bluuebunny/crossref_metadata_2025 huggingface dataset:
A study of transient responses on nonuniform conductors by FDTD simulations
Authors: Asada Takashi , Ametani Akihiro , Baba Yoshihiro , Nagaoka Naoto
Published: May 2016

Surge propagation on nonuniform conductors has been investigated on the basis of finite‐difference time‐domain (FDTD) simulations. It has been confirmed that an inclined conductor above the earth is represented following the image theory based on transverse electromagnetic (TEM) wave propagation by two angled (nonparallel) conductors in a free space. Nonparallel conductor systems above the earth show a wave propagation characteristic quite different from that of the TEM mode, and thus steady‐state and transient phenomena on the nonparallel conductors cannot be appropriately analyzed by a circuit theory and by simulation tools such as the EMTP based on the circuit theory. © 2016 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.
Hybrid Chinese text classification approach using general knowledge from Baidu Baike
Authors: Ren Fuji , Li Chao
Published: May 2016

Most of the previous studies focused on enriching text representation to address text classification (TC) task. However, conventional classification approaches with VSM (vector space model) on Chinese text study intensively only the words and their relationship in some specific corpus/dataset but ignore the basic concept of categories and the general knowledge behind the words learned and used to recognize entities by people. This paper focuses on enriching text representation and proposes a novel approach, which complements information from the online Chinese encyclopedia Baidu Baike for Chinese TC. The similarities between every text and each concept of categories and the most related words from Baidu Baike are added to the feature space. The performance of the proposed approach is measured on the Fudan University TC corpus, which is an imbalanced Chinese dataset. In the experiments, the proposed Baidu Baike‐based concept similarity approach obtains promising results when compared with a previous research and the conventional method, with macro‐precision of 90.31%, recall of 75.45%, and F1 score 80.32%, which are about 0.02%, 0.15%, 0.12%, respectively, higher than the conventional method, which obviously improves the recall for some small categories while keeping precision at high level and improving the macro F1 score. Moreover, the proposed approach has good expandability, so that many other knowledge bases could be integrated and many other concepts could be referred to improve the effectiveness. © 2016 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.
Comparative efficacy of tulathromycin and tildipirosin for the treatment of experimental Mycoplasma bovis infection in calves
Authors: Bartram David J. , Moyaert Hilde , Vanimisetti Bindu H. , Ramage Clifford P. , Reddick David , Stegemann Michael R.
Published: May 2016

The objective of this negative controlled, blinded, randomised, parallel group study was to compare the efficacy of two injectable macrolide antimicrobials, tulathromycin and tildipirosin, administered by single subcutaneous injection at dose rates of 2.5 and 4.0 mg kg−1 bodyweight, respectively, in the treatment of an experimentally induced Mycoplasma bovis infection in calves. A total of 238 M. bovis‐negative calves were challenged on three consecutive days with M. bovis by endobronchial deposition. Post‐challenge, a total of 126 animals fulfilled the inclusion criteria and were randomly allocated to three treatment groups: tulathromycin, tildipirosin and saline. Clinical observations for signs of respiratory disease and injection site assessments were conducted daily for 14 days post‐treatment. The animals were then killed, the lungs were examined for evidence of lesions, and samples collected for bacterial isolation. Calves treated with tulathromycin had a lower percentage of lung with lesions (P = 0.0079), lower mortality (P = 0.0477), fewer days with depressed demeanour (P = 0.0486) and higher body weight (P = 0.0112) than calves administered tildipirosin.
A longitudinal study of self‐control at the transition to secondary school: Considering the role of pubertal status and parenting
Authors: Ng‐Knight Terry , Shelton Katherine H. , Riglin Lucy , McManus I.C. , Frederickson Norah , Rice Frances
Published: May 2016

