bluuebunny/crossref_metadata_2025 huggingface dataset:
Reversible lysine acetylation is involved in DNA replication initiation by regulating activities of initiator DnaA in Escherichia coli
Authors: Zhang Qiufen , Zhou Aiping , Li Shuxian , Ni Jinjing , Tao Jing , Lu Jie , Wan Baoshan , Li Shuai , Zhang Jian , Zhao Shimin , Zhao Guo-Ping , Shao Feng , Yao Yu-Feng
Published: August 2016

The regulation of chromosomal replication is critical and the activation of DnaA by ATP binding is a key step in replication initiation. However, it remains unclear whether and how the process of ATP-binding to DnaA is regulated. Here, we show that DnaA can be acetylated and its acetylation level varies with cell growth and correlates with DNA replication initiation frequencies in E. coli. Specifically, the conserved K178 in Walker A motif of DnaA can be acetylated and its acetylation level reaches the summit at the stationary phase, which prevents DnaA from binding to ATP or oriC and leads to inhibition of DNA replication initiation. The deacetylation process of DnaA is catalyzed by deacetylase CobB. The acetylation process of DnaA is mediated by acetyltransferase YfiQ and nonenzymatically by acetyl-phosphate. These findings suggest that the reversible acetylation of DnaA ensures cells to respond promptly to environmental changes. Since Walker A motif is universally distributed across organisms, acetylation of Walker A motif may present a novel regulatory mechanism conserved from bacteria to eukaryotes.
Structural evolution and strength change of a metallic glass at different temperatures
Authors: Tong X. , Wang G. , Stachurski Z. H. , Bednarčík J. , Mattern N. , Zhai Q. J. , Eckert J.
Published: August 2016

The structural evolution of a Zr64.13Cu15.75Ni10.12Al10 metallic glass is investigated in-situ by high-energy synchrotron X-ray radiation upon heating up to crystallization. The structural rearrangements on the atomic scale during the heating process are analysed as a function of temperature, focusing on shift of the peaks of the structure factor in reciprocal space and the pair distribution function and radial distribution function in real space which are correlated with atomic rearrangements and progressing nanocrystallization. Thermal expansion and contraction of the coordination shells is measured and correlated with the bulk coefficient of thermal expansion. The characteristics of the microstructure and the yield strength of the metallic glass at high temperature are discussed aiming to elucidate the correlation between the atomic arrangement and the mechanical properties.
microRNA-132/212 deficiency enhances Aβ production and senile plaque deposition in Alzheimer’s disease triple transgenic mice
Authors: Hernandez-Rapp Julia , Rainone Sara , Goupil Claudia , Dorval Véronique , Smith Pascal Y. , Saint-Pierre Martine , Vallée Maxime , Planel Emmanuel , Droit Arnaud , Calon Frédéric , Cicchetti Francesca , Hébert Sébastien S.
Published: August 2016

The abnormal regulation of amyloid-β (Aβ) metabolism (e.g., production, cleavage, clearance) plays a central role in Alzheimer’s disease (AD). Among endogenous factors believed to participate in AD progression are the small regulatory non-coding microRNAs (miRs). In particular, the miR-132/212 cluster is severely reduced in the AD brain. In previous studies we have shown that miR-132/212 deficiency in mice leads to impaired memory and enhanced Tau pathology as seen in AD patients. Here we demonstrate that the genetic deletion of miR-132/212 promotes Aβ production and amyloid (senile) plaque formation in triple transgenic AD (3xTg-AD) mice. Using RNA-Seq and bioinformatics, we identified genes of the miR-132/212 network with documented roles in the regulation of Aβ metabolism, including Tau, Mapk and Sirt1. Consistent with these findings, we show that the modulation of miR-132, or its target Sirt1, can directly regulate Aβ production in cells. Finally, both miR-132 and Sirt1 levels correlated with Aβ load in humans. Overall, our results support the hypothesis that the miR-132/212 network, including Sirt1 and likely other target genes, contributes to abnormal Aβ metabolism and senile plaque deposition in AD. This study strengthens the importance of miR-dependent networks in neurodegenerative disorders and opens the door to multifactorial drug targets of AD by targeting Aβ and Tau.
Genome-wide identification and gene expression profiling of ubiquitin ligases for endoplasmic reticulum protein degradation
Authors: Kaneko Masayuki , Iwase Ikuko , Yamasaki Yuki , Takai Tomoko , Wu Yan , Kanemoto Soshi , Matsuhisa Koji , Asada Rie , Okuma Yasunobu , Watanabe Takeshi , Imaizumi Kazunori , Nomura Yausyuki
Published: August 2016

Endoplasmic reticulum (ER)-associated degradation (ERAD) is a mechanism by which unfolded proteins that accumulate in the ER are transported to the cytosol for ubiquitin–proteasome-mediated degradation. Ubiquitin ligases (E3s) are a group of enzymes responsible for substrate selectivity and ubiquitin chain formation. The purpose of this study was to identify novel E3s involved in ERAD. Thirty-seven candidate genes were selected by searches for proteins with RING-finger motifs and transmembrane regions, which are the major features of ERAD E3s. We performed gene expression profiling for the identified E3s in human and mouse tissues. Several genes were specifically or selectively expressed in both tissues; the expression of four genes (RNFT1, RNF185, CGRRF1 and RNF19B) was significantly upregulated by ER stress. To determine the involvement of the ER stress-responsive genes in ERAD, we investigated their ER localisation, in vitro autoubiquitination activity and ER stress resistance. All were partially localised to the ER, whereas CGRRF1 did not possess E3 activity. RNFT1 and RNF185, but not CGRRF1 and RNF19B, exhibited significant resistance to ER stressor in an E3 activity-dependent manner. Thus, these genes are possible candidates for ERAD E3s.
STAT5 is a key transcription factor for IL-3-mediated inhibition of RANKL-induced osteoclastogenesis
Authors: Lee Jongwon , Seong Semun , Kim Jung Ha , Kim Kabsun , Kim Inyoung , Jeong Byung-chul , Nam Kwang-Il , Kim Kyung Keun , Hennighausen Lothar , Kim Nacksung
Published: August 2016

