bluuebunny/crossref_metadata_2025_split huggingface dataset:
A ZIP6-ZIP10 heteromer controls NCAM1 phosphorylation and integration into focal adhesion complexes during epithelial-to-mesenchymal transition
Authors: Brethour Dylan , Mehrabian Mohadeseh , Williams Declan , Wang Xinzhu , Ghodrati Farinaz , Ehsani Sepehr , Rubie Elizabeth A. , Woodgett James R. , Sevalle Jean , Xi Zhengrui , Rogaeva Ekaterina , Schmitt-Ulms Gerold 
Published: January 2017

AbstractThe prion protein (PrP) evolved from the subbranch of ZIP metal ion transporters comprising ZIPs 5, 6 and 10, raising the prospect that the study of these ZIPs may reveal insights relevant for understanding the function of PrP. Building on data which suggested PrP and ZIP6 are critical during epithelial-to-mesenchymal transition (EMT), we investigated ZIP6 in an EMT paradigm using ZIP6 knockout cells, mass spectrometry and bioinformatic methods. Reminiscent of PrP, ZIP6 levels are five-fold upregulated during EMT and the protein forms a complex with NCAM1. ZIP6 also interacts with ZIP10 and the two ZIP transporters exhibit interdependency during their expression. ZIP6 contributes to the integration of NCAM1 in focal adhesion complexes but, unlike cells lacking PrP, ZIP6 deficiency does not abolish polysialylation of NCAM1. Instead, ZIP6 mediates phosphorylation of NCAM1 on a cluster of cytosolic acceptor sites. Substrate consensus motif features andin vitrophosphorylation data point toward GSK3 as the kinase responsible, and interface mapping experiments identified histidine-rich cytoplasmic loops within the ZIP6/ZIP10 heteromer as a novel scaffold for GSK3 binding. Our data suggests that PrP and ZIP6 inherited the ability to interact with NCAM1 from their common ZIP ancestors but have since diverged to control distinct posttranslational modifications of NCAM1.
Immunoglobulin light chain (IGL) genes in torafugu: Genomic organization and identification of a third teleost IGL isotype
Authors: Fu Xi , Zhang Fengjun , Watabe Shugo , Asakawa Shuichi 
Published: January 2017

AbstractHere, we report a genome-wide survey of immunoglobulin light chain (IGL) genes of torafugu (Takifugu rubripes) revealing multi-clusters spanning three separate chromosomes (v5 assembly) and 45 scaffolds (v4 assembly). Conventional sequence similarity searches and motif scanning approaches based on recombination signal sequence (RSS) motifs were used. We found that three IGL isotypes (L1, L2, and L3) exist in torafugu and that several loci for each isotype are present. The transcriptional orientations of the variable IGL (VL) segments were found to be either the same (in the L2 isotype) or opposite (in the L1 and L3 isotypes) to the IGL joining (JL) and constant (CL) segments, suggesting they can undergo rearrangement by deletion or inversion when expressed. Alignments of expressed sequence tags (ESTs) to corresponding germline gene segments revealed expression of the three IGL isotypes in torafugu. Taken together, our findings provide a genomic framework for torafugu IGL genes and show that the IG diversity of this species could be attributed to at least three distinct chromosomal regions.
Nanoscale measurement of trace element distributions in Spartina alterniflora root tissue during dormancy
Authors: Feng Huan , Qian Yu , Cochran J. Kirk , Zhu Qingzhi , Hu Wen , Yan Hanfei , Li Li , Huang Xiaojing , Chu Yong S. , Liu Houjun , Yoo Shinjae , Liu Chang-Jun 
Published: January 2017

AbstractThis paper reports a nanometer-scale investigation of trace element (As, Ca, Cr, Cu, Fe, Mn, Ni, S and Zn) distributions in the root system Spartina alterniflora during dormancy. The sample was collected on a salt marsh island in Jamaica Bay, New York, in April 2015 and the root was cross-sectioned with 10 μm resolution. Synchrotron X-ray nanofluorescence was applied to map the trace element distributions in selected areas of the root epidermis and endodermis. The sampling resolution was 60 nm to increase the measurement accuracy and reduce the uncertainty. The results indicate that the elemental concentrations in the epidermis, outer endodermis and inner endodermis are significantly (p < 0.01) different. The root endodermis has relatively higher concentrations of these elements than the root epidermis. Furthermore, this high resolution measurement indicates that the elemental concentrations in the outer endodermis are significantly (p < 0.01) higher than those in the inner endodermis. These results suggest that the Casparian strip may play a role in governing the aplastic transport of these elements. Pearson correlation analysis on the average concentrations of each element in the selected areas shows that most of the elements are significantly (p < 0.05) correlated, which suggests that these elements may share the same transport pathways.
Carbon elimination from silicon kerf: Thermogravimetric analysis and mechanistic considerations
Authors: Vazquez-Pufleau Miguel , Chadha Tandeep S. , Yablonsky Gregory , Biswas Pratim 
Published: January 2017

