bluuebunny/crossref_metadata_2025 huggingface dataset:
Long-range coupling between ATP-binding and lever-arm regions in myosin via dielectric allostery
Authors: Sato Takato , Ohnuki Jun , Takano Mitsunori
Published: December 2017

A protein molecule is a dielectric substance, so the binding of a ligand is expected to induce dielectric response in the protein molecule, considering that ligands are charged or polar in general. We previously reported that binding of adenosine triphosphate (ATP) to molecular motor myosin actually induces such a dielectric response in myosin due to the net negative charge of ATP. By this dielectric response, referred to as “dielectric allostery,” spatially separated two regions in myosin, the ATP-binding region and the actin-binding region, are allosterically coupled. In this study, from the statistically stringent analyses of the extensive molecular dynamics simulation data obtained in the ATP-free and the ATP-bound states, we show that there exists the dielectric allostery that transmits the signal of ATP binding toward the distant lever-arm region. The ATP-binding-induced electrostatic potential change observed on the surface of the main domain induced a movement of the converter subdomain from which the lever arm extends. The dielectric response was found to be caused by an underlying large-scale concerted rearrangement of the electrostatic bond network, in which highly conserved charged/polar residues are involved. Our study suggests the importance of the dielectric property for molecular machines in exerting their function.
Monte Carlo analysis of field-dependent electron avalanche coefficients in nitrogen at atmospheric pressure
Authors: Nguyen H. K. , Mankowski J. , Dickens J. C. , Neuber A. A. , Joshi R. P.
Published: December 2017

Calculations of electron impact ionization of nitrogen gas at atmospheric pressure are presented based on the kinetic Monte Carlo technique. The emphasis is on energy partitioning between primary and secondary electrons, and three different energy sharing schemes have been evaluated. The ionization behavior is based on Wannier's classical treatment. Our Monte Carlo results for the field-dependent drift velocities match the available experimental data. More interestingly, the field-dependent first Townsend coefficient predicted by the Monte Carlo calculations is shown to be in close agreement with reported data for E/N values ranging as high as 4000 Td, only when a random assignment of excess energies between the primary and secondary particles is used.
Magnetization reversal mechanism for Co nanoparticles revealed by a magnetic hysteresis scaling technique
Authors: Kobayashi Satoru , Sato Takuma , Li Zhang , Dong Xing-Long , Murakami Takeshi
Published: December 2017

We report results of magnetic hysteresis scaling of minor loops for cobalt nanoparticles with variable mean particle size of 53 and 95 nm. A power-law scaling with an exponent of 1.40±0.05 was found to hold true between minor-loop remanence and hysteresis loss in the wide temperature range of 10 − 300 K, irrespective of particle size and cooling field. A coefficient deduced from the scaling law steeply increases with decreasing temperature and exhibits a cooling field dependence below T ∼ 150 K. The value obtained after field cooling at 5 T was lower than that after zero-field cooling, being opposite to a behavior of major-loop coercivity. These observations were explained from the viewpoint of the exchange coupling between ferromagnetic Co core and antiferromagnetic CoO shell, which becomes effective below T ∼ 150 K.
Communication: Self-assembly of a model supramolecular polymer studied by replica exchange with solute tempering
Authors: Arefi Hadi H. , Yamamoto Takeshi
Published: December 2017

Conventional molecular-dynamics (cMD) simulation has a well-known limitation in accessible time and length scales, and thus various enhanced sampling techniques have been proposed to alleviate the problem. In this paper, we explore the utility of replica exchange with solute tempering (REST) (i.e., a variant of Hamiltonian replica exchange methods) to simulate the self-assembly of a supramolecular polymer in explicit solvent and compare the performance with temperature-based replica exchange MD (T-REMD) as well as cMD. As a test system, we consider a relatively simple all-atom model of supramolecular polymerization (namely, benzene-1,3,5-tricarboxamides in methylcyclohexane solvent). Our results show that both REST and T-REMD are able to predict highly ordered polymer structures with helical H-bonding patterns, in contrast to cMD which completely fails to obtain such a structure for the present model. At the same time, we have also experienced some technical challenge (i.e., aggregation-dispersion transition and the resulting bottleneck for replica traversal), which is illustrated numerically. Since the computational cost of REST scales more moderately than T-REMD, we expect that REST will be useful for studying the self-assembly of larger systems in solution with enhanced rearrangement of monomers.
Atom manipulation method to substitute individual adsorbate atoms into a Si(111)-(7 × 7) substrate at room temperature
Authors: Yurtsever Ayhan , Abe Masayuki , Morita Seizo , Sugimoto Yoshiaki
Published: December 2017

We demonstrate a method to substitute individual adsorbate atoms into a Si(111)-(7 × 7) substrate using the tip of an atomic force microscope (AFM) at room temperature. We show that single Sn atoms diffusing within the half-unit-cells (HUCs) of the Si(111)-(7 × 7) substrate can be substituted into Si adatom sites via a close approach of the tip, whereby the intrinsic Si adatoms are ejected onto the surface of the adjacent HUCs. The Sn atom substitution sites can be precisely controlled by the approach of the AFM tip toward the surface at certain positions near the boundary of the HUCs but slightly shifted away from the HUC with the diffusing Sn atom. This manipulation method is also demonstrated to replace Si adatoms in the Si(111)-(7 × 7) surface with Pb using scanning tunneling microscopy. This method can provide a way to induce single-atom substitutional doping at certain positions from an adsorbate atom diffusing within a confined space provided by a substrate, which would allow for control of the doping sites in nanostructural materials.
Light-activated resistance switching in SiOx RRAM devices
Authors: Mehonic A. , Gerard T. , Kenyon A. J.
Published: December 2017