Among the diverse cytokines involved in osteoclast differentiation, interleukin (IL)-3 inhibits RANKL-induced osteoclastogenesis. However, the mechanism underlying IL-3-mediated inhibition of osteoclast differentiation is not fully understood. Here we demonstrate that the activation of signal transducers and activators of transcription 5 (STAT5) by IL-3 inhibits RANKL-induced osteoclastogenesis through the induction of the expression of Id genes. We found that STAT5 overexpression inhibited RANKL-induced osteoclastogenesis. However, RANKL did not regulate the expression or activation of STAT5 during osteoclast differentiation. STAT5 deficiency prevented IL-3-mediated inhibition of osteoclastogenesis, suggesting a key role of STAT5 in IL-3-mediated inhibition of osteoclast differentiation. In addition, IL-3-induced STAT5 activation upregulated the expression of Id1 and Id2, which are negative regulators of osteoclastogenesis. Overexpression of ID1 or ID2 in STAT5-deficient cells reversed osteoclast development recovered from IL-3-mediated inhibition. Importantly, microcomputed tomography and histomorphometric analysis revealed that STAT5 conditional knockout mice showed reduced bone mass, with an increased number of osteoclasts. Furthermore, IL-3 inhibited RANKL-induced osteoclast differentiation less effectively in the STAT5 conditional knockout mice than in the wild-type mice after RANKL injection. Taken together, our findings indicate that STAT5 contributes to the remarkable IL-3-mediated inhibition of RANKL-induced osteoclastogenesis by activating Id genes and their associated pathways.
Dynamic mRNA and miRNA expression analysis in response to intermuscular bone development of blunt snout bream (Megalobrama amblycephala)
Authors: Wan Shi-Ming , Yi Shao-Kui , Zhong Jia , Nie Chun-Hong , Guan Ning-Nan , Zhang Wei-Zhuo , Gao Ze-Xia
Published: August 2016

Intermuscular bone (IB), which occurs only in the myosepta of lower teleosts, is attracting more attention because they are difficult to remove and make the fish unpleasant to eat. By gaining a better understanding of the genetic regulation of IB development, an integrated analysis of miRNAs and mRNAs expression profiling was performed on Megalobrama amblycephala. Four key development stages were selected for transcriptome and small RNA sequencing. A number of significantly differentially expressed miRNAs/genes associated with bone formation and differentiation were identified and the functional characteristics of these miRNAs/genes were revealed by GO function and KEGG pathway analysis. These were involved in TGF-β, ERK and osteoclast differentiation pathways known in the literature to affect bone formation and differentiation. MiRNA-mRNA interaction pairs were detected from comparison of expression between different stages. The function annotation results also showed that many miRNA-mRNA interaction pairs were likely to be involved in regulating bone development and differentiation. A negative regulation effect of two miRNAs was verified through dual luciferase reporter assay. As a unique public resource for gene expression and regulation during the IB development, this study is expected to provide forwards ideas and resources for further biological researches to understand the IBs’ development.
Decompensated liver cirrhosis and neural regulation of mesenteric vascular tone in rats: role of sympathetic, nitrergic and sensory innervations
Authors: Sastre Esther , Caracuel Laura , Prieto Isabel , Llévenes Pablo , Aller M. Ángeles , Arias Jaime , Balfagón Gloria , Blanco-Rivero Javier
Published: August 2016

We evaluated the possible alterations produced by liver cholestasis (LC), a model of decompensated liver cirrhosis in sympathetic, sensory and nitrergic nerve function in rat superior mesenteric arteries (SMA). The vasoconstrictor response to electrical field stimulation (EFS) was greater in LC animals. Alpha-adrenoceptor antagonist phentolamine and P2 purinoceptor antagonist suramin decreased this response in LC animals more than in control animals. Both non-specific nitric oxide synthase (NOS) L-NAME and calcitonin gene related peptide (CGRP) (8-37) increased the vasoconstrictor response to EFS more strongly in LC than in control segments. Vasomotor responses to noradrenaline (NA) or CGRP were greater in LC segments, while NO analogue DEA-NO induced a similar vasodilation in both experimental groups. The release of NA was not modified, while those of ATP, nitrite and CGRP were increased in segments from LC. Alpha 1 adrenoceptor, Rho kinase (ROCK) 1 and 2 and total myosin phosphatase (MYPT) expressions were not modified, while alpha 2B adrenoceptor, nNOS expression and nNOS and MYPT phosphorylation were increased by LC. Together, these alterations might counteract the increased splanchnic vasodilation observed in the last phases of decompensated liver cirrhosis.
p18 inhibits reprogramming through inactivation of Cdk4/6
Authors: Zhu Shaohua , Cao Jiani , Sun Hongyan , Liu Kun , Li Yaqiong , Zhao Tongbiao
Published: August 2016

Pluripotent stem cells (PSCs), including embryonic and induced pluripotent stem cells (iPSCs), show atypical cell cycle regulation characterized by a high proliferation rate and a shorter G1 phase compared with somatic cells. The mechanisms by which somatic cells remodel their cell cycle to achieve the high proliferation rate of PSCs during reprogramming are unclear. Here we identify that the Ink4 protein p18, which is expressed at high levels in somatic cells but at low levels in PSCs, is a roadblock to successful reprogramming. Mild inhibition of p18 expression enhances reprogramming efficiency, while ectopic expression of p18 completely blocks reprogramming. Mechanistic studies show that expression of wild-type p18, but not a p18D68N mutant which cannot inhibit Cdk4/6, down-regulates expression of Cdk4/6 target genes involved in DNA synthesis (TK, TS, DHFR, PCNA) and cell cycle regulation (CDK1 and CCNA2) and thus inhibits reprogramming. These results indicate that p18 blocks reprogramming by targeting Cdk4/6-mediated cell cycle regulation. Taken together, our results define a novel pathway that inhibits somatic cell reprogramming and provide a new target to enhance reprogramming efficiency.
Ultra-sensitive determination of silver nanoparticles by surface-enhanced Raman spectroscopy (SERS) after hydrophobization-mediated extraction
Authors: Guo Huiyuan , Xing Baoshan , White Jason C. , Mukherjee Arnab , He Lili
Published: August 2016