Higher self‐control in children and adolescents is associated with a range of positive outcomes in adulthood. However, little is known about the naturalistic development of self‐control during early adolescence and the factors that affect this. We examined the role of puberty and parenting style as theoretically important influences on stability and change in self‐control. A longitudinal (3 waves), multiple‐informant dataset of children entering early adolescence (M = 11 years) was used to explore longitudinal change in self‐control using latent growth curve modelling. Children's self‐control declined during the one‐year study period and declines were associated with children's behavioural and social functioning. Associations with self‐control were found for pubertal status and parental warmth and hostility, but not for parental discipline. The findings suggest that during early adolescence, when children make the transition to secondary school, self‐control declines. This is particularly the case for those experiencing puberty earlier than their peers. Parent warmth influences the trajectory of self‐control during this period.
Survey on hand gestures relevance in patient practitioner communication: a homeopathic example
Authors: Büssing Arndt , Ostermann Thomas , Escher Max
Published: May 2016

Background:
Gestures play an important role in medical communication.

Methods:
94 homeopaths (Mean age 49.6 years, 20% male) completed a 20-item questionnaire on utilization and relevance of gestures in patients’ symptom description.

Results:
After excluding nine items due to low validity (n = 4) or low item total correlation (n = 5), factor analysis of the questionnaire resulted in the following three dimensions explaining 66.6% of variance: ‘Hand gestures in relation to verbal expressions’ (5 items; Cronbach’s α = 0.81), ‘Hand Gestures describing the experience of bodily and mental symptoms’ (4 items; Cronbach’s α = 0.74) and ‘practitioners’ behavior and active attitude in observing hand gestures’ (2 items; Cronbach’s α = 0.86).

Conclusion:
The survey shows how homeopathic therapists view patients’ hand gestures, whether they use these diagnostically and how this relates to their homeopathic practice. Practitioners with only homeopathic influence on this topic are highly congruent to findings on hand gestures from other domains.
Protocol of randomized controlled trial of potentized estrogen in homeopathic treatment of chronic pelvic pain associated with endometriosis
Authors: Sérgio Podgaec , Baracat Edmund Chada , Teixeira Marcus Zulian
Published: May 2016

Background: Endometriosis is a chronic inflammatory disease that causes difficult-to-treat pelvic pain. Thus being, many patients seek help in complementary and alternative medicine, including homeopathy. The effectiveness of homeopathic treatment for endometriosis is controversial due to the lack of evidences in the literature. The aim of the present randomized controlled trial is to assess the efficacy of potentized estrogen compared to placebo in the treatment of chronic pelvic pain associated with endometriosis.

Methods/design: The present is a randomized, double-blind, placebo-controlled trial of a homeopathic medicine individualized according to program ‘New Homeopathic Medicines: use of modern drugs according to the principle of similitude’ (http://newhomeopathicmedicines.com). Women with endometriosis, chronic pelvic pain and a set of signs and symptoms similar to the adverse events caused by estrogen were recruited at the Endometriosis Unit of Division of Clinical Gynecology, Clinical Hospital, School of Medicine, University of São Paulo (Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo – HCFMUSP). The participants were selected based on the analysis of their medical records and the application of self-report structured questionnaires. A total of 50 women meeting the eligibility criteria will be randomly allocated to receive potentized estrogen or placebo. The primary clinical outcome measure will be severity of chronic pelvic pain. Statistical analysis will be performed on the intention-to-treat and per-protocol approaches comparing the effect of the homeopathic medicine versus placebo after 24 weeks of intervention.

Discussion: The present study was approved by the research ethics committee of HCFMUSP and the results are expected in 2016.

Trial registration: ClinicalTrials.gov Identifier: https://clinicaltrials.gov/ct2/show/NCT02427386.
Attitudes and behaviors towards risky driving among adolescents in Saudi Arabia
Authors: Ramisetty-Mikler Suhasini , Almakadma Abdulkarim
Published: May 2016

Background and Objectives:

The main objective of the paper is to investigate perceptions and attitudes of school youth concerning risky driving behaviors (i.e.: Tafheet) in Saudi Arabia.