We report a study of light-activated resistance switching in silicon oxide (SiOx) resistive random access memory (RRAM) devices. Our devices had an indium tin oxide/SiOx/p-Si Metal/Oxide/Semiconductor structure, with resistance switching taking place in a 35 nm thick SiOx layer. The optical activity of the devices was investigated by characterising them in a range of voltage and light conditions. Devices respond to illumination at wavelengths in the range of 410–650 nm but are unresponsive at 1152 nm, suggesting that photons are absorbed by the bottom p-type silicon electrode and that generation of free carriers underpins optical activity. Applied light causes charging of devices in the high resistance state (HRS), photocurrent in the low resistance state (LRS), and lowering of the set voltage (required to go from the HRS to LRS) and can be used in conjunction with a voltage bias to trigger switching from the HRS to the LRS. We demonstrate negative correlation between set voltage and applied laser power using a 632.8 nm laser source. We propose that, under illumination, increased electron injection and hence a higher rate of creation of Frenkel pairs in the oxide—precursors for the formation of conductive oxygen vacancy filaments—reduce switching voltages. Our results open up the possibility of light-triggered RRAM devices.
Periodic pattern of liquid crystal molecular orientation induced by ultrasound vibrations
Authors: Shimizu Yuki , Koyama Daisuke , Taniguchi Satoki , Emoto Akira , Nakamura Kentaro , Matsukawa Mami
Published: December 2017

Methods for controlling the periodic molecular orientation of liquid crystals using ultrasound vibrations and estimating the orientational direction are proposed. An ultrasonic liquid crystal cell was used, consisting of a liquid crystal layer sandwiched by two glass plates fitted with piezoelectric ultrasound transducers. The transmitted light intensity distribution through the cell was measured by changing the polarization direction to investigate the orientation direction of the liquid crystal molecules. The transmitted light distributions changed periodically owing to the flexural vibration of the cell at resonance frequencies of 43.9 and 70.7 kHz. The orientational direction of the liquid crystal molecules correlated with the vibrational distribution of the glass substrates, and the molecular orientation was changed periodically by the acoustic radiation force. The interval and intensity of the transmitted light could be controlled by the driving frequency and voltage amplitude, respectively.
Percolative core formation in planetesimals enabled by hysteresis in metal connectivity
Authors: Ghanbarzadeh Soheil , Hesse Marc A. , Prodanović Maša
Published: December 2017

Significance

It has long been thought that percolative core formation is prevented by high dihedral angles that trap the majority of the metallic phases in the mantle, even if the percolation threshold is overcome. Here we use pore-scale simulations to show that hysteresis in melt network topology allows the melt to remain connected during drainage, suggesting that percolative core formation is possible on bodies that contain enough metallic phases to overcome the percolation threshold.
Kras
mutant genetically engineered mouse models of human cancers are genomically heterogeneous
Authors: Chung Wei-Jen , Daemen Anneleen , Cheng Jason H. , Long Jason E. , Cooper Jonathan E. , Wang Bu-er , Tran Christopher , Singh Mallika , Gnad Florian , Modrusan Zora , Foreman Oded , Junttila Melissa R.
Published: December 2017

Significance

RAS
mutant cancers represent a large unmet clinical need.
Kras
mutant genetically engineered mouse models (GEMMs) of cancer recapitulate disease characteristics and are relied upon preclinically to validate targets and test therapies. Our integrative analysis of GEMM tumors revealed significantly evolved genetic heterogeneity, a common feature of human tumors that undermines therapeutic responses. Moreover, interspecies comparative analyses showed the extent of gene-level fidelity between altered oncogenes and tumor suppressors. The genomic diversity represents an unrecognized opportunity to identify therapeutically susceptible genomic subsets preclinically. Moreover, this more-thorough understanding of the unappreciated complexity in these model systems ultimately allows for better interpretation and translatability of preclinical GEMM data for the benefit of cancer patients.
Early childhood stress exposure, reward pathways, and adult decision making
Authors: Birn Rasmus M. , Roeber Barbara J. , Pollak Seth D.
Published: December 2017

Significance

Individuals who have experienced high levels of stress in early childhood are at risk for a wide range of behavioral problems, yet the neurobiological processes underlying these associations are poorly understood. In this experiment, we uncover a potential mechanism leading to maladaptive decision making: altered brain activation during anticipation of rewards and losses. Individual differences in neural responses to cues of potential reward or loss were associated with early life stress and both laboratory and real-world measures of risk-taking behaviors. These effects were predicted only by childhood stress exposure, not by current levels of stress in the participants’ adult lives. Early life stress was assessed prospectively, when the participants were children, thereby avoiding the potential biases associated with adult retrospective recall.
Molecular and functional resemblance of differentiated cells derived from isogenic human iPSCs and SCNT-derived ESCs
Authors: Zhao Ming-Tao , Chen Haodong , Liu Qing , Shao Ning-Yi , Sayed Nazish , Wo Hung-Ta , Zhang Joe Z. , Ong Sang-Ging , Liu Chun , Kim Youngkyun , Yang Huaxiao , Chour Tony , Ma Hong , Gutierrez Nuria Marti , Karakikes Ioannis , Mitalipov Shoukhrat , Snyder Michael P. , Wu Joseph C.
Published: December 2017