An innovative and ultra-sensitive SERS method that uses a triple-functional surfactant ligand for nanoparticle surface binding, phase transfer and SERS signal reporting was developed for silver nanoparticle (AgNP) detection.
A novel near-infrared colorimetric probe for fluoride anions based on a heptamethine dye
Authors: Jin Di , Zhao Xu , Li Yang , Yan Xilong , Chen Ligong
Published: August 2016

A new colorimetric probe for rapid, selective and sensitive detection of fluoride anions was reported.
Investigation of the co-identification of hexogen and pentrite as particles and co-adsorbed on copper oxide nanoparticles by using nanocalorimetry
Authors: Bonnot K. , Schlur L. , Spitzer D.
Published: August 2016

When both RDX and PETN are present in air, their competition for detection can be determined by fast heating nanocalorimetry.
Thermally induced recrystallization of MAPbI3 perovskite under methylamine atmosphere: an approach to fabricating large uniform crystalline grains
Authors: Jacobs Daniel L. , Zang Ling
Published: August 2016

A liquid–solid phase transition of MAPbI3 under methylamine gas was used to fabricate highly crystalline grains tens of microns large.
Hexanuclear tin(ii) and mixed valence tin(ii,iv) oxide clusters within polyoxometalates
Authors: Suzuki Kosuke , Hanaya Takumi , Sato Rinta , Minato Takuo , Yamaguchi Kazuya , Mizuno Noritaka
Published: August 2016

A hexanuclear mixed valence tin oxide cluster [Sn32+Sn34+O15]12− was synthesized by selective oxidation of a tin oxide cluster within polyoxometalates.
Probing protein adsorption on a nanoparticle surface using second harmonic light scattering
Authors: Das A. , Chakrabarti A. , Das P. K.
Published: August 2016

A new application of second harmonic light scattering to probe protein adsorption on gold nanoparticle is reported.
True ferroelectric switching in thin films of trialkylbenzene-1,3,5-tricarboxamide (BTA)
Authors: Gorbunov A. V. , Putzeys T. , Urbanavičiūtė I. , Janssen R. A. J. , Wübbenhorst M. , Sijbesma R. P. , Kemerink M.
Published: August 2016

The true ferroelectric nature of the dipolar switching in trialkylbenzene-1,3,5-tricarboxamide (BTA) is demonstrated.
Kinetics of self-assembled monolayer formation on individual nanoparticles
Authors: Smith Jeremy G. , Jain Prashant K.
Published: August 2016

New insights into the complex dynamics of self-assembled monolayer formation are obtained by monitoring the process on individual nanoparticles.
First-principles prediction of a new planar hydrocarbon material: half-hydrogenated 14,14,14-graphyne
Authors: Zhang Hongyu , Pan Hongzhe , Zhang Meng , Luo Youhua
Published: August 2016

A new strictly planar semiconducting hydrocarbon, formed by hydrogenating half of the sp-hybridized carbon atoms in 14,14,14-graphyne, is predicted.
Performance enhancement of organic photovoltaic devices enabled by Au nanoarrows inducing surface plasmonic resonance effect
Authors: Li Shujun , Li Zhiqi , Zhang Xinyuan , Zhang Zhihui , Liu Chunyu , Shen Liang , Guo Wenbin , Ruan Shengping
Published: August 2016

The significant performance enhancement of organic photovoltaic devices was achieved upon incorporating Au nanoarrows in a ZnO buffer layer.
Infrared spectroscopy of the ν2 band of the water monomer and small water clusters (H2O)n=2,3,4 in helium droplets
Authors: Schwan Raffael , Kaufmann Matin , Leicht Daniel , Schwaab Gerhard , Havenith Martina
Published: August 2016

Ro-vibrational transitions of water and water clusters (H2O)n=1,2,3,4 for the ν2 bending vibration were observed and assigned to distinct structures.
Tribotronic control of friction in oil-based lubricants with ionic liquid additives
Authors: Cooper P. K. , Li H. , Rutland M. W. , Webber G. B. , Atkin R.
Published: August 2016

Atomic force microscopy (AFM) reveals that tribotronic control of friction using an external potential applied to a gold surface is possible for ionic liquid (IL) concentrations as low as 5 mol% in hexadecane.
From bulk to plasmonic nanoparticle surfaces: the behavior of two potent therapeutic peptides, octreotide and pasireotide
Authors: Hernández Belén , López-Tobar Eduardo , Sanchez-Cortes Santiago , Coïc Yves-Marie , Baron Bruno , Chenal Alexandre , Kruglik Sergei G. , Pflüger Fernando , Cohen Régis , Ghomi Mahmoud
Published: August 2016

Structural dynamics of two potent somatostatin analogues in an aqueous environment and their binding sites on plasmonic nanoparticles were described.
Single oxygen vacancies of (TiO2)35as a prototype reduced nanoparticle: implication for photocatalytic activity
Authors: Kim Sunkyung , Ko Kyoung Chul , Lee Jin Yong , Illas Francesc
Published: August 2016