Abstract40% of ultrapure silicon is lost as kerf during slicing to produce wafers. Kerf is currently not being recycled due to engineering challenges and costs associated with removing its abundant impurities. Carbon left behind from the lubricant remains as one of the most difficult contaminants to remove in kerf without significant silicon oxidation. The present work enables to better understand the mechanism of carbon elimination in kerf which can aid the design of better processes for kef recycling and low cost photovoltaics. In this paper, we studied the kinetics of carbon elimination from silicon kerf in two atmospheres: air and N2, under a regime of no-diffusion-limitation. We report the apparent activation energy in both atmospheres using three methods: Kissinger, and two isoconversional approaches. In both atmospheres, a bimodal apparent activation energy is observed, suggesting a two stage process. A reaction mechanism is proposed in which (a) C-C and C-O bond cleavage reactions occur in parallel with polymer formation; (b) at higher temperatures, this polymer fully degrades in air but leaves a tarry residue in N2 that accounts for about 12% of the initial total carbon.
Stochastic evolution in populations of ideas
Authors: Nicole Robin , Sollich Peter , Galla Tobias 
Published: January 2017

AbstractIt is known that learning of players who interact in a repeated game can be interpreted as an evolutionary process in a population of ideas. These analogies have so far mostly been established in deterministic models, and memory loss in learning has been seen to act similarly to mutation in evolution. We here propose a representation of reinforcement learning as a stochastic process in finite ‘populations of ideas’. The resulting birth-death dynamics has absorbing states and allows for the extinction or fixation of ideas, marking a key difference to mutation-selection processes in finite populations. We characterize the outcome of evolution in populations of ideas for several classes of symmetric and asymmetric games.
Crystal growth of Dirac semimetal ZrSiS with high magnetoresistance and mobility
Authors: Sankar Raman , Peramaiyan G. , Muthuselvam I. Panneer , Butler Christopher J. , Dimitri Klauss , Neupane Madhab , Rao G. Narsinga , Lin M.-T. , Chou F. C. 
Published: January 2017

AbstractHigh quality single crystal ZrSiS as a theoretically predicted Dirac semimetal has been grown successfully using a vapor phase transport method. The single crystals of tetragonal structure are easy to cleave into perfect square-shaped pieces due to the van der Waals bonding between the sulfur atoms of the quintuple layers. Physical property measurement results including resistivity, Hall coefficient (RH), and specific heat are reported. The transport and thermodynamic properties suggest a Fermi liquid behavior with two Fermi pockets at low temperatures. At T = 3 K and magnetic field of Hǁc up to 9 Tesla, large magneto-resistance up to 8500% and 7200% for Iǁ(100) and Iǁ(110) were found. Shubnikov de Haas (SdH) oscillations were identified from the resistivity data, revealing the existence of two Fermi pockets at the Fermi level via the fast Fourier transform (FFT) analysis. The Hall coefficient (RH) showed hole-dominated carriers with a high mobility of 3.05 × 104 cm2V−1s−1 at 3 K. ZrSiS has been confirmed to be a Dirac semimetal by the Dirac cone mapping near the X-point via angle resolved photoemission spectroscopy (ARPES) with a Dirac nodal line near the Fermi level identified using scanning tunneling spectroscopy (STS).
Correlated electronic decay in expanding clusters triggered by intense XUV pulses from a Free-Electron-Laser
Authors: Oelze Tim , Schütte Bernd , Müller Maria , Müller Jan P. , Wieland Marek , Frühling Ulrike , Drescher Markus , Al-Shemmary Alaa , Golz Torsten , Stojanovic Nikola , Krikunova Maria 
Published: January 2017