Significance

Patient-specific pluripotent stem cells (PSCs) can be derived by two nuclear reprogramming methods: somatic cell nuclear transfer (SCNT) using unfertilized eggs and transcription factor-based reprogramming (i.e., induced pluripotent stem cells, iPSCs). The direct comparison of differentiated cells generated by SCNT and iPSC has yet to be assessed. In this study, we employ cutting-edge technologies to evaluate the similarities and differences between isogenic human iPSCs and SCNT-ESC derivatives. We provide proof-of-concept that differentiated cells derived from human iPSCs are comparable to nuclear transfer-derived ESC counterparts with regard to transcriptional, epigenetic, physiological, and pharmacological features, given that they are genetically identical. We conclude that human iPSCs are capable of replacing SCNT for generating differentiated cells for drug testing and disease modeling.
Electrostatic confinement and manipulation of DNA molecules for genome analysis
Authors: Kounovsky-Shafer Kristy L. , Hernandez-Ortiz Juan P. , Potamousis Konstantinos , Tsvid Gene , Place Michael , Ravindran Prabu , Jo Kyubong , Zhou Shiguo , Odijk Theo , de Pablo Juan J. , Schwartz David C.
Published: December 2017

Significance

Repeated sequences make up approximately two-thirds of the human genome, which become fully accountable when very large DNA molecules are analyzed. Long, single DNA molecules are problematic using common experimental techniques and fluidic devices because of mechanical considerations that include breakage, dealing with the massive size of these coils, or the huge length of stretched DNAs. Accordingly, we harness analyte “issues” as exploitable advantages by invention and characterization of the “molecular gate,” which controls and synchronizes formation of stretched molecules as DNA dumbbells within nanoslit geometries that may also offer new routes to separation. This was accomplished by theoretical studies and experiments leveraging a series of electrical forces acting on DNA molecules, device walls, and the fluid flows within our devices.
Structural studies of Chikungunya virus maturation
Authors: Yap Moh Lan , Klose Thomas , Urakami Akane , Hasan S. Saif , Akahata Wataru , Rossmann Michael G.
Published: December 2017

Significance

Chikungunya virus (CHIKV) belongs to the alphavirus family, the members of which have enveloped icosahedral capsids. The maturation process of alphaviruses involves proteolysis of some of the structural proteins before assembling with nucleocapsids to produce mature virions. We mutated the proteolytic cleavage site on E2 envelope protein, which is necessary in initiating the maturation process. Noninfectious virus-like particles (VLP) equivalent to “immature” fusion incompetent particles were produced to study the immature conformation of CHIKV. We describe the 6.8-Å resolution electron microscopy structure of “immature” CHIK VLPs. Structural differences between the mature and immature VLPs show that posttranslational processing of the envelope proteins and nucleocapsid is necessary to allow exposure of the fusion loop on glycoprotein E1 to produce an infectious virus.
Islet cells share promoter hypomethylation independently of expression, but exhibit cell-type–specific methylation in enhancers
Authors: Neiman Daniel , Moss Joshua , Hecht Merav , Magenheim Judith , Piyanzin Sheina , Shapiro A. M. James , de Koning Eelco J. P. , Razin Aharon , Cedar Howard , Shemer Ruth , Dor Yuval
Published: December 2017

Significance

We have studied the dynamics of DNA methylation in pancreatic α- and β-cells and reached surprising insights into the establishment of islet cell identity. Different islet cell types share lack of methylation in cell-type–specific gene promoters, while DNA methylation differences between islet cell types are concentrated in enhancer regions. The findings support the fundamental role of enhancer methylation in determining cell identity, and have implications for the understanding of islet cell plasticity in diabetes.
Development and validation of a high-throughput transcriptomic biomarker to address 21st century genetic toxicology needs
Authors: Li Heng-Hong , Chen Renxiang , Hyduke Daniel R. , Williams Andrew , Frötschl Roland , Ellinger-Ziegelbauer Heidrun , O’Lone Raegan , Yauk Carole L. , Aubrecht Jiri , Fornace Albert J.
Published: December 2017

Significance

Standard in vitro assays to assess genotoxicity frequently generate positive results that are subsequently found to be irrelevant for in vivo carcinogenesis and human cancer risk assessment. Currently used follow-up methods, such as animal testing, are expensive and time-consuming, and the development of approaches enabling more accurate mechanism-based risk assessment is essential. We developed an in vitro transcriptomic biomarker-based approach that provides a robust biomarker reflecting stress-signaling responses. The biomarker correctly identifies the vast majority of irrelevant genotoxicity results from in vitro chromosome damage assays. TGx-DDI, a multigene biomarker for DNA damage-inducing agents, is the first biomarker that not only shows convincing interlaboratory and intralaboratory reproducibility, but also performs accurately in a system suitable for high-throughput screening.
Multiple oscillatory rhythms determine the temporal organization of perception
Authors: Ronconi Luca , Oosterhof Nikolaas N. , Bonmassar Claudia , Melcher David
Published: December 2017