Design

and Setting: This was a school-based cross-sectional study of adolescents in Riyadh that employed a multistage probability sampling scheme.

Subjects and Methods:

The self-administered survey included questions adapted from the school-based studies conducted by the Centers for Disease Control and Prevention in the United States. The survey inquired about adolescents’ behaviors and attitudes toward driving, perceptions of school and family, and leisure time activities.

Results:

Nearly 40% of the students surveyed reported engaging in the risky driving behavior called Tafheet. Fifty-one percent of those who engage in dangerous activities also reported engaging in Tafheet. A higher proportion (70%) among those who believe Tafheet is a talent or a cool activity also engaged in Tafheet. Multivariate analyses indicate that students who are willing to engage in dangerous activities even when they are known to be dangerous (OR = 2.7; 95% CI = 1.55-4.72), those who think there is no harm in not wearing seat belts are at higher speeds (OR = 2.77; 95% CI = 1.24-6.21), and those who use a mobile telephone while driving are nearly three times (OR = 2.96; 95% CI = 1.41-6.23) at risk for engaging in Tafheet. Lack of respect towards traffic laws is also a risk factor.

Conclusion:

Our study unequivocally points to pro-attitudes and behavior including a daring personality, not wearing a seat belt and using a mobile telephone while driving are significant factors associated with risky driving activity. Our study calls for a strategic intervention plan to change the culture of risky driving through a structured and stringent driving curriculum in school settings. A curriculum of this nature is currently non-existent in the Kingdom of Saudi Arabia (KSA). Multilevel and multifaceted interventions may hold great promise in reducing unintended motor vehicle injuries and changing the culture as a whole.
Serum From Patients with Erectile Dysfunction and Vascular Risk Factors Triggered an Oxidative Stress-Dependent Mitochondrial Apoptotic Pathway in Ex Vivo Expanded Circulating Angiogenic Cells of Healthy Men
Authors: D'Andrea Settimio , Micillo Alessandro , Francavilla Felice , Di Emidio Giovanna , Tatone Carla , Francavilla Sandro , Barbonetti Arcangelo
Published: May 2016

Introduction

Serum from men with erectile dysfunction (ED) and vascular risk factors inhibits circulating mononuclear cells (MNCs) from expanding ex vivo and differentiating circulating angiogenic cells (CACs), which are putatively involved in the repair of endothelial damage.

Aim

To explore the involvement of apoptosis in the inhibition of CAC differentiation from MNCs of healthy men exerted by serum from men with ED and vascular risk factors.

Methods

MNCs from healthy men were cultured in serum from 10 healthy men (median age = 45 years, 25th–75th quartiles = 38.5–48.5) and from 14 patients (median age = 58.0 years, 25th–75th quartiles = 52.5–62.0). CACs were identified by the uptake of 1,1′-dioctadecyl-3,3,3′,3′-tetramethylindocarbocyanine–labeled acetylated low-density lipoprotein (DiLDL) and concomitant Ulex europaeus agglutinin I binding assessed by fluorescence microscopy.

Main Outcome Measures

Flow cytometric evaluation of mitochondrial membrane potential, assessed with 5,5′,6,6′-tetrachloro-1,1′,3,3′-tetraethyl-benimidazolyl carbocyanine iodide dye, and of activated caspase-8, -9, and -3 in DiLDL-positive cells.

Results

The number of CACs was significantly decreased by serum from patients compared with controls. This was associated with suppression of the mitochondrial membrane potential and activation of caspase-9 and -3 but not of caspase-8. This suggests an activation of the intrinsic (mitochondrial) pathway of apoptosis, whereas the death receptor activation of apoptosis was not involved. Activation of caspase-9 and -3 induced by serum from patients with ED was prevented by the exposure of MNCs to Trolox, a hydrophilic cell-permeable vitamin E analog with high antioxidant capacity.