AbstractIrradiation of nanoscale clusters and large molecules with intense laser pulses transforms them into highly-excited non- equilibrium states. The dynamics of intense laser-cluster interaction is encoded in electron kinetic energy spectra, which contain signatures of direct photoelectron emission as well as emission of thermalized nanoplasma electrons. In this work we report on a so far not observed spectrally narrow bound state signature in the electron kinetic energy spectra from mixed Xe core - Ar shell clusters ionized by intense extreme-ultraviolet (XUV) pulses from a free-electron-laser. This signature is attributed to the correlated electronic decay (CED) process, in which an excited atom relaxes and the excess energy is used to ionize the same or another excited atom or a nanoplasma electron. By applying the terahertz field streaking principle we demonstrate that CED-electrons are emitted at least a few picoseconds after the ionizing XUV pulse has ended. Following the recent finding of CED in clusters ionized by intense near-infrared laser pulses, our observation of CED in the XUV range suggests that this process is of general relevance for the relaxation dynamics in laser produced nanoplasmas.
Vanillic acid attenuates Aβ1-42-induced oxidative stress and cognitive impairment in mice
Authors: Amin Faiz Ul , Shah Shahid Ali , Kim Myeong Ok 
Published: January 2017

AbstractIncreasing evidence demonstrates that β-amyloid (Aβ) elicits oxidative stress, which contributes to the pathogenesis and disease progression of Alzheimer’s disease (AD). The aims of the present study were to determine and explore the antioxidant nature and potential mechanism of vanillic acid (VA) in Aβ1-42-induced oxidative stress and neuroinflammation mediated cognitive impairment in mice. An intracerebroventricular (i.c.v.) injection of Aβ1-42 into the mouse brain triggered increased reactive oxygen species (ROS) levels, neuroinflammation, synaptic deficits, memory impairment, and neurodegeneration. In contrast, the i.p. (intraperitoneal) administration of VA (30 mg/kg, for 3 weeks) after Aβ1-42-injection enhanced glutathione levels (GSH) and abrogated ROS generation accompanied by an induction of the endogenous nuclear factor erythroid 2-related factor 2 (Nrf2) and heme oxygenase 1 (HO-1) via the activation of Akt and glycogen synthase kinase 3β (GSK-3β) in the brain mice. Additionally, VA treatment decreased Aβ1-42-induced neuronal apoptosis and neuroinflammation and improved synaptic and cognitive deficits. Moreover, VA was nontoxic to HT22 cells and increased cell viability after Aβ1-42 exposure. To our knowledge, this study is the first to reveal the neuroprotective effect of VA against Aβ1-42-induced neurotoxicity. Our findings demonstrate that VA could potentially serve as a novel, promising, and accessible neuroprotective agent against progressive neurodegenerative diseases such as AD.
Hepatitis B virus X protein is capable of down-regulating protein level of host antiviral protein APOBEC3G
Authors: Chen Ruidong , Zhao Xue , Wang Yongxiang , Xie Youhua , Liu Jing 
Published: January 2017

AbstractThe apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC) family proteins bind RNA and single-stranded DNA, and create C-to-U base modifications through cytidine deaminase activity. APOBEC3G restricts human immunodeficiency virus 1 (HIV-1) infection by creating hypermutations in proviral DNA, while HIV-1-encoded vif protein antagonizes such restriction by targeting APOBEC3G for degradation. APOBEC3G also inhibits hepatitis B virus (HBV): APOBEC3G co-expression inhibits HBV replication and evidences exist indicating APOBEC3G-mediated HBV hypermutations in patients. HBV encodes a small non-structural X protein (HBx) with a recognized activating effect on HBV life cycle. In this work, we report the discovery that HBx selectively and dose-dependently decreases the protein level of co-expressed APOBEC3G in transfected Huh-7 cells. The effect was shown to take place post-translationally, but does not rely on protein degradation via proteasome or lysosome. Further work demonstrated that intracellular APOBEC3G is normally exported via exosome secretion and inhibition of exosome biogenesis causes retention of intracellular APOBEC3G. Finally, HBx co-expression specifically enhanced externalization of APOBEC3G via exosomes, resulting in decrease of intracellular APOBEC3G protein level. These data suggest the possibility that in addition to other mechanisms, HBx-mediated activation of HBV might also involve antagonizing of intracellular restriction factor APOBEC3G through promotion of its export.
Different Volumetric Measurement Methods for Pituitary Adenomas and Their Crucial Clinical Significance
Authors: Chuang Chi-Cheng , Lin Shinn-Yn , Pai Ping-Ching , Yan Jiun-Lin , Toh Cheng-Hong , Lee Shih-Tseng , Wei Kuo-Chen , Liu Zhuo-Hao , Chen Chung-Ming , Wang Yu-Chi , Lee Cheng-Chi 
Published: January 2017

