bluuebunny/crossref_metadata_2025 huggingface dataset:
Nonadiabatic effects in electronic and nuclear dynamics
Authors: Bircher Martin P. , Liberatore Elisa , Browning Nicholas J. , Brickel Sebastian , Hofmann Cornelia , Patoz Aurélien , Unke Oliver T. , Zimmermann Tomáš , Chergui Majed , Hamm Peter , Keller Ursula , Meuwly Markus , Woerner Hans-Jakob , Vaníček Jiří , Rothlisberger Ursula
Published: January 2018

Due to their very nature, ultrafast phenomena are often accompanied by the occurrence of nonadiabatic effects. From a theoretical perspective, the treatment of nonadiabatic processes makes it necessary to go beyond the (quasi) static picture provided by the time-independent Schrödinger equation within the Born-Oppenheimer approximation and to find ways to tackle instead the full time-dependent electronic and nuclear quantum problem. In this review, we give an overview of different nonadiabatic processes that manifest themselves in electronic and nuclear dynamics ranging from the nonadiabatic phenomena taking place during tunnel ionization of atoms in strong laser fields to the radiationless relaxation through conical intersections and the nonadiabatic coupling of vibrational modes and discuss the computational approaches that have been developed to describe such phenomena. These methods range from the full solution of the combined nuclear-electronic quantum problem to a hierarchy of semiclassical approaches and even purely classical frameworks. The power of these simulation tools is illustrated by representative applications and the direct confrontation with experimental measurements performed in the National Centre of Competence for Molecular Ultrafast Science and Technology.
Experiment study of mud to the moving process influent about viscous debris flow along slope
Authors: Jun JiXian , Ying Liang , Li Pan Hua , Qiang OuGuo
Published: January 2018

Mud is the main component of viscous debris flow. The physical model experiments of viscous debris flow were carried out through the mixing mud with different density and fixed components of coarse particles. The width, longitudinal movement distance and motion velocity were recorded by video cameras during experiment. Through viscous debris flow physical model experiments, the influence of mud to transverse width, longitudinal movement distance and motion velocity was discussed. The physical model experiment results show that the motion forms change from inviscid particle flow to viscous debris flow and to the whole mass sliding with the increase of mud density; the width and the length along the slope decrease with mud density increasing; the movement process has classified phenomena about viscous debris flow composed by different mud densities: the velocity increases rapidly with time and the change gradient is steady when the density of mud is lower than 1.413g/cm3; the movement process can be divided into two stages when the density of mud is higher than 1.413g/cm3: the movement velocity is lower and the gradient change is small in the initial stage; but in the second stage, the movement velocity increases quickly, and the gradient is higher than the first stage, and with steady value.
Exchange bias effect in hybrid improper ferroelectricity Ca2.94Na0.06Mn2O7
Authors: Li Songyang , Wang Shouyu , Lu Yangong , Zhang Chuang , Yang Xiaoxia , Gao Ju , Li Dejun , Zhu Yun , Liu Weifang
Published: January 2018

The hybrid improper ferroelectricity Ca3Mn2O7 (CMO) has been a subject of remarkable interest due to potential multiferroicity. In this paper we synthesized CMO and Ca2.94Na0.06Mn2O7 (CNMO) ceramics and investigated their structural and magnetic properties. It is found that Na doping effectively weakens the structural distortion as decreasing the orthorhombic distortion and Jahn-Teller distortion. Although both samples undergo an antiferromagnetic transition at temperature around 111 K, the exchange bias and coercive fields increase in CNMO. Such increased exchange bias field could be explained within a model of size-variable nanoscale ferromagnetic clusters embedded in an antiferromagnetic matrix.
Strain effect on the magnetic and transport properties of LaCoO3 thin films
Authors: Li Y. , Peng S. J. , Wang D. J. , Wu K. M. , Wang S. H.
Published: January 2018

LaCoO3 (LCO) has attracted much attention due to the unique magnetic transition and spin transition of Co3+ ions. Epitaxial LCO film exhibits an unexpected ferromagnetism, in contrast to the non-magnetism of bulk LCO. An in-depth study on the property of strained LCO film is of great importance. We have fabricated 30 nm LCO films on various substrates and studied the magnetic and transport properties of films in different strain states (compressed strain for LCO/LaAlO3, tensile strain for LCO/(LaAlO3)0.3(Sr2TaAlO6)0.35, SrTiO3). The in-plane tensiled LCO films exhibit ferromagnetic ground state at 5K and magnetic transition with TC around 85K, while compressed LCO/LaAlO3 film has a negligibly small moment signal. Our results reveal that in-plane tensile strain and tetragonal distortion are much more favorable for stabilizing the FM order in LCO films.
Non-iterative triple excitations in equation-of-motion coupled-cluster theory for electron attachment with applications to bound and temporary anions
Authors: Jagau Thomas-C.
Published: January 2018