Conclusion

An oxidative stress-dependent mitochondrial dysfunction was triggered in ex vivo expanded CACs of healthy men by serum from men with vascular risk factors and ED, the only clinical correlate for diffuse vascular disease. The activation of apoptosis and inhibition of CAC differentiation might generate a defective mechanism of vascular repair.
Endogenous growth theory and regional performance: The moderating effects of special economic zones
Authors: Pan Wei-Hwa , Ngo Xuan-Thang
Published: May 2016

Previous studies have explored regional performance from the perspective of endogenous growth theory. This empirical investigation is conducted on a panel dataset of 64 Vietnamese provinces and integrates moderated regression analysis. Statistically, the empirical results did not fully support the endogenous growth model in cases in which regional per capita income tended to converge across different regions, while improved foreign direct investment (FDI) inflow, capital investment, and degree of openness did have significant positive impacts on GDP growth. This study questions the validity of endogenous growth theory in the early stage of a less developed country. Furthermore, results indicate that internationalization activities positively affect regional performance for provinces that have established special economic zones (SEZs) through liberal state regulation.
Structural basis of the signalling through a bacterial membrane receptor HasR deciphered by an integrative approach
Authors: Wojtowicz Halina , Prochnicka-Chalufour Ada , de Amorim Gisele Cardoso , Roudenko Olga , Simenel Catherine , Malki Idir , Pehau-Arnaudet Gérard , Gubellini Francesca , Koutsioubas Alexandros , Pérez Javier , Delepelaire Philippe , Delepierre Muriel , Fronzes Rémi , Izadi-Pruneyre Nadia
Published: May 2016

Bacteria use diverse signalling pathways to adapt gene expression to external stimuli. In Gram-negative bacteria, the binding of scarce nutrients to membrane transporters triggers a signalling process that up-regulates the expression of genes of various functions, from uptake of nutrient to production of virulence factors. Although proteins involved in this process have been identified, signal transduction through this family of transporters is not well understood. In the present study, using an integrative approach (EM, SAXS, X-ray crystallography and NMR), we have studied the structure of the haem transporter HasR captured in two stages of the signalling process, i.e. before and after the arrival of signalling activators (haem and its carrier protein). We show for the first time that the HasR domain responsible for signal transfer: (i) is highly flexible in two stages of signalling; (ii) extends into the periplasm at approximately 70–90 Å (1 Å=0.1 nm) from the HasR β-barrel; and (iii) exhibits local conformational changes in response to the arrival of signalling activators. These features would favour the signal transfer from HasR to its cytoplasmic membrane partners.
Phase-resolved two-dimensional terahertz spectroscopy including off-resonant interactions beyond the χ(3) limit
Authors: Somma Carmine , Folpini Giulia , Reimann Klaus , Woerner Michael , Elsaesser Thomas
Published: May 2016

We present the first two-dimensional (2D) terahertz (THz) experiment with three phase-locked THz pulses and a fully phase-resolved detection of the nonlinearly emitted field by electrooptic sampling. In a prototype experiment we study the ultrafast dynamics of nonlinear two-phonon and two-photon interband coherences in the narrow-gap semiconductor InSb. Due to the extraordinarily large optical interband dipole of InSb the experiments were performed in the strongly nonperturbative regime of light-matter interaction allowing for impulsive off-resonant excitation of both two-phonon coherences and two-photon interband coherences, the ultrafast dynamics of which is experimentally observed as a function of the waiting time in the three-pulse 2D experiment. Our novel three-pulse 2D THz spectroscopy paves the way for the detailed investigation of nonlinear quantum coherences in solids and holds potential for an extension to other systems.
Electronic Transport Through N24B24 Molecular Junction
Authors: Yaghobi Mojtaba , Ramzanpour Mohammad Ali , Nyazian Mohammad Reza
Published: May 2016