Significance

To reduce the complexity of our sensory environment, the perceptual system discretizes information in different ways. In the time domain, this is evident when stimuli that are presented very close in time are sometimes faithfully perceived as different entities, whereas they are integrated into a single event at other times. Using multivariate decoding of electroencephalography data, we show that integration and segregation of stimuli over different time scales (a few tens vs. a few hundreds of milliseconds) do not rely on a single sampling rhythm; instead, they depend on the phase of prestimulus oscillations at different frequency bands in right posterior-parietal channels. These findings suggest the existence of a specific mapping between oscillations and temporal windows in perception.
Terminal attack trajectories of peregrine falcons are described by the proportional navigation guidance law of missiles
Authors: Brighton Caroline H. , Thomas Adrian L. R. , Taylor Graham K.
Published: December 2017

Significance

Renowned as nature’s fastest predators, peregrines are famous for their high-speed stooping and swooping attack behaviors. We used miniature GPS receivers to track peregrines attacking dummy targets thrown by a falconer or towed by a drone and fitted a simulation describing the dynamics of the guidance system used in interception. We collected onboard video giving a falcon’s-eye view of the attacks and used this to validate our conclusions for attacks on live targets. Remarkably, we find that the terminal attack trajectories of peregrines are described by the same feedback law used by visually guided missiles, but with a tuning appropriate to their lower flight speed. Our findings have application to drones designed to remove other drones from protected airspace.
Enigmatic origin of the poxvirus membrane from the endoplasmic reticulum shown by 3D imaging of vaccinia virus assembly mutants
Authors: Weisberg Andrea S. , Maruri-Avidal Liliana , Bisht Himani , Hansen Bryan T. , Schwartz Cindi L. , Fischer Elizabeth R. , Meng Xiangzhi , Xiang Yan , Moss Bernard
Published: December 2017

Significance

Poxviruses cause human and epizootic diseases and are employed as vaccine vectors. The present investigation provides insights into a key step in poxvirus replication, the assembly of infectious virus particles. Enveloped viruses acquire membranes from cellular organelles; nevertheless, the source of the poxvirus membrane has been an enigma. Poxvirus assembly occurs in cytoplasmic factories, and the first recognizable structures are membrane crescents without discernible connections to cellular membranes. The key to demonstrating connections was isolation of vaccinia virus mutants that are defective in assembly. Electron tomographic analyses of cells infected with the mutants unambiguously demonstrated continuity between viral membranes and the endoplasmic reticulum and suggested that viral proteins induce or stabilize membrane scissions during a normal infection.
Structure and function of a compound eye, more than half a billion years old
Authors: Schoenemann Brigitte , Pärnaste Helje , Clarkson Euan N. K.
Published: December 2017

Significance

An exceptionally well-preserved arthropod fossil from near the base of the lower Cambrian shows the internal sensory structures of a compound eye, more than half a billion years old. The trilobite to which it belongs is found in a zone where the first complete organisms appear in the fossil record; thus, it is probably the oldest record of a visual system that ever will be available. This compound eye proved to possess the same kind of structure as the eyes of bees and dragonflies living today, but it lacks the lenses that are typical of modern eyes of this type. There is an elegant physical solution, however, of how to develop a quality image of modern type.
Evidence for sortilin modulating regional accumulation of human tau prions in transgenic mice
Authors: Johnson Noah R. , Condello Carlo , Guan Shenheng , Oehler Abby , Becker Julia , Gavidia Marta , Carlson George A. , Giles Kurt , Prusiner Stanley B.
Published: December 2017

Significance

Human neurodegenerative diseases such as Alzheimer’s disease develop in a highly stereotyped fashion, suggesting intrinsic differences among brain regions determine whether they are affected or spared. Here, we employed a widely used line of transgenic (Tg) mice expressing mutant (P301S) human tau and exhibiting robust tauopathy. By examining brain regions affected by and spared of tau prions, we found that localization of human tau prion formation in Tg mice arises from regional inhibition of tau prion replication. Using a cell-based bioassay, we identified an inhibitor of tau prion propagation in the forebrain. These discoveries may lead to the identification of key mediators of brain vulnerability involved in human tauopathies, a promising strategy for the development of targeted therapeutics for these diseases.
Unusual zinc-binding mode of HDAC6-selective hydroxamate inhibitors
Authors: Porter Nicholas J. , Mahendran Adaickapillai , Breslow Ronald , Christianson David W.
Published: December 2017

Significance

Histone deacetylase 6 (HDAC6) is a zinc metalloenzyme that serves as the tubulin deacetylase in the cell cytosol. Inhibition of tubulin deacetylase activity leads to suppression of microtubule dynamics, causing cell cycle arrest and apoptosis, which is a validated strategy for cancer chemotherapy. Selective inhibition of HDAC6 is clinically preferable, since unwanted inhibition of other HDAC isozymes can lead to undesirable off-target effects. Here, X-ray crystal structures of HDAC6-inhibitor complexes reveal molecular features responsible for the isozyme selectivity measured in inhibition assays, including an unusual monodentate hydroxamate-Zn
2+
coordination mode as well as intermolecular interactions of bulky inhibitor substituents. These observations will inform the design of HDAC6-selective inhibitors with improved properties.
Argument by multimodal metaphor as strategic maneuvering in video advertising
Authors: Chuanrui Zhang , Cihua Xu
Published: December 2017