The impact of residual electron correlation beyond the equation-of-motion coupled-cluster singles and doubles (EOM-CCSD) approximation on positions and widths of electronic resonances is investigated. To establish a method that accomplishes this task in an economical manner, several approaches proposed for the approximate treatment of triple excitations are reviewed with respect to their performance in the electron attachment (EA) variant of EOM-CC theory. The recently introduced EOM-CCSD(T)(a)* method [D. A. Matthews and J. F. Stanton, J. Chem. Phys. 145, 124102 (2016)], which includes non-iterative corrections to the reference and the target states, reliably reproduces vertical attachment energies from EOM-EA-CC calculations with single, double, and full triple excitations in contrast to schemes in which non-iterative corrections are applied only to the target states. Applications of EOM-EA-CCSD(T)(a)* augmented by a complex absorbing potential (CAP) to several temporary anions illustrate that shape resonances are well described by EOM-EA-CCSD, but that residual electron correlation often makes a non-negligible impact on their positions and widths. The positions of Feshbach resonances, on the other hand, are significantly improved when going from CAP-EOM-EA-CCSD to CAP-EOM-EA-CCSD(T)(a)*, but the correct energetic order of the relevant electronic states is still not achieved.
Improved thermal stability of TbF3-coated sintered Nd–Fe–B magnets by electrophoretic deposition
Authors: Cao X. J. , Chen L. , Guo S. , Di J. H. , Ding G. F. , Chen R. J. , Yan A. R. , Chen K. Z.
Published: January 2018

Using electrophoretic deposition (EPD) method, the impact of TbF3 diffusion on the coercivity, microstructure and thermal stability of sintered Nd–Fe–B magnets with different rare earth (RE) content was investigated. In the diffused magnets with the RE content of 34 wt.%, the maximum coercivity about 28.12 kOe with less than 1.44 wt.% Tb was achieved, the coercivity temperature coefficient (β) was improved to -0.50 %/°C from -0.58 %/°C within the temperature interval 25-160 °C, and the maximum operating temperature further increased to about 160 °C. It suggested that TbF3 diffused magnets had much superior thermal stability than the annealed samples. This was attributed to the formation of the Tb-rich (Nd, Tb)2Fe14B phase in the outer region of the matrix grains and the improved Nd-rich grain boundary phase after TbF3 diffusion.
Disordered kagomé spin ice
Authors: Greenberg Noah , Kunz Andrew
Published: January 2018

Artificial spin ice is made from a large array of patterned magnetic nanoislands designed to mimic naturally occurring spin ice materials. The geometrical arrangement of the kagomé lattice guarantees a frustrated arrangement of the islands’ magnetic moments at each vertex where the three magnetic nanoislands meet. This frustration leads to a highly degenerate ground state which gives rise to a finite (residual) entropy at zero temperature. In this work we use the Monte Carlo simulation to explore the effects of disorder in kagomé spin ice. Disorder is introduced to the system by randomly removing a known percentage of magnetic islands from the lattice. The behavior of the spin ice changes as the disorder increases; evident by changes to the shape and locations of the peaks in heat capacity and the residual entropy. The results are consistent with observations made in diluted physical spin ice materials.
Effects of an adjacent metal surface on spin wave propagation
Authors: Trossman Jonathan , Lim Jinho , Bang Wonbae , Ketterson J. B. , Tsai C. C. , Lee S. J.
Published: January 2018

We experimentally investigate and model the effects of a copper surface adjacent to a surface on which spin waves propagate in a thin film of yttrium iron garnet (YIG). Investigation was performed using a phase detection method, which can map out the spin wave velocity as a function wavevector for small wavevector with high resolution. This velocity is in good agreement with a simple model and allows for extraction of the separation between the YIG film and the copper.
In-situ magnetization/heating electron holography to study the magnetic ordering in arrays of nickel metallic nanowires
Authors: Ortega Eduardo , Santiago Ulises , Giuliani Jason G. , Monton Carlos , Ponce Arturo
Published: January 2018

Magnetic nanostructures of different size, shape, and composition possess a great potential to improve current technologies like data storage and electromagnetic sensing. In thin ferromagnetic nanowires, their magnetization behavior is dominated by the competition between magnetocrystalline anisotropy (related to the crystalline structure) and shape anisotropy. In this way electron diffraction methods like precession electron diffraction (PED) can be used to link the magnetic behavior observed by Electron Holography (EH) with its crystallinity. Using off-axis electron holography under Lorentz conditions, we can experimentally determine the magnetization distribution over neighboring nanostructures and their diamagnetic matrix. In the case of a single row of nickel nanowires within the alumina template, the thin TEM samples showed a dominant antiferromagnetic arrangement demonstrating long-range magnetostatic interactions playing a major role.
Reading magnetic ink patterns with magnetoresistive sensors
Authors: Merazzo K. J. , Costa T. , Franco F. , Ferreira R. , Zander M. , Türr M. , Becker T. , Freitas P. P. , Cardoso S.
Published: January 2018