We have investigated the electron transport properties of a N24B24 molecule coupled to two metallic contacts with a combination of GW approximation and the non-equilibrium Green's-function technique. The calculations indicate that the four and three resonant tunneling peaks are seen for the density of states (DOS) curves in the cases of single and multiple atomic contacts, respectively. The off state and negative differential resistance (NDR) effect are observed in the I-V characteristics of the N24B24 molecule. The NDR behavior is also observed in voltages of about ∓4.5, ∓4, ∓4.6, and ∓4.3 V for one, four, six, and eight atomic contacts. Also, the I-V characteristics of N24B24 are in off state at low voltages that is independent of the contact types. The current curves against the gate voltage depend on contact types and indicate that N24B24 molecule behaves as a semiconductor.
Preparation, Characterization and Photocatalytic Activity of Fe, La Co-doped Nanometer Titanium Dioxide Photocatalysts
Authors: Shi Zhong-liang , Guo Man , Wang Lin-jun , Yao Shu-hua
Published: May 2016

A series of photocatalysts of un-doped, single-doped and co-doped nanometer titanium dioxide (TiO2) have been successfully prepared by template method using Fe(NO3)3·9H2O, La(NO3)3·6H2O, and tetrabutyl titanate as precursors and glucan as template. Scanning electron microscopy, X-ray diffraction, and N2 adsorption-desorption measurement were employed to characterize the morphology, crystal structure and surface structure of the samples. The photo-absorbance of the obtained catalysts was measured by UV-Vis absorption spectroscopy, and the photocatalytic activities of the prepared samples under UV and visible light were estimated by measuring the degradation rate of methyl orange in an aqueous solution. The characterizations indicated that the prepared photocatalysts consisted of anatase phase and possessed high surface area of ca. 163–176 m2/g. It was shown that the Fe and La co-doped nano-TiO2 could be activated by visible light and could thus be used as an effective catalyst in photo-oxidation reactions. The synergistic effect of Fe and La co-doping played an important role in improving the photocatalytic activity. In addition, the possibility of cyclic usage of co-doped nano-TiO2 was also confirmed, the photocatalytic activity of codoped nano-TiO2 remained above 89.6% of the fresh sample after being used four times.
Response Ability to External Signal Enhanced by Biological Spatial Configuration in Coupled Hindmarsh-Rose Neural System
Authors: Huang Shou-fang , Zhang Ji-qian , Wang Mao-sheng
Published: May 2016

The effect of realistic topology configuration of intercellular connections on the response ability in coupled cell system is numerically investigated by using the Hindmarsh-Rose model. For the proper coupling intensity, we set the control parameter to be near the critical value, and the external stimulus is introduced to the first cell in coupled system. It is found that, on one hand, when the cells are coupled with some proper topological structures, the external stimulus could transmit through the system, and shows better response ability and higher sensitivity. On the other hand, the influence of topological configuration on the synchronous ability and selection effect of neural system are also discussed. Our results display that the topology of coupled system may play an important role in the process of signal propagation, which could help us to understand the coordinated performance of cells in tissue.
Fast Photodegradation of Malachite Green using Nano-ZnO on Ceramic MgAl Carbonate Layered Double Hydroxides Support
Authors: Yan Rui-qiang , Liu Gui-hua , Wang Qing-feng , Liu Wei , Song Chun-lin
Published: May 2016

The nanopowders of Mg-Al carbonate layered double hydroxides (MgAl-LDH) were prepared via coprecipitation process. ZnO nanoparticles were homogeneously coated on the ceramic MgAl-LDH surface. After calcination at 500 °C for 4 h, X-ray diffraction and scanning electron microscopy were employed to investigate the crystal structure and morphology, respectively. It was demonstrated that ZnO nanoparticles were successfully prepared on ceramic MgAl-LDH support. The obtained nano-ZnO photocatalyst showed a high photocatalytic degradation of malachite green. The enhanced photocatalytic property can be attributed to both high photocatalytic activity of ZnO and good adsorption behavior of ceramic MgAl-LDH, in which the flaky structure of MgAl-LDH plays an important role.
Crystallization Behavior and Properties of B-Doped ZnO Thin Films Prepared by Sol-Gel Method with Different Pyrolysis Temperatures
Authors: Wen Bin , Liu Chao-qian , Wang Nan , Wang Hua-lin , Liu Shi-min , Jiang Wei-wei , Ding Wan-yu , Fei Wei-dong , Chai Wei-ping
Published: May 2016