The properties of single oxygen vacancies of (TiO2)35, a prototype of an anatase nanoparticle, were investigated by DFT calculations.
Quantum phase transitions in Sn bilayer based interfacial systems by an external strain
Authors: Chen Li , Zhuang Qiandong , Chen Yeqing , Shi Changmin , Wang Dongchao
Published: August 2016

Using first-principle calculations, we report for the first time, the changes in electronic structures of a single bilayer Sn stacked on a single bilayer Sb(Bi) and on a single quintuple layer Sb2Te3 induced by both interface polarization and strain.
Why are sec-alkylperoxyl bimolecular self-reactions orders of magnitude faster than the analogous reactions of tert-alkylperoxyls? The unanticipated role of CH hydrogen bond donation
Authors: Lee Richmond , Gryn'ova Ganna , Ingold K. U. , Coote Michelle L.
Published: August 2016

Theory reveals that pri- and sec-alkylperoxyl bimolecular self-reactions are orders of magnitude faster than the analogous tert-alkylperoxyl reactions, because of the formation of 5-center cyclic CH⋯O hydrogen bonding.
Micro-heterogeneity versus clustering in binary mixtures of ethanol with water or alkanes
Authors: Požar Martina , Lovrinčević Bernarda , Zoranić Larisa , Primorać Tomislav , Sokolić Franjo , Perera Aurélien
Published: August 2016

Snapshots of the difference in complex disorder, with analogy with direct (ethanol–water) and inverse (ethanol–alkanes) emulsions.
Defect energetics of concentrated solid-solution alloys from ab initio calculations: Ni0.5Co0.5, Ni0.5Fe0.5, Ni0.8Fe0.2and Ni0.8Cr0.2
Authors: Zhao Shijun , Stocks G. Malcolm , Zhang Yanwen
Published: August 2016

The distribution of migration energies of vacancies and interstitials in Ni0.5Fe0.5has a region of overlap, an indication of their comparable mobility compared to pure Ni (indicated by dotted line), which will greatly facilitate the recombination of Frenkel pairs.
Synergistic photomagnetic effects in coordination polymer heterostructure particles of Hofmann-like Fe(4-phenylpyridine)2[Ni(CN)4]·0.5H2O and K0.4Ni[Cr(CN)6]0.8·nH2O
Authors: Gros Corey R. , Peprah Marcus K. , Felts Ashley C. , Brinzari Tatiana V. , Risset Olivia N. , Cain John M. , Ferreira Cauê F. , Meisel Mark W. , Talham Daniel R.
Published: August 2016

A coordination polymer heterostructure exhibits light-switchable magnetism with the photoevent in one component influencing the magnetization of the other.
Aluminum alkoxide, amide and halide complexes supported by a bulky dipyrromethene ligand: synthesis, characterization, and preliminary ε-caprolactone polymerization activity
Authors: Gianopoulos Christopher G. , Kumar Nishant , Zhao Yihong , Jia Li , Kirschbaum Kristin , Mason Mark R.
Published: August 2016

The synthesis, characterization, and ε-caprolactone polymerization activity of aluminum complexes supported by the bulky dipyrromethene (1) ligand are reported.
Titanium-based zeolitic imidazolate framework for chemical fixation of carbon dioxide
Authors: Verma Sanny , Baig R. B. Nasir , Nadagouda Mallikarjuna N. , Varma Rajender S.
Published: August 2016

A titanium-based zeolitic imidazolate framework (Ti-ZIF) with a high surface area and porosity has been synthesized and its application has been demonstrated in the synthesis of cyclic carbonates from carbon dioxide.
One-pot conversion of furfural to alkyl levulinate over bifunctional Au-H4SiW12O40/ZrO2 without external H2
Authors: Zhu Shanhui , Cen Youliang , Guo Jing , Chai Jiachun , Wang Jianguo , Fan Weibin
Published: August 2016

An unprecedented 80.2% yield of alkyl levulinate was obtained via one-pot conversion of furfural with 2-propanol over Au-H4SiW12O40/ZrO2.
Continuous flow biocatalysis: production and in-line purification of amines by immobilised transaminase from Halomonas elongata
Authors: Planchestainer Matteo , Contente Martina Letizia , Cassidy Jennifer , Molinari Francesco , Tamborini Lucia , Paradisi Francesca
Published: August 2016

The continuous flow synthesis of a series of amines was successfully achieved by exploiting the enhanced stability and broad substrate scope of an immobilised transaminase from Halomonas elongata (HEWT).
A comparative analysis reveals the dosage sensitivity and regulatory patterns of lncRNA in prostate cancer
Authors: Liu Yongjing , Zhang Rui , Zhao Ning , Zhang Qiang , Yan Zichuang , Chang Zhiqiang , Wei Yunzhen , Wu Cheng , Xu Jin , Xu Yan
Published: August 2016

Although the key roles of long non-coding RNAs (lncRNAs) in multiple diseases are well documented, the relationship between the lncRNA copy number and expression is unknown.
Various structures of complexes fabricated using transition metals and triazole ligands and their inhibition effects on xanthine luminescence
Authors: Shang Di , Ni Juechen , Gao Xinyu , Li Chengren , Lin Xiaomeng , Wang Zhinan , Du Ning , Li Shuang , Xing Yongheng
Published: August 2016

The interaction between novel transition metal complexes and xanthine luminescence was studied for the first time.
Mesoporous titanosilicate nanoparticles: facile preparation and application in heterogeneous epoxidation of cyclohexene
Authors: Jiang Yanqiu , Zhao Yong , Xu Xianzhu , Lin Kaifeng , Wang Dan
Published: August 2016

Mesoporous titanosilicate nanoparticles were hydrothermally synthesized from a titanosilicate solution with cetyltrimethylammonium bromide as the template and with a cationic polymer as the size-controlling agent.
Probing high temperature ferromagnetism and its paramagnetic phase change due to Eu3+ incorporation in ZnO nanophosphors
Authors: Rajan K. Jayanthi , Ganesan Kausalya , Lanka Satyanaryana , Bishnoi Swati , Sunkara Manorama V.
Published: August 2016