Information storage and monitoring relies on sensitive transducers with high robustness and reliability. This paper shows a methodology enabling the qualification of magnetic sensors for magnetic pattern readout, in applications different than hard disk magnetic recording. A magnetic tunnel junction MTJ sensor was incorporated in a reader setup for recognition of the magnetization of patterned arrays made of CoCrPt thin films and magnetic ink. The geometry of the sensor (in particular, the footprint and vertical distance to the media) was evaluated for two sensor configurations. The readout conditions were optimized to cope for variable media field intensity, resulting from CoCrPt film or magnetic ink thickness, with fixed reading distance and dimensions of the pattern. The calibration of the ink magnetic signal could be inferred from the analytical calculations carried out to validate the CoCrPt results.
Tailoring magnetic properties of self-biased hexaferrites using an alternative copolymer of isobutylene and maleic anhydride
Authors: Wu Chuanjian , Yu Zhong , Sokolov Alexander S. , Yu Chengju , Sun Ke , Jiang Xiaona , Lan Zhongwen , Harris Vincent G.
Published: January 2018

Discussed is a novel self-biased hexaferrite gelling system based on a nontoxic and water-soluble copolymer of isobutylene and maleic anhydride. This copolymer simultaneously acts as a dispersant and gelling agent, and recently received much attention from the ceramics community. Herein its effects on the rheological conditions throughout magnetic-field pressing, and consequently, orientation, density and magnetic properties of textured hexaferrites were investigated. Ka-band FMR linewidths were measured, and the crystalline anisotropy and porosity induced linewidth broadening were estimated according to Schlömann’s theory. The copolymer allowed to reduce the friction between micron-sized magnetic particulates, resulting in higher density and degree of crystalline orientation, and lower FMR linewidth.
The band structures of three-dimensional nonlinear plasma photonic crystals
Authors: Zhang Hai-Feng
Published: January 2018

In this paper, the properties of the photonic band gaps (PBGs) for three-dimensional (3D) nonlinear plasma photonic crystals (PPCs) are theoretically investigated by the plane wave expansion method, whose equations for calculations also are deduced. The configuration of 3D nonlinear PPCs is the Kerr nonlinear dielectric spheres (Kerr effect is considered) inserted in the plasma background with simple-cubic lattices. The inserted dielectric spheres are Kerr nonlinear dielectrics whose relative permittivities are the functions of the external light intensity. Three different Kerr nonlinear dielectrics are considered, which can be expressed as the functions of space coordinates. The influences of the parameters for the Kerr nonlinear dielectrics on the PBGs also are discussed. The calculated results demonstrate that the locations, bandwidths and number of PBGs can be manipulated with the different Kerr nonlinear dielectrics. Compared with the conventional 3D dielectric PCs and PPCs with simple-cubic lattices, the more PBGs or larger PBG can be achieved in the 3D nonlinear PPCs. Those results provide a new way to design the novel devices based on the PPCs.
Optical observation of single layer graphene on silicon nitride substrate
Authors: An Jin Yong , Kahng Yung Ho
Published: January 2018

Optical observation of graphene on substrates is an important aspect of graphene research. However, while graphene visibility on SiO2/Si substrates has already been thoroughly investigated, that on Si3N4/Si substrates, which excludes background oxygen, requires further investigation. Here, we present theoretical and experimental results of graphene visibility on Si3N4/Si substrates. On these substrates, the graphene contrast that diverges and changes sign over narrow ranges, which makes it more difficult to observe graphene on them, was predicted and experimentally verified. Under appropriate conditions, it was possible to observe single layer graphene on these substrates, as demonstrated by our experimentally observed results. Our findings will be useful for enabling the use of Si3N4/Si substrates in characterizing functionalized graphenes.
Effects of vacuum rapid thermal annealing on the electrical characteristics of amorphous indium gallium zinc oxide thin films
Authors: Lee Hyun-Woo , Cho Won-Ju
Published: January 2018

We investigated the effects of vacuum rapid thermal annealing (RTA) on the electrical characteristics of amorphous indium gallium zinc oxide (a-IGZO) thin films. The a-IGZO films deposited by radiofrequency sputtering were subjected to vacuum annealing under various temperature and pressure conditions with the RTA system. The carrier concentration was evaluated by Hall measurement; the electron concentration of the a-IGZO film increased and the resistivity decreased as the RTA temperature increased under vacuum conditions. In a-IGZO thin-film transistors (TFTs) with a bottom-gate top-contact structure, the threshold voltage decreased and the leakage current increased as the vacuum RTA temperature increased. As the annealing pressure decreased, the threshold voltage decreased, and the leakage current increased. X-ray photoelectron spectroscopy indicated changes in the lattice oxygen and oxygen vacancies of the a-IGZO films after vacuum RTA. At higher annealing temperatures, the lattice oxygen decreased and oxygen vacancies increased, which suggests that oxygen was diffused out in a reduced pressure atmosphere. The formation of oxygen vacancies increased the electron concentration, which consequently increased the conductivity of the a-IGZO films and reduced the threshold voltage of the TFTs. The results showed that the oxygen vacancies and electron concentrations of the a-IGZO thin films changed with the vacuum RTA conditions and that high-temperature RTA treatment at low pressure converted the IGZO thin film to a conductor.
Parametric excitation of a SiN membrane via piezoelectricity
Authors: Wu Shuhui , Sheng Jiteng , Zhang Xiaotian , Wu Yuelong , Wu Haibin
Published: January 2018

