21 and 28 after HSCT, mice were sacrificed for analysis of liver inflammation, cytokine secretion, NLRP3 expression and caspase-1 activation as well as release of ATP and high-mobility group protein B1 (HMGB1). Furthermore, NLRP3 selective inhibitor (BAY 11-7082) was administrated into mice after HSCT to evaluate its effects on liver inflammation. Severe liver inflammation and damage with elevated secretion of IL-1β and IL-18 were found in mice after HSCT. Meanwhile, elevated expressions of NLRP3 and caspase-1 activation in liver were found. In addition, increased release of ATP and HMGB1 were observed. Selective inhibition of NLRP3 decreased caspase-1 activation and secretion of IL-1β and IL-18. Furthermore, NLRP3 inhibition also reduced infiltration of macrophages and neutrophils and improved liver function. In conclusion, NLRP3 was involved in BU/CY-induced liver inflammation after HSCT and selectively inhibited it ameliorated liver inflammation and improved liver function, suggesting targeting NLRP3 might be a new approach in the prophylaxis of liver inflammation after HSCT.