The present study analyzes the strategic maneuvering in theLin Dan Commercial(LDC), an anti-corruption advertisement broadcasted on China Central Television, with the help of pragma-dialectics and conceptual metaphor theory. In order to evaluate theLDC’s reasonableness and effectiveness, this research aims to establish how an argument by multimodal metaphor is used in practice for disseminating of an anti-corruption view. A pragma-dialectical analysis is provided of theLDCadvertisement viewed as a multimodal metaphor. According to the research, theLDCadvertisement multimodally contains a conceptual metaphor,career is a match,to enhance the advertisement’s effectiveness by maneuvering strategically. In this endeavor, a sense of identity created by the multimodally-expressed conceptual metaphor is utilized to ensure its reasonableness.
Strategic maneuvering by personal attacks in spokespersons’ argumentative replies at diplomatic press conferences
Authors: Peng Wu
Published: December 2017

Within the framework of Pragma-Dialectics, this article analyzes personal attacks in the spokespersons’ replies at the press conferences held by the Chinese Ministry of Foreign Affairs between 2012 and 2015. The research results show that, to cut down the credibility of their opponents in attempting to dismiss them, spokespersons adopt three subtypes of personal attack: the direct, the indirect, and theYou toosubtypes. Each of them can be further divided into several variants. Taking account of the institutional preconditions for making argumentative replies at governmental press conferences, this article analyzes how spokespersons maneuver strategically in attacking a secondary audience by means of the various subtypes and variants of personal attack. It then explains how these strategic maneuvers assist the spokespersons in convincing their primary audience.
The verbal prefix u- in Croatian and Bulgarian
Authors: Šarić Ljiljana , Nedelcheva Svetlana
Published: December 2017

This study compares the semantic networks of the verbal prefix
u- in two South Slavic languages, Bulgarian (blg.) and
Croatian (cro.), in a cognitive linguistics framework using two
databases of prefixed verbs drawn from dictionaries and corpora. We point to
similarities and overlapping categories in the semantic networks of
u- in blg. and cro., as well as to
differences. When accounting for the differences, we consider prefixes
semantically similar to u- (within one language and in both
languages) that combine with the same base verbs forming either prefixed
near-synonyms (e.g., blg. uvehna, zavehna, izvehna
‘wither, fade’; cro. umastiti, omastiti, zamastiti
‘grease, stain’) or prefixed verbs that are only seemingly near-synonyms (e.g.,
blg. ukaža ‘indicate, show’, okaža
se ‘turn out’; cro. ocrniti ‘denigrate,
slander’, ucrniti (se) ‘color black, wear
black’). We examine how the meaning networks of individual semantically related
prefixes (e.g., u- and za-,
iz-) overlap within one language and across the two
languages, as well as how different construals of the same event affect the
prefix choice.
“No news is good news?”
Authors: Sakamoto Akiko , Foedisch Melanie
Published: December 2017

Professional translation is now predominantly carried out in virtual-team-style production networks where communication between language service providers (LSPs) and freelance translators’ practice is increasingly restricted to computerised methods. Although some literature deals with interactions between different participants in the translation production network, little attention has been paid to the ways in which they exchange feedback on translation products. Using observation and interview methods, this article examines how feedback is perceived and dealt with by freelance translators and LSPs’ project managers. Our results suggest that, although both groups share the value of feedback to some extent, feedback does not always reach translators and the translators are not always aware of the rationale behind it. By drawing on the Job Characteristics Model (JCM) (Hackman and Oldham 1980), which was developed in organisational psychology, we argue that incorporating feedback in the job constructs of freelance translators’ work may help to enhance translators’ motivation.
Effects of homogenisation treatment on microstructure and grain refinement of Al–1.2Mn alloy
Authors: Chen X. P. , Mei L. , Li S. , Shang L. M.
Published: December 2017

The effects of a homogenisation treatment on precipitation, recrystallisation, grain refinement and texture in an Al–1.2Mn alloy were investigated. Based on hardness and electrical conductivity measurements, a precipitation–recrystallisation diagram was generated, which described the sequence of recrystallisation and precipitation. The results showed that recrystallisation was significantly retarded during the annealing treatment for the cold-rolled alloys with a supersaturated solid solution or with dense pre-existing dispersoids. If precipitation occurred prior to recrystallisation, the precipitates caused a strong resistance to recrystallisation, resulting in a coarse and elongated grain structure with a dominant normal direction-rotated cube texture. In contrast, when recrystallisation was completed before precipitation, recrystallisation was little affected by the precipitates, leading to a fine-grained structure with a weak cube texture.
Hot tensile deformation and fracture behaviours of Hastelloy C-276 alloy
Authors: Huang Yuanchun , Liu Chang , Xiao Zhengbing
Published: December 2017

The uniaxial tensile tests of Hastelloy C-276 were performed under elevated temperature and strain rate. Considering the effects of different deformation parameters, the flow behaviour, microstructure and fracture characteristics were analysed based on the experimental data. From the rheological curves, the typical characteristics of dynamic recrystallisation were observed at a relatively high deformation temperature and low strain rate. Optical microstructures show that the degree of dynamic recrystallisation increases with an increase in temperature. The SEM micrographs show that the amount of precipitates increases with an increase in deformation temperature. Examination of the fracture morphology at high magnifications revealed that the coalescence of microscopic voids is responsible for the fracture failure.
Physical, mechanical, and ablation properties of Cu–Ti3AlC2 composites with various Ti3AlC2 contents
Authors: Huang Xiaochen , Feng Yi , Qian Gang , Zhao Hao , Zhang Jingcheng , Zhang Xuebin
Published: December 2017