We develop a stoichiometric silicon nitride (SiN) membrane-based electromechanical system, in which the spring constant of the mechanical resonator can be dynamically controlled via piezoelectric actuation. The degenerate parametric amplifier is studied in this configuration. We observe the splitting of mechanical mode in the response spectra of a phase-sensitive parametric amplifier. In addition, we demonstrate that the quality factor Q of the membrane oscillator can be significantly enhanced by more than two orders of magnitude due to the coherent amplification, reaching an effective Q factor of ∼3 × 108 at room temperature. The nonlinear effect on the parametric amplification is also investigated, as well as the thermomechanical noise squeezing. This system offers the possibility to integrate electrical, optical and mechanical degrees of freedom without compromising the exceptional material properties of SiN membranes, and can be a useful platform for studying cavity optoelectromechanics.
Perovskite-based solar cells with inorganic inverted hybrid planar heterojunction structure
Authors: Lai Wei-Chih , Lin Kun-Wei , Guo Tzung-Fang , Chen Peter , Liao Yuan-Yu
Published: January 2018

We demonstrated the good performance of inorganic inverted CH3NH3PbI3 perovskite-based solar cells (SCs) with glass/ITO/NiOx/CH3NH3PbI3 perovskite/C60/ room temperature (RT)-sputtered ZnO/Al structure. We adopted spin coating and RT sputtering for the deposition of NiOx and ZnO, respectively. The inorganic hole and electron transport layer of NiOx and RT-sputtered ZnO, respectively, could improve the open-circuit voltage (VOC), short-circuit current density (JSC), and power conversion efficiency (η%) of the SCs. We obtained inorganic inverted CH3NH3PbI3 perovskite-based SCs with a JSC of 21.96 A/cm2, a VOC of 1.02 V, a fill factor (FF%) of 68.2%, and an η% of 15.3% despite the sputtering damage of the RT-sputtered ZnO deposition. Moreover, the RT-sputtered ZnO could function as a diffusion barrier for Al, moisture, and O2. The inorganic inverted CH3NH3PbI3 perovskite-based SCs demonstrated improved storage reliability.
Silica-coated gadolinium-doped lanthanum strontium manganite nanoparticles for self-controlled hyperthermia applications
Authors: Ahmad Ashfaq , Bae Hongsub , Rhee Ilsu
Published: January 2018

Gadolinium-doped lanthanum strontium manganite (LSM) nanoparticles were synthesized by using a citrate-gel technique. The particles were then annealed at 850 oC to remove defects for a good crystallinity, followed by coating with silica for possible biomedical application to magnetic hyperthermia. The chemical composition was determined to be La0.54Sr0.27Gd0.19MnO3 using an inductively coupled plasma mass spectrometer. The nanoparticles were characterized by X-ray diffraction, transmission electron microscope, and Fourier transform infrared spectrometer to check the perovskite crystalline structure and to observe the particles size and coating status of silica on the surface of the particles. The Curie temperature of the particles was found to be about 280 K. The saturation temperature of the aqueous solution of the particles remained at the hyperthermia target temperature of 42 oC with increasing concentration of particles from 6 to 60 mg/mL in the dispersion. This saturation temperature for a highly concentrated 120-mg/mL-sample increased further, but less than the dangerous temperature of 47 oC for normal tissues. The saturation temperature of the powder sample reached only up to 53 oC. These results showed that the gadolinium-doped LSM nanoparticles can be used for the self-controlled hyperthermia in which the temperature does not exceed the target temperature of hyperthermia even at the tissue site of highly accumulated nanoparticles.
Fabrication of triple-layered bifurcated vascular scaffold with a certain degree of three-dimensional structure
Authors: Liu Yuanyuan , Jiang Weijian , Yang Yang , Pu Huayan , Peng Yan , Xin Liming , Zhang Yi , Sun Yu
Published: January 2018

Constructing vascular scaffolds is important in tissue engineering. However, scaffolds with characteristics such as multiple layers and a certain degree of spatial morphology still cannot be readily constructed by current vascular scaffolds fabrication techniques. This paper presents a three-layered bifurcated vascular scaffold with a curved structure. The technique combines 3D printed molds and casting hydrogel and fugitive ink to create vessel-mimicking constructs with customizable structural parameters. Compared with other fabrication methods, the technique can create more native-like 3D geometries. The diameter and wall thickness of the fabricated constructs can be independently controlled, providing a feasible approach for vascular scaffold construction. Enzymatically-crosslinked gelatin was used as the scaffold material. The morphology and mechanical properties were evaluated. Human umbilical cord derived endothelial cells (HUVECs) were seeded on the scaffolds and cultured for 72 h. Cell viability and morphology were assessed. The results showed that the proposed process had good application potentials, and will hopefully provide a feasible approach for constructing vascular scaffolds.
A helical charge simulation based 3-D calculation model for corona loss of AC stranded conductors in the corona cage
Authors: Liu Yunpeng , Huang Shilong , Liu Shugang , Liu Daran
Published: January 2018