Ferromagnetic oxide semiconductors exhibiting efficient luminescent properties together with robust ferromagnetism above room temperature form an exclusive class of spintronic materials endowed with both charge and spin degrees of freedom.
One-step in situ synthesis of a novel α-zirconium phosphate/graphene oxide hybrid and its application in phenolic foam with enhanced mechanical strength, flame retardancy and thermal stability
Authors: Li Xiaoyan , Wang Zhengzhou , Wu Lixin , Tsai Tsungyen
Published: August 2016

A novel α-zirconium phosphate/graphene oxide hybrid was synthesized, and its incorporation into phenolic foam can greatly improve mechanical strengths, thermal stability and flame retardancy of the foam.
New chloramphenicol Schiff base ligands for the titanium-mediated asymmetric aldol reaction of α,β-unsaturated aldehydes with diketene: a short synthesis of atorvastatin calcium
Authors: Wang Haifeng , Yan Linjie , Xiong Fangjun , Wu Yan , Chen Fener
Published: August 2016

Several novel chiral Schiff base ligands were prepared from a commercially available chloramphenicol base and applied to the titanium-mediated asymmetric aldol reaction of diketene with various α,β-unsaturated aldehydes.
Polyvinylidene fluoride hollow fiber mixed matrix membrane contactor incorporating modified ZSM-5 zeolite for carbon dioxide absorption
Authors: Shirzadeh-Gharacheh Afsaneh , Rahbari-Sisakht Masoud
Published: August 2016

PVDF/ ZSM-5 hollow fiber mixed matrix membrane.
Multicomponent synthesis of dithiocarbamates starting from vinyl sulfones/sulfoxides and their use in polymerization reactions
Authors: Halimehjani Azim Ziyaei , Mohtasham Reza , Shockravi Abbas , Martens Jürgen
Published: August 2016

Synthesis of dithiocarbamates from vinyl sulfones/sulfoxides and the corresponding polymers with a dithiocarbamate backbone using divinyl sulfone and diamines is reported.
Spatially-controlled laser-induced decoration of 2D and 3D substrates with plasmonic nanoparticles
Authors: Bashouti M. Y. , Povolotckaia A. V. , Povolotskiy A. V. , Tunik S. P. , Christiansen S. H. , Leuchs G. , Manshina A. A.
Published: August 2016

We demonstrate a new approach which can be used for targeted imparting of plasmonic properties for wide range of different substrates which may have any 2D or 3D topological structure created independently in a prior step with some other technology.
The role of caffeine as an inhibitor in the aggregation of amyloid forming peptides: a unified molecular dynamics simulation and experimental study
Authors: Sharma Bhanita , Kalita Sourav , Paul Ashim , Mandal Bhubaneswar , Paul Sandip
Published: August 2016

10 : 1 or more caffeine to SwP ratio can prevent the formation of β-sheet conformation.
Nitroxide-mediated polymerization of methyl methacrylate by 4,4′-dimethoxydiphenyl-based alkoxyamine
Authors: Zhu Zhecheng , Shan Guorong , Pan Pengju
Published: August 2016

4,4′-Dimethoxydiphenyl nitroxide-based alkoxyamine was prepared and used to control the polymerization of methyl methacrylate. Linear increase in molecular weight with conversion and narrow molecular weight distribution was up to 65% conversion.
Keto-polymethines: a versatile class of dyes with outstanding spectroscopic properties for in cellulo and in vivo two-photon microscopy imaging
Authors: Pascal Simon , Denis-Quanquin Sandrine , Appaix Florence , Duperray Alain , Grichine Alexei , Le Guennic Boris , Jacquemin Denis , Cuny Jérôme , Chi San-Hui , Perry Joseph W. , van der Sanden Boudewijn , Monnereau Cyrille , Andraud Chantal , Maury Olivier
Published: August 2016

The keto-heptamethine family has been expanded to various symmetrical and asymmetrical structures.
Hierarchical multi-component nanofiber separators for lithium polysulfide capture in lithium–sulfur batteries: an experimental and molecular modeling study
Authors: Zhu Jiadeng , Yildirim Erol , Aly Karim , Shen Jialong , Chen Chen , Lu Yao , Jiang Mengjin , Kim David , Tonelli Alan E. , Pasquinelli Melissa A. , Bradford Philip D. , Zhang Xiangwu
Published: August 2016

A multi-functional nanofiber membrane significantly improves the overall performance of Li–S batteries.
Recent progress in Pd-based composite membranes
Authors: Li H. , Caravella A. , Xu H. Y.
Published: August 2016

This review covers both experimental and modeling progress of Pd-based composite membranes, focusing on thermal and chemical stability issues.
Intermolecular disulfide bond influences unphosphorylated STAT3 dimerization and function
Authors: Butturini Elena , Gotte Giovanni , Dell'Orco Daniele , Chiavegato Giulia , Marino Valerio , Canetti Diana , Cozzolino Flora , Monti Maria , Pucci Piero , Mariotto Sofia
Published: August 2016

Signal transducer and activator of transcription 3 (STAT3) is a transcription factor activated by the phosphorylation of tyrosine 705 in response to many cytokines and growth factors. Recently, the roles for unphosphorylated STAT3 (U-STAT3) have been described in response to cytokine stimulation, in cancers, and in the maintenance of heterochromatin stability. It has been reported that U-STAT3 dimerizes, shuttles between the cytoplasm and nucleus, and binds to DNA, thereby driving genes transcription. Although many reports describe the active role of U-STAT3 in oncogenesis in addition to phosphorylated STAT3, the U-STAT3 functional pathway remains elusive.