The effects of Ti3AlC2 content on the physical, mechanical, and arc ablation resistance properties of a fabricated Cu–Ti3AlC2 composite are investigated in detail. Composite samples containing 10, 15, 20, 25, 30, and 35 vol.-% Ti3AlC2 are sintered at 800°C without decomposition of Ti3AlC2. It is demonstrated that with increasing Ti3AlC2 content, the relative density, electrical conductivity, and flexural strength of Cu–Ti3AlC2 decrease but the Brinell hardness first increases and then decreases. After eroded by an electric arc, Cu–Ti3AlC2 oxidises to CuO, TiO2, and Al2O3. Meanwhile, field emission-SEM observations reveal that the dimensions of protrusions and the percentage of TiO2 increase with increasing Ti3AlC2 content. Remarkably, the electric arc mainly occurs at the Ti3AlC2 particles, and the Cu matrix remains well protected.
Undecaprenyl phosphate metabolism in Gram-negative and Gram-positive bacteria
Authors: Kawakami Naoki , Fujisaki Shingo
Published: December 2017

Undecaprenyl phosphate (UP) is essential for the biosynthesis of bacterial extracellular polysaccharides. UP is produced by the dephosphorylation of undecaprenyl diphosphate (UPP) via de novo synthetic and recycling pathways. Gram-positive bacteria contain remarkable amounts of undecaprenol (UOH), which is phosphorylated to UP, although UOH has not been found in Gram-negative bacteria. Here, current knowledge about UPP phosphatase and UOH kinase is reviewed. Dephosphorylation of UPP is catalyzed by a BacA homologue and a type-2 phosphatidic acid phosphatase (PAP2) homologue. The presence of one of these UPP phosphatases is essential for bacterial growth. The catalytic center of both types of enzyme is located outside the cytoplasmic membrane. In Gram-positive bacteria, an enzyme homologous to DgkA, which is the diacylglycerol kinase of Escherichia coli, catalyzes UOH phosphorylation. The possible role of UOH and the significance of systematic construction of Staphylococcus aureus mutants to determine UP metabolism are discussed.
Improvement of the activity and thermostability of microbial transglutaminase by multiple-site mutagenesis
Authors: Mu Dongdong , Lu Jiaojiao , Shu Chang , Li Haowen , Li Xingjiang , Cai Jing , Luo Shuizhong , Yang Peizhou , Jiang Shaotong , Zheng Zhi
Published: December 2017

Microbial transglutaminase (MTG) is an enzyme widely used in the food industry. Mutiple-site mutagenesis of Streptomyces mobaraensis transglutaminase was performed in Escherichia coli. According to enzymatic assay and thermostability study, among three penta-site MTG mutants (DM01-03), DM01 exhibited the highest enzymatic activity of 55.7 ± 1.4 U/mg and longest half-life at 50 °C (418.2 min) and 60 °C (24.8 min).
Characterization of moderately halotolerant selenate- and tellurite-reducing bacteria isolated from brackish areas in Osaka
Authors: Soda Satoshi , Ma Wenbo , Kuroda Masashi , Nishikawa Hiroshi , Zhang Yuanyuan , Ike Michihiko
Published: December 2017

Moderately halotolerant selenate- and tellurite-reducing bacteria were characterized for wastewater treatment applications. A selenate-reducing strain 9a was isolated from the biofilm of a leachate treatment plant at a sea-based waste disposal site. A tellurite-reducing strain Taa was isolated from an enrichment culture derived from brackish sediment. Both bacterial strains were Shewanella species. Strain 9a could anaerobically remove 45–70% of 1.0 mM selenate and selenite from water containing up to 3% NaCl within 4 days, while strain Taa could anaerobically and aerobically remove 70–90% of 0.4 mM tellurite from water containing up to 6% NaCl within 3 days. Globular particles of insoluble selenium were observed both outside and inside the cells of strain 9a. The insoluble tellurium formed by strain Taa was globular under microaerobic conditions but nanorod under aerobic conditions. These bacteria will yield a range of useful selenium and tellurium nanomaterials as well as wastewater treatment applications.
Social Class, Gender and Ethnic Differences in Subjects Taken at Age 14.
Authors: Henderson Morag , Sullivan Alice , Anders Jake , Moulton Vanessa
Published: December 2017

In this paper, we identify patterns of subject and qualification choices made at age 14. Much of the previous research on ‘subject choice’ has focussed on the later stages of educational trajectories, particularly Higher Education. However, the choices made at early branching points can limit pupils’ subsequent options, potentially contributing to educational inequalities. This paper identifies the patterns of General Certificate of Secondary Education (GCSE) subjects chosen by a cohort of young people born in 1989/1990. We make use of the Next Steps data (formerly the Longitudinal Study of Young People in England (LSYPE)) which is linked to the National Pupil Database. We develop an approach to measuring the academic selectivity of subjects and qualifications. We examine the roles of social class, parental education, income, gender and ethnicity in determining participation in these curriculum groupings. Using measures of prior attainment from age thirteen, we address the question of whether curriculum differentials simply reflect differences in prior attainment or whether they actually operate above and beyond existing inequalities. We find clear socio‐economic, gender, ethnic and school‐level differences in subjects studied which cannot be accounted for by prior attainment.
Effect of upset pressure on texture evolution and its correlation to toughness in flash butt joints
Authors: Shajan Nikhil , Arora Kanwer Singh , Sharma Vikram , Shome Mahadev
Published: December 2017