Corona loss generated from conductors is an indispensable factor in the design of alternating current(AC) transmission lines. Based on a helical charge simulation method, a 3-D calculation model for corona loss considering the outer strands of the conductor in the corona cage was established. Compared to the 2-D corona-loss calculation method, the calculation model proposed in this study incorporates the heterogeneity of the electric fields strength along the axial direction of the stranded conductor. Furthermore, it was also able to calculate the corona loss when the conductor had sagged. The calculation results of the LGJ-300/40 and LGJ-400/35 in the small corona cage show close agreement with the measurement results indicating that the corona-loss calculation model was accurate. In addition, the corona loss of the bundle conductors 4 × LGJ720 with sag in the UHV corona cage was also analyzed.
Sphingolipids activate the endoplasmic reticulum stress surveillance pathway
Authors: Piña Francisco , Yagisawa Fumi , Obara Keisuke , Gregerson J.D. , Kihara Akio , Niwa Maho
Published: January 2018

Proper inheritance of functional organelles is vital to cell survival. In the budding yeast, Saccharomyces cerevisiae, the endoplasmic reticulum (ER) stress surveillance (ERSU) pathway ensures that daughter cells inherit a functional ER. Here, we show that the ERSU pathway is activated by phytosphingosine (PHS), an early biosynthetic sphingolipid. Multiple lines of evidence support this: (1) Reducing PHS levels with myriocin diminishes the ability of cells to induce ERSU phenotypes. (2) Aureobasidin A treatment, which blocks conversion of early intermediates to downstream complex sphingolipids, induces ERSU. (3) orm1Δorm2Δ cells, which up-regulate PHS, show an ERSU response even in the absence of ER stress. (4) Lipid analyses confirm that PHS levels are indeed elevated in ER-stressed cells. (5) Lastly, the addition of exogenous PHS is sufficient to induce all ERSU phenotypes. We propose that ER stress elevates PHS, which in turn activates the ERSU pathway to ensure future daughter-cell viability.
Key comparison BIPM.RI(I)-K5 of the air-kerma standards of the SMU, Slovakia and the BIPM in 137Cs gamma radiation
Authors: Kessler C , Burns D , Durný N
Published: January 2018

The first direct comparison of the standards for air kerma of the Slovak Institute of Metrology (SMU), Slovakia and of the Bureau International des Poids et Mesures (BIPM) was carried out in the 137Cs radiation beam of the BIPM in June 2017. The comparison result, evaluated as a ratio of the SMU and the BIPM standards for air kerma, is 1.0051 with a combined standard uncertainty of 2.7 × 10−3. The results for an indirect comparison made at the same time are consistent with the direct results at the level of 2 parts in 104. The results are analysed and presented in terms of degrees of equivalence, suitable for entry in the BIPM key comparison database.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCRI, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
International comparison CCQM-K119 liquefied petroleum gas
Authors: Brewer P J , Downey M L , Atkins E , Brown R J C , Brown A S , Zalewska E T , van der Veen A M H , Smeulders D E , McCallum J B , Satumba R T , Kim Y D , Kang N , Bae H K , Woo J C , Konopelko L A , Popova T A , Meshkov A V , Efremova O V , Kustikov Y
Published: January 2018

Liquefied hydrocarbon mixtures with traceable composition are required in order to underpin measurements of the composition and other physical properties of LPG (liquefied petroleum gas), thus meeting the needs of an increasingly large industrial market.

This comparison aims to assess the analytical capabilities of laboratories for measuring the composition of a Liquid Petroleum Gas (LPG) mixture when sampled in the liquid phase from a Constant Pressure Cylinder. Mixtures contained ethane, propane, propene, i-butane, n-butane, but-1-ene and i-pentane with nominal amount fractions of 2, 71, 9, 4, 10, 3 and 1 cmol mol−1 respectively.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Retailer Proximity and Nutrition Program Redemptions: Evidence From the Summer Electronic Benefit Transfer For Children Program
Authors: Furey Jane , Klerman Jacob Alex , Grindal Todd
Published: January 2018

Although nearly all Supplemental Nutrition Assistance Program benefits are redeemed, a moderate share of Special Supplemental Nutrition Program for Women, Infant, and Children (WIC) benefits go unredeemed. Some hypothesize that the redemption rate differences are due to the lower density of WIC‐authorized retailers. For the 2012 Summer Electronic Benefit Transfer for Children sites, this paper finds no consistent evidence of a relationship between redemption rates and retailer proximity. In fact, households often travel past the closest participating retailer to redeem their benefits. These findings are consistent with recent “food deserts” literature, which suggests that correlations between retailer environment and nutritional outcomes are not causal. Rather, it appears that differences in redemption rates may be related to the restrictions on what foods can be redeemed in what form with WIC.
Presence of Myocardial Damage Predicts Future Development of Hypertension in a Normotensive Japanese General Population: The Yamagata (Takahata) Study
Authors: Honda Yuki , Watanabe Tetsu , Tamura Harutoshi , Nishiyama Satoshi , Takahashi Hiroki , Arimoto Takanori , Shishido Tetsuro , Miyamoto Takuya , Shibata Yoko , Konta Tsuneo , Kayama Takamasa , Kubota Isao
Published: January 2018

BACKGROUND

A modest rise in blood pressure (BP) reportedly increases cardiovascular mortality despite not reaching obvious hypertension, suggesting that target organ damages are latently induced by slight BP rising. The goal of this study was to determine whether presence of subclinical myocardial damage can predict the future development of hypertension in the normotensive general population.