In this report, we describe the molecular mechanism of U-STAT3 dimerization, and we identify the presence of two intermolecular disulfide bridges between Cys367 and Cys542 and Cys418 and Cys426, respectively. Recently, we reported that the same cysteines contribute to the redox regulation of STAT3 signaling pathway both in vitro and in vivo. The presence of these disulfides is here demonstrated to largely contribute to the structure and the stability of U-STAT3 dimer as the dimeric form rapidly dissociates upon reduction in the S–S bonds. In particular, the Cys367–Cys542 disulfide bridge is shown to be critical for U-STAT3 DNA-binding activity. Mutation of the two Cys residues completely abolishes the DNA-binding capability of U-STAT3. Spectroscopic investigations confirm that the noncovalent interactions are sufficient for proper folding and dimer formation, but that the interchain disulfide bonds are crucial to preserve the functional dimer. Finally, we propose a reaction scheme of U-STAT3 dimerization with a first common step followed by stabilization through the formation of interchain disulfide bonds.
Mushroom meta‐material based substrate integrated waveguide cavity backed slot antenna with broadband and reduced back radiation
Authors: Kang Hyunseong , Park Seong‐Ook
Published: August 2016

A novel substrate integrated waveguide (SIW) cavity backed slot antenna with low back radiation is proposed in this study. This newly proposed meta‐mushroom antenna uses a SIW cavity to decrease the back radiation. It is fed by the SIW cavity backed slot and radiates by meta‐mushroom structure. This antenna exhibits broadband characteristics due to the meta‐mushroom structure and a bow‐tie slot on the SIW. The back radiation of the proposed antenna is considerably diminished by the SIW cavity located at the back side maintaining high gain performance. After all, its front‐to‐back ratio is increased and maintained over 19.2 dB in the operating frequency band, 4.5–5.6 GHz. Full‐wave simulation and experiments results of the proposed antenna are demonstrated.
Calibrating for the satellite attitude jitter in multistatic SAR using a subspace method
Authors: Li Chenlei , Liu Mei , Wang Pengfei , Wang Zhigui
Published: August 2016

With respect to a spaceborne multistatic synthetic aperture radar (SAR) system, satellite attitude jitter, consisting of yaw‐, pitch‐, and roll‐angle components, undermines the coherent cooperation among the satellites and results in degraded imaging performance. In order to calibrate the system to compensate for the jitter, a parametric method is proposed in this study. The approach starts by deriving the echo signal with unknown jitter received by each satellite as a bistatic extended space–time model. Then, the high‐order instantaneous moment of the model is obtained, which is in the form of a high‐order polynomial phase array signal. Finally, the unknown jitter is estimated using the multiple signal classification method, which is a subspace method. The proposed method can improve the imaging performance by correctly calibrating the system to compensate for the jitter. Furthermore, the authors demonstrate that the proposed method outperforms conventional autofocus algorithms using the simulated raw data of a Cartwheel constellation, which is a typical flying formation of a multistatic SAR system.
Radiologie Trendreport: Spracherkennung steht oben auf der Wunschliste
Authors: Mau Jens
Published: August 2016

Ob E-Arztbrief, Spracherkennung oder Telemedizin – Radiologen sind die Vorreiter unter den Fachärzten. Was bei den IT-Trendsettern im Krankenhaus oben auf ihrer Agenda steht, zeigt der Trendreport Radiologie.
High Spatial Inhomogeneity in the Intima-Media Thickness of the Common Carotid Artery is Associated with a Larger Degree of Stenosis in the Internal Carotid Artery: The PARISK Study
Authors: Steinbuch Jeire , van Dijk Anouk , Schreuder Floris , Truijman Martine , de Rotte Alexandra , Nederkoorn Paul , van der Lugt Aad , Hermeling Evelien , Hoeks Arnold , Mess Werner
Published: August 2016

Purpose Inhomogeneity of arterial wall thickness may be indicative of distal plaques. This study investigates the intra-subject association between relative spatial intima-media thickness (IMT) inhomogeneity of the common carotid artery (CCA) and the degree of stenosis of plaques in the internal carotid artery (ICA).

Materials and Methods We included 240 patients with a recent ischemic stroke or transient ischemic attack and mild-to-moderate stenosis in the ipsilateral ICA. IMT inhomogeneity was extracted from B-mode ultrasound recordings. The degree of ICA stenosis was assessed on CT angiography according to the European Carotid Surgery Trial method. Patients were divided into groups with a low (≤ 2 %) and a high (> 2 %) IMT inhomogeneity scaled with respect to the local end-diastolic diameter.

Results 182 patients had suitable CT and ultrasound measurements. Relative CCA-IMT inhomogeneity was similar for the symptomatic and asymptomatic side (difference: 0.02 %, p = 0.85). High relative IMT inhomogeneity was associated with a larger IMT (difference: 235 µm, p < 0.001) and larger degree of ICA stenosis (difference: 5 %, p = 0.023) which remained significant (p = 0.016) after adjustment for common risk factors.

Conclusion Regardless of common risk factors, high relative CCA-IMT inhomogeneity is associated with a greater degree of ICA stenosis and is therefore indicative of atherosclerotic disease. The predictive value of CCA-IMT inhomogeneity for plaque progression and recurrence of cerebrovascular symptoms will be determined in the follow-up phase of PARISK.
Signal and background considerations for the MRSt on the National Ignition Facility (NIF)
Authors: Wink C. W. , Frenje J. A. , Hilsabeck T. J. , Bionta R. , Khater H. Y. , Gatu Johnson M. , Kilkenny J. D. , Li C. K. , Séguin F. H. , Petrasso R. D.
Published: August 2016