Effect of upset pressure on the weld zone microstructure, texture evolution and its effect on toughness were investigated. It was observed that an increase in upset pressure leads to a decrease in the heat-affected zone width and also the grain size as a result of recrystallisation. It was also observed that insufficient upset pressure leads to porosity in the joints. Electron backscattered diffraction study on the weld zone showed that an increase in the upset pressure resulted in a sharp rise in (110)[001] and (110) [Formula: see text] component. Shear deformation at the plate edges due to the constrained flow of material led to the evolution of Goss fibre component parallel to the fracture plane. The presence of Goss fibre components that are generated during welding as a result of upsetting operation played a critical role in decreasing the toughness at the weld zone compared to the parent material.
High mobility group box 1 orchestrates tissue regeneration via CXCR4
Authors: Tirone Mario , Tran Ngoc Lan , Ceriotti Chiara , Gorzanelli Andrea , Canepari Monica , Bottinelli Roberto , Raucci Angela , Di Maggio Stefania , Santiago César , Mellado Mario , Saclier Marielle , François Stéphanie , Careccia Giorgia , He Mingzhu , De Marchis Francesco , Conti Valentina , Ben Larbi Sabrina , Cuvellier Sylvain , Casalgrandi Maura , Preti Alessandro , Chazaud Bénédicte , Al-Abed Yousef , Messina Graziella , Sitia Giovanni , Brunelli Silvia , Bianchi Marco Emilio , Vénéreau Emilie
Published: December 2017

Inflammation and tissue regeneration follow tissue damage, but little is known about how these processes are coordinated. High Mobility Group Box 1 (HMGB1) is a nuclear protein that, when released on injury, triggers inflammation. We previously showed that HMGB1 with reduced cysteines is a chemoattractant, whereas a disulfide bond makes it a proinflammatory cytokine. Here we report that fully reduced HMGB1 orchestrates muscle and liver regeneration via CXCR4, whereas disulfide HMGB1 and its receptors TLR4/MD-2 and RAGE (receptor for advanced glycation end products) are not involved. Injection of HMGB1 accelerates tissue repair by acting on resident muscle stem cells, hepatocytes, and infiltrating cells. The nonoxidizable HMGB1 mutant 3S, in which serines replace cysteines, promotes muscle and liver regeneration more efficiently than the wild-type protein and without exacerbating inflammation by selectively interacting with CXCR4. Overall, our results show that the reduced form of HMGB1 coordinates tissue regeneration and suggest that 3S may be used to safely accelerate healing after injury in diverse clinical contexts.
Novel and shared neoantigen derived from histone 3 variant H3.3K27M mutation for glioma T cell therapy
Authors: Chheda Zinal S. , Kohanbash Gary , Okada Kaori , Jahan Naznin , Sidney John , Pecoraro Matteo , Yang Xinbo , Carrera Diego A. , Downey Kira M. , Shrivastav Shruti , Liu Shuming , Lin Yi , Lagisetti Chetana , Chuntova Pavlina , Watchmaker Payal B. , Mueller Sabine , Pollack Ian F. , Rajalingam Raja , Carcaboso Angel M. , Mann Matthias , Sette Alessandro , Garcia K. Christopher , Hou Yafei , Okada Hideho
Published: December 2017

The median overall survival for children with diffuse intrinsic pontine glioma (DIPG) is less than one year. The majority of diffuse midline gliomas, including more than 70% of DIPGs, harbor an amino acid substitution from lysine (K) to methionine (M) at position 27 of histone 3 variant 3 (H3.3). From a CD8+ T cell clone established by stimulation of HLA-A2+ CD8+ T cells with synthetic peptide encompassing the H3.3K27M mutation, complementary DNA for T cell receptor (TCR) α- and β-chains were cloned into a retroviral vector. TCR-transduced HLA-A2+ T cells efficiently killed HLA-A2+H3.3K27M+ glioma cells in an antigen- and HLA-specific manner. Adoptive transfer of TCR-transduced T cells significantly suppressed the progression of glioma xenografts in mice. Alanine-scanning assays suggested the absence of known human proteins sharing the key amino acid residues required for recognition by the TCR, suggesting that the TCR could be safely used in patients. These data provide us with a strong basis for developing T cell–based therapy targeting this shared neoepitope.
Food Insecurity Research in the United States: Where We Have Been and Where We Need to Go
Authors: Gundersen Craig , Ziliak James P
Published: December 2017

Food insecurity is now recognized as a major health crisis in the United States. This is due to the size of the problem—more than 42 million persons were food insecure in 2015—as well as the multiple negative health outcomes and higher health care costs attributable to food insecurity. An extensive body of literature from multiple fields has examined the causes and consequences of food insecurity and the efficacy of food assistance programs—especially the Supplemental Nutrition Assistance Program. We review this literature and provide suggestions for future research directions. We suggest examining the distribution of food insecurity within households, the impact of the food distribution system on food insecurity, the coping mechanisms of low‐income food secure families, food insecurity among American Indians, the effects of charitable food assistance, the causal relationship between food insecurity and health outcomes, the declining age gradient in food insecurity among Seniors, the effects of labor force participation and the Great Recession on food insecurity, and the long‐term consequences of food insecurity. In addition, the impact of two recent policy recommendations on food insecurity – the minimum wage and the Affordable Care – Act should be considered.
Patient Experience With Care and Its Association With Adherence to Hypertension Medications
Authors: Fortuna Robert J , Nagel Angela K , Rocco Thomas A , Legette-Sobers Sharon , Quigley Denise D
Published: December 2017

BACKGROUND

Medication adherence is crucial to effective chronic disease management, yet little is known about the influence of the patient–provider interaction on medication adherence to hypertensive regimens. We aimed to examine the association between the patient’s experience with care and medication adherence.