METHODS AND RESULTS

The cohort study was conducted with subjects who participated in a community-based annual health check. Normotensive subjects without prior cardiovascular diseases at baseline were eligible for analyses (n = 524, mean age 58 ± 9 years; 53% women). We measured heart-type fatty acid binding protein (H-FABP) at baseline as a biomarker of ongoing myocardial damage. Longitudinal changes in BP were examined during median follow-up period of 6.2 years, and we investigated the association between the baseline H-FABP level and longitudinal BP changes.

RESULTS

During the follow-up, 177 subjects (34%) developed hypertension. In multivariate Cox proportional hazard analysis adjusted for potential confounders including age and baseline BP, presence of myocardial damage was significantly associated with the development of hypertension (hazard ratio 1.80, 95% confidence interval, 1.26–2.54; P = 0.0014). Furthermore, relative risk of myocardial damage for incident hypertension was higher in younger subjects and lower BP category.

CONCLUSIONS

Presence of subclinical myocardial damage was independently associated with the future development of hypertension in the normotensive general population.
Characteristics and evolution of the ecosystem of software tools supporting research in molecular biology
Authors: Pazos Florencio , Chagoyen Monica
Published: January 2018

Daily work in molecular biology presently depends on a large number of computational tools. An in-depth, large-scale study of that ‘ecosystem’ of Web tools, its characteristics, interconnectivity, patterns of usage/citation, temporal evolution and rate of decay is crucial for understanding the forces that shape it and for informing initiatives aimed at its funding, long-term maintenance and improvement. In particular, the long-term maintenance of these tools is compromised because of their specific development model. Hundreds of published studies become irreproducible de facto, as the software tools used to conduct them become unavailable. In this study, we present a large-scale survey of >5400 publications describing Web servers within the two main bibliographic resources for disseminating new software developments in molecular biology. For all these servers, we studied their citation patterns, the subjects they address, their citation networks and the temporal evolution of these factors. We also analysed how these factors affect the availability of these servers (whether they are alive). Our results show that this ecosystem of tools is highly interconnected and adapts to the ‘trendy’ subjects in every moment. The servers present characteristic temporal patterns of citation/usage, and there is a worrying rate of server ‘death’, which is influenced by factors such as the server popularity and the institutions that hosts it. These results can inform initiatives aimed at the long-term maintenance of these resources.
pyHVis3D: visualising molecular simulation deduced H-bond networks in 3D: application to T-cell receptor interactions
Authors: Knapp Bernhard , Alcala Marta , Zhang Hao , West Clare E , van der Merwe P Anton , Deane Charlotte M
Published: January 2018

Motivation

Hydrogen bonds (H-bonds) play an essential role for many molecular interactions but are also often transient, making visualising them in a flexible system challenging.

Results

We provide pyHVis3D which allows for an easy to interpret 3D visualisation of H-bonds resulting from molecular simulations. We demonstrate the power of pyHVis3D by using it to explain the changes in experimentally measured binding affinities for three T-cell receptor/peptide/MHC complexes and mutants of each of these complexes.

Availability and implementation

pyHVis3D can be downloaded for free from http://opig.stats.ox.ac.uk/resources.

Supplementary information

Supplementary data are available at Bioinformatics online.
MAGNAMWAR: an R package for genome-wide association studies of bacterial orthologs
Authors: Sexton Corinne E , Smith Hayden Z , Newell Peter D , Douglas Angela E , Chaston John M
Published: January 2018

Here we report on an R package for genome-wide association studies of orthologous genes in bacteria. Before using the software, orthologs from bacterial genomes or metagenomes are defined using local or online implementations of OrthoMCL. These presence–absence patterns are statistically associated with variation in user-collected phenotypes using the Mono-Associated GNotobiotic Animals Metagenome-Wide Association R package (MAGNAMWAR). Genotype-phenotype associations can be performed with several different statistical tests based on the type and distribution of the data.

Availability and implementation

MAGNAMWAR is available on CRAN.
A network approach to exploring the functional basis of gene–gene epistatic interactions in disease susceptibility
Authors: Yip Danny Kit-Sang , Chan Landon L , Pang Iris K , Jiang Wei , Tang Nelson L S , Yu Weichuan , Yip Kevin Y
Published: January 2018

Motivation

Individual genetic variants explain only a small fraction of heritability in some diseases. Some variants have weak marginal effects on disease risk, but their joint effects are significantly stronger when occurring together. Most studies on such epistatic interactions have focused on methods for identifying the interactions and interpreting individual cases, but few have explored their general functional basis. This was due to the lack of a comprehensive list of epistatic interactions and uncertainties in associating variants to genes.

Results

We conducted a large-scale survey of published research articles to compile the first comprehensive list of epistatic interactions in human diseases with detailed annotations. We used various methods to associate these variants to genes to ensure robustness. We found that these genes are significantly more connected in protein interaction networks, are more co-expressed and participate more often in the same pathways. We demonstrate using the list to discover novel disease pathways.