AbstractConfirming the status of residual tumors is crucial. In stationary or spontaneous regression cases, early treatments are inappropriate. The long-used geometric calculation formula is 1/2 (length × width × height). However, it yields only rough estimates and is particularly unreliable for irregularly shaped masses. In our study, we attempted to propose a more accurate method. Between 2004 and 2014, 94 patients with pituitary tumors were enrolled in this retrospective study. All patients underwent transsphenoidal surgery and received magnetic resonance imaging (MRI). The pre- and postoperative volumes calculated using the traditional formula were termed A1 and A2, and those calculated using the proposed method were termed O1 and O2, respectively. Wilcoxon signed rank test revealed no significant difference between the A1 and O1 groups (P = 0.1810) but a significant difference between the A2 and O2 groups (P < 0.0001). Significant differences were present in the extent of resection (P < 0.0001), high-grade cavernous sinus invasion (P = 0.0312), and irregular shape (P = 0.0116). Volume is crucial in evaluating tumor status and determining treatment. Therefore, a more scientific method is especially useful when lesions are irregularly shaped or when treatment is determined exclusively based on the tumor volume.
New hydrate formation methods in a liquid-gas medium
Authors: Chernov A. A. , Pil’nik A. A. , Elistratov D. S. , Mezentsev I. V. , Meleshkin A. V. , Bartashevich M. V. , Vlasenko M. G. 
Published: January 2017

AbstractConceptually new methods of hydrate formation are proposed. The first one is based on the shock wave impact on a water-bubble medium. It is shown that the hydrate formation rate in this process is typically very high. A gas hydrate of carbon dioxide was produced. The process was experimentally studied using various initial conditions, as well as different external action magnitudes. The obtained experimental data are in good agreement with the proposed model. Other methods are based on the process of boiling liquefied gas in an enclosed volume of water (explosive boiling of a hydrating agent and the organization of cyclic boiling-condensation process). The key features of the methods are the high hydrate formation rate combined with a comparatively low power consumption leading to a great expected efficiency of the technologies based on them. The set of experiments was carried out. Gas hydrates of refrigerant R134a, carbon dioxide and propane were produced. The investigation of decomposition of a generated gas hydrate sample was made. The criteria of intensification of the hydrate formation process are formulated.
Chemical bonding in aqueous hexacyano cobaltate from photon- and electron-detection perspectives
Authors: Lalithambika Sreeju Sreekantan Nair , Atak Kaan , Seidel Robert , Neubauer Antje , Brandenburg Tim , Xiao Jie , Winter Bernd , Aziz Emad F. 
Published: January 2017

AbstractThe electronic structure of the [Co(CN)6]3− complex dissolved in water is studied using X-ray spectroscopy techniques. By combining electron and photon detection methods from the solutions ionized or excited by soft X-rays we experimentally identify chemical bonding between the metal center and the CN ligand. Non-resonant photoelectron spectroscopy provides solute electron binding energies, and nitrogen 1 s and cobalt 2p resonant core-level photoelectron spectroscopy identifies overlap between metal and ligand orbitals. By probing resonances we are able to qualitatively determine the ligand versus metal character of the respective occupied and non-occupied orbitals, purely by experiment. For the same excitations we also detect the emitted X-rays, yielding the complementary resonant inelastic X-ray scattering spectra. For a quantitative interpretation of the spectra, we perform theoretical electronic-structure calculations. The latter provide both orbital energies and orbital character which are found to be in good agreement with experimental energies and with experimentally inferred orbital mixing. We also report calculated X-ray absorption spectra, which in conjunction with our orbital-structure analysis, enables us to quantify various bonding interactions with a particular focus on the water-solvent – ligand interaction and the strength of π-backbonding between metal and ligand.
Clinical Roles of Lung Volumes Detected by Body Plethysmography and Helium Dilution in Asthmatic Patients: A Correlation and Diagnosis Analysis
Authors: Luo Jian , Liu Dan , Chen Guo , Liang Binmiao , Liu Chuntao 
Published: January 2017

AbstractRoles of lung volumes in asthma remain controversial. We aimed to evaluate the efficacy of lung volumes in differentiating asthma severity levels. Consecutive outpatients with chronic persistent asthma were enrolled, and body plethysmography (BP) and helium dilution (HD) were performed simultaneously to extract RV%pred, TLC%pred, and RV/TLC. Significant negative correlations were found between FEV1%pred and RV%pred (r = −0.557, P < 0.001), TLC%pred (r = −0.387, P < 0.001), and RV/TLC (r = −0.485, P < 0.001) measured by BP, as well as difference in volumes between these two techniques (ΔRV%pred, ΔTLC%pred and ΔRV/TLC). In mild and moderate asthma, AUC of RV%pred detected by BP and ΔTLC%pred was 0.723 (95%CI 0.571–0.874, P = 0.005) and 0.739 (95%CI 0.607–0.872, P = 0.002) with sensitivity and specificity being 79.41% and 88.24%, and 65.22% and 56.52% at cut-off of 145.40% and 14.23%, respectively. In moderate and severe asthma, AUC of RV%pred detected by BP and ΔTLC%pred was 0.782 (95%CI 0.671–0.893, P < 0.001) and 0.788 (95%CI 0.681–0.894, P < 0.002) with sensitivity and specificity being 77.78% and 97.22%, and 73.53% and 52.94% at cut-off of 179.85% and 20.22%, respectively. In conclusion, lung volumes are reliable complement of FEV1 in identifying asthma severity levels.
Optogenetic Modulation of Urinary Bladder Contraction for Lower Urinary Tract Dysfunction
Authors: Park Jae Hong , Hong Jin Ki , Jang Ja Yun , An Jieun , Lee Kyu-Sung , Kang Tong Mook , Shin Hyun Joon , Suh Jun-Kyo Francis 
Published: January 2017