METHODS

We collected 2,128 surveys over 4 years from a convenience sample of hypertensive patients seeking care at three urban safety-net practices in upstate New York. The survey collected adherence measures using the Morisky Medication Adherence Scale (MMAS-8) and patient experience measures. We used regression models to adjust for age, gender, race/ethnicity, self-reported health status, and clustering by patients. The primary outcome was reporting of medium-to-high adherence (MMAS ≥ 6) vs. low adherence

RESULTS

A total of 62.5% of respondents reported medium-to-high medication adherence. The concern the provider demonstrated for patient questions or worries (adjusted odds ratio [AOR] 1.4; 95% confidence interval [CI] 1.1–1.7), provider efforts to include the patient in decisions (AOR 1.5; 95% CI 1.8–1.9), information given (AOR 1.3; 95% CI 1.0–1.6), and the overall rating of care received (AOR 1.4; 95% CI 1.1–1.8) were associated with higher medication adherence. The amount of time the provider spent was not associated with medication adherence (AOR 1.2; 95% CI 0.9–1.4). Medium-to-high medication adherence was in turn associated with increased hypertension control rates.

CONCLUSIONS

Overall, better experiences with care were associated with higher adherence to hypertension regimens. However, the amount of time the provider spent with the patient was not statistically associated with medication adherence, suggesting that the quality of communication may be more important than the absolute quantity of time.
SANA NetGO: a combinatorial approach to using Gene Ontology (GO) terms to score network alignments
Authors: Hayes Wayne B , Mamano Nil
Published: December 2017

Motivation

Gene Ontology (GO) terms are frequently used to score alignments between protein–protein interaction (PPI) networks. Methods exist to measure GO similarity between proteins in isolation, but proteins in a network alignment are not isolated: each pairing is dependent on every other via the alignment itself. Existing measures fail to take into account the frequency of GO terms across networks, instead imposing arbitrary rules on when to allow GO terms.

Results

Here we develop NetGO, a new measure that naturally weighs infrequent, informative GO terms more heavily than frequent, less informative GO terms, without arbitrary cutoffs, instead downweighting GO terms according to their frequency in the networks being aligned. This is a global measure applicable only to alignments, independent of pairwise GO measures, in the same sense that the edge-based EC or S3 scores are global measures of topological similarity independent of pairwise topological similarities. We demonstrate the superiority of NetGO in alignments of predetermined quality and show that NetGO correlates with alignment quality better than any existing GO-based alignment measures. We also demonstrate that NetGO provides a measure of taxonomic similarity between species, consistent with existing taxonomic measuresa feature not shared with existing GObased network alignment measures. Finally, we re-score alignments produced by almost a dozen aligners from a previous study and show that NetGO does a better job at separating good alignments from bad ones.

Availability and implementation

Available as part of SANA.

Supplementary information

Supplementary data are available at Bioinformatics online.
Using the Markov chain Monte Carlo method to study the physical properties of GeV–TeV BL Lac objects
Authors: Qin Longhua , Wang Jiancheng , Yang Chuyuan , Yuan Zunli , Mao Jirong , Kang Shiju
Published: December 2017

We fit the spectral energy distributions (SEDs) of 46 GeV–TeV BL Lac objects in the frame of leptonic one-zone synchrotron self-Compton (SSC) model and investigate the physical properties of these objects. We use the Markov chain Monte Carlo (MCMC) method to obtain the basic parameters, such as magnetic field (B), the break energy of the relativistic electron distribution ($\gamma ^{\prime }_{\rm {b}}$), and the electron energy spectral index. Based on the modeling results, we support the following scenarios for GeV–TeV BL Lac objects. (1) Some sources have large Doppler factors, implying other radiation mechanism should be considered. (2) Compared with flat spectrum quasars (FSRQs), GeV–TeV BL Lac objects have weaker magnetic fields and larger Doppler factors, which cause the ineffective cooling and shift the SEDs to higher bands. Their jet powers are around 4.0 × 1045 erg s−1, compared with radiation power, 5.0 × 1042 erg s−1, indicating that only a small fraction of jet power is transformed into the emission power. (3) For some BL Lacs with large Doppler factors, their jet components could have two substructures, e.g., the fast core and the slow sheath. For most GeV–TeV BL Lacs, Kelvin–Helmholtz instabilities are suppressed by their higher magnetic fields, leading to micro-variability or intro-day variability in the optical bands. (4) Combined with a sample of FSRQs, an anti-correlation between the peak luminosity, Lpk, and the peak frequency, νpk, is obtained, favoring the blazar sequence scenario. In addition, an anti-correlation between the jet power, Pjet, and the break Lorentz factor, γb, also supports the blazar sequence.