Boron-doped zinc oxide transparent (BZO) films were prepared by sol-gel method. The effect of pyrolysis temperature on the crystallization behavior and properties was systematically investigated. XRD patterns revealed that the BZO films had wurtzite structure with a preferential growth orientation along the c-axis. With the increase of pyrolysis temperature, the particle size and surface roughness of the BZO films increased, suggesting that pyrolysis temperature is the critical factor for determining the crystallization behavior of the BZO films. Moreover, the carrier concentration and the carrier mobility increased with increasing the pyrolysis temperature, and the mean transmittance for every film is over 90% in the visible range.
Confinement Induced Ordering in Fluid of Hard Ellipsoids
Authors: Miao Han , Ma Hong-ru
Published: May 2016

The ordering configurations of a fluid of anisotropic ellipsoids under the confinement of two apposing impenetrable walls are studied by Monte Carlo simulations. The excess adsorption of the fluid on the walls with respect to the aspect ratio has a maximum at the critical aspect ratio of 2.9 in high-density ellipsoid fluids, indicating an orientational ordering in the adjacent region of the walls, which is confirmed by probing into the density configurations and the orientational order parameter in the adjacent region of the walls for varying aspect ratios. In addition, the orientational order parameter in the bulk fluid at the same density is calculated, and it indicates an isotropic state as the bulk density is still below the bulk isotropic-to-nematic transition. Therefore, it can be concluded that the anisotropic ordering near the walls in the ellipsoid fluid that exhibits isotropic in the bulk is induced by the confinement effect of the walls.
Tunneling Electron Induced Fluorescence from Single Porphyrin Molecules Decoupled by Striped-Phase Octanethiol Self-assembled Monolayer
Authors: Kuang Yan-min , Yu Yun-jie , Luo Yang , Zhu Jia-zhe , Liao Yuan , Zhang Yang , Dong Zhen-chao
Published: May 2016

We investigate tunneling electron induced luminescence from isolated single porphyrin molecules that are decoupled by striped-phase self-assembled monolayer of octanethiol from the underneath Au(111) substrate. Intrinsic single-molecule electroluminescence has been realized by such decoupling at both bias polarities. The photon emission intensity acquired from the molecular lobe is found stronger than that from the molecular center. These results provide useful information on the understanding of electroluminescent behavior and mechanism in molecular tunnel junctions.
Electronic and Optical Properties of O-Terminated Armchair Graphene Nanoribbons
Authors: Lu Dao-bang , Luo Chang-geng , Song Yu-ling , Pan Qun-na , Pu Chun-ying
Published: May 2016

The structure, electromagnetic and optical properties of the O-terminated graphene nanoribbons with armchair edge are studied using first-principles theory. The results show that the O-terminated armchair edge are more stable than the H-terminated ribbons and show metallic character. Spin-polarized calculations reveal that the antiferromagnetic state are more stable than the ferromagnetic state. The energy band and density of states analyses show that the O-terminated armchair edge are antiferromagnetic semiconductors. Because of the terminated O atoms, the dielectric function has an evident red shift and the first peak is the strongest with its main contribution derived from the highest valence band. The peaks of the dielectric function, reflection, absorption, energy loss are related to the transition of electrons. Our results suggest that the O-terminated graphene nanoribbons have potential applications in nanoelectronics, opto-electric devices.
Synthesis and Surface Activity of Heterogemini Imidazolium Surfactants
Authors: Zhao Xiao-hui , Ye Zhi-wen
Published: May 2016