A Magnetic Recoil Spectrometer (MRSt) has been conceptually designed for time-resolved measurements of the neutron spectrum at the National Ignition Facility. Using the MRSt, the goals are to measure the time-evolution of the spectrum with a time resolution of ∼20-ps and absolute accuracy better than 5%. To meet these goals, a detailed understanding and optimization of the signal and background characteristics are required. Through ion-optics, MCNP simulations, and detector-response calculations, it is demonstrated that the goals and a signal-to background >5–10 for the down-scattered neutron measurement are met if the background, consisting of ambient neutrons and gammas, at the MRSt is reduced 50–100 times.
Dynamical analysis of strongly nonlinear fractional-order Mathieu-Duffing equation
Authors: Wen Shao-Fang , Shen Yong-Jun , Wang Xiao-Na , Yang Shao-Pu , Xing Hai-Jun
Published: August 2016

In this paper, the computation schemes for periodic solutions of the forced fractional-order Mathieu-Duffing equation are derived based on incremental harmonic balance (IHB) method. The general forms of periodic solutions are founded by the IHB method, which could be useful to obtain the periodic solutions with higher precision. The comparisons of the approximate analytical solutions by the IHB method and numerical integration are fulfilled, and the results certify the correctness and higher precision of the solutions by the IHB method. The dynamical analysis of strongly nonlinear fractional-order Mathieu-Duffing equation is investigated by the IHB method. Then, the effects of the excitation frequency, fractional order, fractional coefficient, and nonlinear stiffness coefficient on the complex dynamical behaviors are analyzed. At last, the detailed results are summarized and the conclusions are made, which present some useful information to analyze and/or control the dynamical response of this kind of system.
A fast feedback controlled magnetic drive for the ASDEX Upgrade fast-ion loss detectors
Authors: Ayllon-Guerola J. , Gonzalez-Martin J. , Garcia-Munoz M. , Rivero-Rodriguez J. , Herrmann A. , Vorbrugg S. , Leitenstern P. , Zoletnik S. , Galdon J. , Garcia Lopez J. , Rodriguez-Ramos M. , Sanchis-Sanchez L. , Dominguez A. D. , Kocan M. , Gunn J. P. , Garcia-Vallejo D. , Dominguez J.
Published: August 2016

A magnetically driven fast-ion loss detector system for the ASDEX Upgrade tokamak has been designed and will be presented here. The device is feedback controlled to adapt the detector head position to the heat load and physics requirements. Dynamic simulations have been performed taking into account effects such as friction, coil self-induction, and eddy currents. A real time positioning control algorithm to maximize the detector operational window has been developed. This algorithm considers dynamical behavior and mechanical resistance as well as measured and predicted thermal loads. The mechanical design and real time predictive algorithm presented here may be used for other reciprocating systems.
How wet should be the reaction coordinate for ligand unbinding?
Authors: Tiwary Pratyush , Berne B. J.
Published: August 2016

We use a recently proposed method called Spectral Gap Optimization of Order Parameters (SGOOP) [P. Tiwary and B. J. Berne, Proc. Natl. Acad. Sci. U. S. A. 113, 2839 (2016)], to determine an optimal 1-dimensional reaction coordinate (RC) for the unbinding of a bucky-ball from a pocket in explicit water. This RC is estimated as a linear combination of the multiple available order parameters that collectively can be used to distinguish the various stable states relevant for unbinding. We pay special attention to determining and quantifying the degree to which water molecules should be included in the RC. Using SGOOP with under-sampled biased simulations, we predict that water plays a distinct role in the reaction coordinate for unbinding in the case when the ligand is sterically constrained to move along an axis of symmetry. This prediction is validated through extensive calculations of the unbinding times through metadynamics and by comparison through detailed balance with unbiased molecular dynamics estimate of the binding time. However when the steric constraint is removed, we find that the role of water in the reaction coordinate diminishes. Here instead SGOOP identifies a good one-dimensional RC involving various motional degrees of freedom.
Stochastic level-set variational implicit-solvent approach to solute-solvent interfacial fluctuations
Authors: Zhou Shenggao , Sun Hui , Cheng Li-Tien , Dzubiella Joachim , Li Bo , McCammon J. Andrew
Published: August 2016

Recent years have seen the initial success of a variational implicit-solvent model (VISM), implemented with a robust level-set method, in capturing efficiently different hydration states and providing quantitatively good estimation of solvation free energies of biomolecules. The level-set minimization of the VISM solvation free-energy functional of all possible solute-solvent interfaces or dielectric boundaries predicts an equilibrium biomolecular conformation that is often close to an initial guess. In this work, we develop a theory in the form of Langevin geometrical flow to incorporate solute-solvent interfacial fluctuations into the VISM. Such fluctuations are crucial to biomolecular conformational changes and binding process. We also develop a stochastic level-set method to numerically implement such a theory. We describe the interfacial fluctuation through the “normal velocity” that is the solute-solvent interfacial force, derive the corresponding stochastic level-set equation in the sense of Stratonovich so that the surface representation is independent of the choice of implicit function, and develop numerical techniques for solving such an equation and processing the numerical data. We apply our computational method to study the dewetting transition in the system of two hydrophobic plates and a hydrophobic cavity of a synthetic host molecule cucurbit[7]uril. Numerical simulations demonstrate that our approach can describe an underlying system jumping out of a local minimum of the free-energy functional and can capture dewetting transitions of hydrophobic systems. In the case of two hydrophobic plates, we find that the wavelength of interfacial fluctuations has a strong influence to the dewetting transition. In addition, we find that the estimated energy barrier of the dewetting transition scales quadratically with the inter-plate distance, agreeing well with existing studies of molecular dynamics simulations. Our work is a first step toward the inclusion of fluctuations into the VISM and understanding the impact of interfacial fluctuations on biomolecular solvation with an implicit-solvent approach.
Dynamical transition between weak and strong coupling in Brillouin laser pulse amplification
Authors: Schluck F. , Lehmann G. , Müller C. , Spatschek K. H.
Published: August 2016