Contact

kevinyip@cse.cuhk.edu.hk

Supplementary information

Supplementary data are available at Bioinformatics online.
PyChimera: use UCSF Chimera modules in any Python 2.7 project
Authors: Rodríguez-Guerra Pedregal Jaime , Maréchal Jean-Didier
Published: January 2018

Motivation

UCSF Chimera is a powerful visualization tool remarkably present in the computational chemistry and structural biology communities. Built on a C++ core wrapped under a Python 2.7 environment, one could expect to easily import UCSF Chimera’s arsenal of resources in custom scripts or software projects. Nonetheless, this is not readily possible if the script is not executed within UCSF Chimera due to the isolation of the platform. UCSF ChimeraX, successor to the original Chimera, partially solves the problem but yet major upgrades need to be undergone so that this updated version can offer all UCSF Chimera features.

Results

PyChimera has been developed to overcome these limitations and provide access to the UCSF Chimera codebase from any Python 2.7 interpreter, including interactive programming with tools like IPython and Jupyter Notebooks, making it easier to use with additional third-party software.

Availability and implementation

PyChimera is LGPL-licensed and available at https://github.com/insilichem/pychimera.

Supplementary information

Supplementary data are available at Bioinformatics online.
Older Patients Have Better Pain Outcomes Following Microvascular Decompression for Trigeminal Neuralgia
Authors: Bick Sarah K , Huie David , Sneh Gabriel , Eskandar Emad N
Published: January 2018

BACKGROUND

Trigeminal neuralgia (TN) increases in prevalence with age. Although microvascular decompression (MVD) is the most effective long-term operative treatment for TN, its use in older patient populations has been debated due to its invasive nature. Recent studies have demonstrated safety of MVD in older patients; however, efficacy data are more limited.

OBJECTIVE

To determine the relationship between age and pain outcomes following MVD for TN.

METHODS

Subjects underwent MVD for TN at our institution between 1/1/2004 and 12/31/2013, had typical TN, and demonstrated neurovascular compression on preoperative imaging. We performed a retrospective case series study by reviewing the electronic medical records and performing phone interviews to determine long-term outcomes. We divided patients into 2 groups for analysis, under 60 and 60 yr of age and older.

RESULTS

One hundred twenty-four subjects were included in the study, 82 under 60, and 42 60 yr of age and older. The average length of follow-up was 42.4 mo. Patients in the older age group had average pain score of 1.57 at most recent follow-up, while for the younger age group it was 2.18 (P = .0084). Multiple regression analysis found that older age, male gender, and preoperative medication responsiveness were significantly correlated with lower long-term pain scores, while V2 dermatome involvement was correlated with higher long-term pain scores.

CONCLUSION

Patients 60 yr of age and older have significantly better long-term pain outcomes following MVD than younger patients.
Acute Appendicitis as the Initial Clinical Presentation of Primary HIV-1 Infection
Authors: Schleimann Mariane H , Leth Steffen , Krarup Astrid R , Mortensen Jesper , Barstad Bente , Zaccarin Matthias , Denton Paul W , Mohey Rajesh
Published: January 2018

We report a case of an adolescent who presented at our emergency department with acute abdominal pain. While the initial diagnosis was acute appendicitis, a secondary and coincidental diagnosis of primary HIV-1 infection was made. Concurrent and subsequent clinical and molecular biology findings form the basis of our argument that primary HIV-1 infection was the cause of acute appendicitis in this individual.
Magnetic field analysis of the bow and terminal shock of the SS 433 jet
Authors: Sakemi Haruka , Machida Mami , Akahori Takuya , Nakanishi Hiroyuki , Akamatsu Hiroki , Kurahara Kohei , Farnes Jamie
Published: January 2018

We report a polarization analysis of the eastern region of W 50, observed with the Australia Telescope Compact Array (ATCA) at 1.4–3.0 GHz. In order to study the physical structures in the region where the SS 433 jet and W 50 interact, we obtain an intrinsic magnetic field vector map of that region. We find that the orientation of the intrinsic magnetic field vectors are aligned along the total intensity structures, and that there are characteristic, separate structures related to the jet, the bow shock, and the terminal shock. The Faraday rotation measures (RMs), and the results of Faraday tomography suggest that a high-intensity, filamentary structure in the north–south direction of the eastern-edge region can be separated into at least two parts to the north and south. The results of Faraday tomography also show that there are multiple components along the line of sight and/or within the beam area. In addition, we analyze the X-ray ring-like structure observed with XMM-Newton. While the possibility still remains that this X-ray ring is “real”, it seems that the structure is not ring-like at radio wavelengths. Finally, we suggest that the structure is a part of the helical structure that coils the eastern ear of W 50.
Self-help cognitive behavior therapy for working women with problematic hot flushes and night sweats (MENOS@Work): a multicenter randomized controlled trial
Authors: Hardy Claire , Griffiths Amanda , Norton Sam , Hunter Myra S.
Published: January 2018

Objective:

The aim of the study was to examine the efficacy of an unguided, self-help cognitive behavior therapy (SH-CBT) booklet on hot flush and night sweat (HFNS) problem rating, delivered in a work setting.