A series of heterogemini imidazolium surfactants with two-methylene spacer groups ([Cm-2-Cnim]Br2, m, n=8, 10, 12, 14, 16; m≠n) have been synthesized and characterized by 1H NMR and ESI-MS spectroscopy. The effects of various reaction parameters, including stoichiometry, reaction temperature and time, were investigated. In addition, the surface activity study about heterogemini imidazolium surfactants was carried out and the influences of dissymmetric degree on the surface properties were also discussed.
Ab initio Study on Formation Mechanism of Spiro-Si-Heterocyclic Ring Compound Involving Ge from H2Ge=Si: and Formaldehyde
Authors: Lu Xiu-hui , Wang Dang-sheng , Ming Jing-jing
Published: May 2016

H2Ge=Si: and its derivatives (X2Ge=Si:, X=H, Me, F, Cl, Br, Ph, Ar, …) are new species. Its cycloaddition reactions are new area for the study of silylene chemistry. The cycloaddition reaction mechanism of singlet H2Ge=Si: and formaldehyde has been investigated with the MP2/aug-cc-pVDZ method. From the potential energy profile, it could be predicted that the reaction has one dominant reaction pathway. The reaction rule is that two reactants firstly form a four-membered Ge-heterocyclic ring silylene through the [2+2] cycloaddition reaction. Because of the 3p unoccupied orbital of Si: atom in the four-membered Ge-heterocyclic ring silylene and the π orbital of formaldehyde forming a π→p donor-acceptor bond, the four-membered Ge-heterocyclic ring silylene further combines with formaldehyde to form an intermediate. Because the Si: atom in the intermediate undergoes sp3 hybridization after transition state, then the intermediate isomerizes to a spiro-Si-heterocyclic ring compound involving Ge via a transition state. The result indicates the laws of cycloaddition reaction between H2Ge=Si: or its derivatives (X2Ge=Si:, X=H, Me, F, Cl, Br, Ph, Ar, …) and asymmetric π-bonded compounds are significant for the synthesis of small-ring involving Si and Ge and spiro-Si-heterocyclic ring compounds involving Ge.
First Principles Investigation of Electronic Property and High Pressure Phase Stability of SmN
Authors: Hao Ai-min , Bai Jing , Luo Shao-hua , Qi Xi-wei
Published: May 2016

An investigation of electronic property and high pressure phase stability of SmN has been conducted using first principles calculations based on density functional theory. The electronic properties of SmN show a striking feature of a half metal, the majority-spin electrons are metallic and the minority-spin electrons are semiconducting. It was found that SmN undergoes a pressure-induced phase transition from NaCl-type (B1) to CsCl-type structure (B2) at 117 GPa. The elastic constants of SmN satisfy Born conditions at ambient pressure, indicating that B1 phase of SmN is mechanically stable at 0 GPa. The result of phonon spectra shows that B1 structure is dynamically stable at ambient pressure, which agrees with the conclusion derived from the elastic constants.
Dynamics of Tripartite Entanglement and Intramolecular Energy in Symmetric Trimer Molecule
Authors: Yi Di , Jian Xing-lin , Hou Xi-wen
Published: May 2016

The dynamics of tripartite entanglement and intramolecular energy for one harmonic- and two anharmonic-vibrational modes in a symmetric trimer molecule is studied for various initial states, where the entanglement is quantified in terms of concurrence and the interacting energy among three modes is calculated to establish a link between entanglement and energy. It is shown that the concurrence and the interacting energy behave dominantly positive correlation for the localized state in the anharmonic-vibrational mode, while they are dominantly anti-correlated for the localized state in the harmonic-vibrational mode. The relation between bipartite entanglement and the energy in a subsystem is discussed as well. Those are useful for quantum computing and quantum information in high dimensional states prepared in polyatomic molecules.
Performances of Five Representative Force Fields on Gaseous Amino Acids with Different Termini
Authors: Chen Xin , Lin Zi-jing
Published: May 2016