Short laser pulse amplification via stimulated Brillouin backscattering in plasma is considered. Previous work distinguishes between the weakly and strongly coupled regime and treats them separately. It is shown here that such a separation is not generally applicable because strong and weak coupling interaction regimes are entwined with each other. An initially weakly coupled amplification scenario may dynamically transform into strong coupling. This happens when the local seed amplitude grows and thus triggers the strongly driven plasma response. On the other hand, when in a strong coupling scenario, the pump pulse gets depleted, and its amplitude might drop below the strong coupling threshold. This may cause significant changes in the final seed pulse shape. Furthermore, experimentally used pump pulses are typically Gaussian-shaped. The intensity threshold for strong coupling may only be exceeded around the maximum and not in the wings of the pulse. Also here, a description valid in both strong and weak coupling regimes is required. We propose such a unified treatment which allows us, in particular, to study the dynamic transition between weak and strong coupling. Consequences for the pulse forms of the amplified seed are discussed.
Second order gyrokinetic theory for particle-in-cell codes
Authors: Tronko Natalia , Bottino Alberto , Sonnendrücker Eric
Published: August 2016

The main idea of the gyrokinetic dynamical reduction consists in a systematical removal of the fast scale motion (the gyromotion) from the dynamics of the plasma, resulting in a considerable simplification and a significant gain of computational time. The gyrokinetic Maxwell–Vlasov equations are nowadays implemented in for modeling (both laboratory and astrophysical) strongly magnetized plasmas. Different versions of the reduced set of equations exist, depending on the construction of the gyrokinetic reduction procedure and the approximations performed in the derivation. The purpose of this article is to explicitly show the connection between the general second order gyrokinetic Maxwell–Vlasov system issued from the modern gyrokinetic theory and the model currently implemented in the global electromagnetic Particle-in-Cell code ORB5. Necessary information about the modern gyrokinetic formalism is given together with the consistent derivation of the gyrokinetic Maxwell–Vlasov equations from first principles. The variational formulation of the dynamics is used to obtain the corresponding energy conservation law, which in turn is used for the verification of energy conservation diagnostics currently implemented in ORB5. This work fits within the context of the code verification project VeriGyro currently run at IPP Max-Planck Institut in collaboration with others European institutions.
Dependence of SERS enhancement on the chemical composition and structure of Ag/Au hybrid nanoparticles
Authors: Chaffin Elise , O’Connor Ryan T. , Barr James , Huang Xiaohua , Wang Yongmei
Published: August 2016

Noble metal nanoparticles (NPs) such as silver (Ag) and gold (Au) have unique plasmonic properties that give rise to surface enhanced Raman scattering (SERS). Generally, Ag NPs have much stronger plasmonic properties and, hence, provide stronger SERS signals than Au NPs. However, Ag NPs lack the chemical stability and biocompatibility of comparable Au NPs and typically exhibit the most intense plasmonic resonance at wavelengths much shorter than the optimal spectral region for many biomedical applications. To overcome these issues, various experimental efforts have been devoted to the synthesis of Ag/Au hybrid NPs for the purpose of SERS detections. However, a complete understanding on how the SERS enhancement depends on the chemical composition and structure of these nanoparticles has not been achieved. In this study, Mie theory and the discrete dipole approximation have been used to calculate the plasmonic spectra and near-field electromagnetic enhancements of Ag/Au hybrid NPs. In particular, we discuss how the electromagnetic enhancement depends on the mole fraction of Au in Ag/Au alloy NPs and how one may use extinction spectra to distinguish between Ag/Au alloyed NPs and Ag-Au core-shell NPs. We also show that for incident laser wavelengths between ∼410 nm and 520 nm, Ag/Au alloyed NPs provide better electromagnetic enhancement than pure Ag, pure Au, or Ag-Au core-shell structured NPs. Finally, we show that silica-core Ag/Au alloy shelled NPs provide even better performance than pure Ag/Au alloy or pure solid Ag and pure solid Au NPs. The theoretical results presented will be beneficial to the experimental efforts in optimizing the design of Ag/Au hybrid NPs for SERS-based detection methods.
Far-forward collective scattering measurements by FIR polarimeter-interferometer on J-TEXT tokamak
Authors: Shi P. , Chen J. , Gao L. , Liu Y. , Liu H. , Zhou Y. N. , Zhuang G.
Published: August 2016

The multi-channel three-wave polarimeter-interferometer system on J-TEXT tokamak has been exploited to measure far-forward collective scattering from electron density fluctuations. The diagnostic utilizes far infrared lasers operated at 432 μm with 17-channel vertical chords (3 cm chord spacing), covering the entire cross section of plasma. Scattering laser power is measured using a high-sensitivity Schottky planar diode mixer which can also detect polarimetric and interferometric phase simultaneously. The system provides a line-integrated measurement of density fluctuations with maximum measurable wave number: k⊥max ≤ 2 cm−1 and time response up to 350 kHz. Feasibility of the diagnostic has been tested, showing higher sensitivity to detect fluctuation than interferometric measurement. Capability of providing spatial-resolved information of fluctuation has also been demonstrated in preliminary experimental applications.
A synthetic diagnostic for beam emission spectroscopy in the helically symmetric experiment stellarator
Authors: Dobbins T. J. , Kumar S. T. A. , Anderson D. T.
Published: August 2016

The Helically Symmetric Experiment (HSX) has a number of active spectroscopy diagnostics. Due to the relatively large beam width compared to the plasma minor radius, it is difficult to achieve good spatial resolution at the core of the HSX plasma. This is due to the fact that the optical sightline cuts through many flux surfaces with varying field vectors within the beam. In order to compare the experimental results with theoretical models it is important to accurately model the beam width effects. A synthetic diagnostic has been developed for this purpose. This synthetic diagnostic calculates the effect of spot size and beam width on the measurements of quantities of interest, including radial electric field, flow velocity, and Stark polarization.