AbstractAs current clinical approaches for lower urinary tract (LUT) dysfunction such as pharmacological and electrical stimulation treatments lack target specificity, thus resulting in suboptimal outcomes with various side effects, a better treatment modality with spatial and temporal target-specificity is necessary. In this study, we delivered optogenetic membrane proteins, such as channelrhodopsin-2 (ChR2) and halorhodopsin (NpHR), to bladder smooth muscle cells (SMCs) of mice using either the Cre-loxp transgenic system or a viral transfection method. The results showed that depolarizing ChR2-SMCs with blue light induced bladder contraction, whereas hyperpolarizing NpHR-SMCs with yellow light suppressed PGE2-induced overactive contraction. We also confirmed that optogenetic contraction of bladder smooth muscles in this study is not neurogenic, but solely myogenic, and that optogenetic light stimulation can modulate the urination in vivo. This study thus demonstrated the utility of optogenetic modulation of smooth muscle as a means to actively control the urinary bladder contraction with spatial and temporal accuracy. These features would increase the efficacy of bladder control in LUT dysfunctions without the side effects of conventional clinical therapies.
Comparative Transcriptome Analysis of Raccoon Dog Skin to Determine Melanin Content in Hair and Melanin Distribution in Skin
Authors: Du Zhanyu , Huang Kai , Zhao Jiaping , Song Xingchao , Xing Xiumei , Wu Qiong , Zhang Linbo , Xu Chao 
Published: January 2017

AbstractThe raccoon dog (Nyctereutes procyonoides) is an important canid fur-bearing animal species worldwide. Chinese raccoon dogs that present a white mutation, especially those with a white coat. Exploring melanin biosynthesis in the hair and skin of raccoon dogs is important for understanding the survival and evolutionary mechanisms of them. In this study, we measured the content of melanin in the hair of two types of raccoon dog and generated stained slices of skin tissue. The results indicated that melanin biosynthesis occurs in the wild-type (W) and white-type (B) raccoon dog skin, although less melanin is produced in B skin. We then sequenced the skin transcriptomes of W and B, compared the similarities and differences in expressed genes. A comparison of the gene expression showed 60 up-regulated genes and 127 down-regulated genes in B skin. We analyzed the unigenes and pathways related to the melanogenesis pathway and found that TYR, TYRP1, MC1R, SLC24a5, SLC45a2 and OCA2 were significantly down-regulated in B skin and these results were verified via qRT-PCR. We surmised that the phenotypic characteristics of the white mutation might be caused by the reduced expression of these genes and this finding provides new insights for future experiments in raccoon dogs.
Crystal structure of Sec10, a subunit of the exocyst complex
Authors: Chen Jianxing , Yamagata Atsushi , Kubota Keiko , Sato Yusuke , Goto-Ito Sakurako , Fukai Shuya 
Published: January 2017

AbstractThe exocyst complex is a heterooctameric protein complex composed of Sec3, Sec5, Sec6, Sec8, Sec10, Sec15, Exo70 and Exo84. This complex plays an essential role in trafficking secretory vesicles to the plasma membrane through its interaction with phosphatidylinositol 4,5-bisphosphate and small GTPases. To date, the near-full-length structural information of each subunit has been limited to Exo70, although the C-terminal half structures of Sec6, Sec15 and Exo84 and the structures of the small GTPase-binding domains of Sec3, Sec5 and Exo84 have been reported. Here, we report the crystal structure of the near-full-length zebrafish Sec10 (zSec10) at 2.73 Å resolution. The structure of zSec10 consists of tandem antiparallel helix bundles that form a straight rod, like helical core regions of other exocyst subunits. This structure provides the first atomic details of Sec10, which may be useful for future functional and structural studies of this subunit and the exocyst complex.