Methods:

Women aged 45 to 60 years, having 10 or more problematic HFNS a week, were recruited to a multicenter randomized controlled trial, via the occupational health/human resources departments of eight organizations. Participants were 1:1 randomized to SH-CBT or no treatment waitlist control (NTWC). The primary outcome was HFNS problem rating; secondary outcomes included HFNS frequency, work and social adjustment, sleep, mood, beliefs and behaviors, and work-related variables (absence, performance, turnover intention, and work impairment due to presenteeism). Intention-to-treat analysis was used, and between-group differences estimated using linear mixed models.

Results:

A total of 124 women were randomly allocated to SH-CBT (n = 60) and NTWC (n = 64). 104 (84%) were assessed for primary outcome at 6 weeks and 102 (82%) at 20 weeks. SH-CBT significantly reduced HFNS problem rating at 6 weeks (SH-CBT vs NTWC adjusted mean difference, −1.49; 95% CI, −2.11 to −0.86; P < 0.001) and at 20 weeks (−1.09; 95% CI, −1.87 to −0.31; P < 0.01). SH-CBT also significantly reduced HFNS frequency, improved work and social adjustment; sleep, menopause beliefs, HFNS beliefs/behaviors at 6 and 20 weeks; improved wellbeing and somatic symptoms and reduced work impairment due to menopause-related presenteeism at 20 weeks, compared with the NTWC. There was no difference between groups in other work-related outcomes.

Conclusions:

A brief, unguided SH-CBT booklet is a potentially effective management option for working women experiencing problematic HFNS.
An In-Vitro Insertion-Force Study of Magnetically Guided Lateral-Wall Cochlear-Implant Electrode Arrays
Authors: Leon Lisandro , Warren Frank M. , Abbott Jake J.
Published: January 2018

Hypothesis:

Insertion forces can be reduced by magnetically guiding the tip of lateral-wall cochlear-implant electrode arrays during insertion via both cochleostomy and the round window.

Background:

Steerable electrode arrays have the potential to minimize intracochlear trauma by reducing the severity of contact between the electrode-array tip and the cochlear wall. However, steerable electrode arrays typically have increased stiffness associated with the steering mechanism. In addition, steerable electrode arrays are typically designed to curve in the direction of the basal turn, which is not ideal for round-window insertions, as the cochlear hook's curvature is in the opposite direction. Lateral-wall electrode arrays can be modified to include magnets at their tips, augmenting their superior flexibility with a steering mechanism. By applying magnetic torque to the tip, an electrode array can be navigated through the cochlear hook and the basal turn.

Methods:

Automated insertions of candidate electrode arrays are conducted into a scala-tympani phantom with either a cochleostomy or round-window opening. The phantom is mounted on a multi-degree-of-freedom force sensor. An external magnet applies the necessary magnetic bending torque to the magnetic tip of a modified clinical electrode array, coordinated with the insertion, with the goal of directing the tip down the lumen. Steering of the electrode array is verified through a camera.

Results:

Statistical t-test results indicate that magnetic guidance does reduce insertion forces by as much as 50% with certain electrode-array models. Direct tip contact with the medial wall through the cochlear hook and the lateral wall of the basal turn is completely eliminated. The magnetic field required to accomplish these insertions varied from 77 to 225 mT based on the volume of the magnet at the tip of the electrode array. Alteration of the tip to accommodate a tiny magnet is minimal and does not change the insertion characteristic of the electrode array unless the tip shape is altered.

Conclusion:

Magnetic guidance can eliminate direct tip contact with the medial walls through the cochlear hook and the lateral walls of the basal turn. Insertion-force reduction will vary based on the electrode-array model, but is statistically significant for all models tested. Successful steering of lateral-wall electrode arrays is accomplished while maintaining its superior flexibility.
Utilization of Nerve Integrity Monitor for Promontory Stimulation Testing Prior to Cochlear Implant
Authors: Kelly Elizabeth A. , Levine Samuel , Gravel Kristin E. , Hart Dianna L. , Huang Tina
Published: January 2018

Objective:

To demonstrate the feasibility of a nerve integrity monitor as a tool for promontory stimulation testing in patients with profound sensorineural hearing loss considering cochlear implantation.

Patients:

Adult patients considered for cochlear implantation with no auditory response on audiometric testing

Intervention:

Promontory stimulation testing using the nerve integrity monitor.

Main Outcome Measure:

By using a facial nerve stimulator and the nerve integrity monitor, transtympanic promontory stimulation testing was performed to assess auditory nerve function and determine candidacy for cochlear implantation. Patients indicated if they heard the stimulus.

Results:

Of the four patients completing the promontory stimulation tests, three patients heard the stimulus and one patient did not hear the stimulus. Of the three patients with a positive stimulation test, two patients have a history of progressive profound sensorineural hearing loss and one patient had a history of severe blunt temporal bone trauma. Two of these patients proceeded with cochlear implantation. The patient who had a negative promontory stimulation test has a history of neurofibromatosis type 2.

Conclusion:

The nerve integrity monitor is a convenient tool that can be used in the clinic setting to perform promontory stimulation tests and aid in determining cochlear implant candidates, specifically in those patients who require verification of auditory nerve function. This tool is a feasible and reasonable method for promontory stimulation testing.