There is a growing interest in the study of structures and properties of biomolecules in gas phase. Applications of force fields are highly desirable for the computational efficiency of the gas phase study. To help the selection of force fields, the performances of five representative force fields for gaseous neutral, protonated, deprotonated and capped amino acids are systematically examined and compared. The tested properties include relative conformational energies, energy differences between cis and trans structures, the number and strength of predicted hydrogen bonds, and the quality of the optimized structures. The results of BHandHLYP/6-311++G(d,p) are used as the references. GROMOS53A6 and ENCADS are found to perform poorly for gaseous biomolecules, while the performance of AMBER99SB, CHARMM27 and OPLSAA/L are comparable when applicable. Considering the general availability of the force field parameters, CHARMM27 is the most recommended, followed by OPLSAA/L, for the study of biomolecules in gas phase.
Ion Product of Pure Water Characterized by Physics-Based Water Model
Authors: Jie Bin-bin , Sah Chihtang
Published: May 2016

Pure water has been characterized for nearly a century, by its dissociation into hydronium (H3O)1+ and hydroxide (HO)1− ions. As a chemical equilibrium reaction, the equilibrium constant, known as the ion product or the product of the equilibrium concentration of the two ion species, has been extensively measured by chemists over the liquid water temperature and pressure range. The experimental data have been nonlinear least-squares fitted to chemical thermodynamic-based equilibrium equations, which have been accepted as the industrial standard for 35 years. In this study, a new and statistical-physics-based water ion product equation is presented, in which, the ions are the positively charged protons and the negatively charged proton-holes or prohols. Nonlinear least squares fits of our equation to the experimental data in the 0–100 °C pure liquid water range, give a factor of two better precision than the 35-year industrial standard.
Structural and Magnetic Properties of Chemically Synthesized Pd-Modified NiFe2O4 Nanoparticles
Authors: Atiq Shahid , Ramay Shahid M. , Mahmood Asif , Riaz Saira , Naseem Shahzad
Published: May 2016

Magnetic nanoparticles of NiFe2O4-Pd composites have been synthesized using a simple, low cost, sol-gel auto-combustion method. As-prepared samples were sintered at 800 °C for 6 h in order to develop the crystalline phase. X-ray diffraction confirmed the spinel structure of the ferrite samples. Structural morphology and size of the nanoparticles were evaluated using a field emission scanning electron microscope. Magnetic hysteresis loops were obtained at 300 and 100 K using a physical properties measurement system. The value of saturation magnetization was observed to decrease at the temperatures with the increase of Pd contents up to 5% but then a sudden rise in saturation magnetization was observed for the addition of 10% Pd in NiFe2O4.
Substituent Effects on Reduction Potentials of Meta-substituted and Para-substituted Benzylideneanilines
Authors: Wang Lin-yan , Cao Chao-tun , Cao Chen-zhong
Published: May 2016

Effects of meta-substituent of 3,4′/4,3′/3,3′-substituted benzylideneanilines (XBAYs) on the electrochemical reduction potentials (E(Red)) were investigated, in which 49 samples of target compounds were synthesized, and their reduction potentials were measured by cyclic voltammetry. The substituent effects on the E(Red) of target compounds were analyzed and an optimality equation with four parameters (Hammett constant σ of X, Hammett constant σ of Y, excited-state substituent constant σCCex of X, and the substituent specific cross-interaction effect ΔσCCex 2 between X and Y) was obtained. The results show that the factors affecting the E(Red) of 3,4′/4,3′/3,3′-substituted XBAYs are different from those of 4,4′-substituted XBAYs. For 3,4′/4,3′/3,3′-substituted XBAYs, σ(X) and σ(Y) must be employed, and the contribution of ΔσCCex 2 is important and not negligible. Compared with 4,4′-substituted XBAYs, X group contributes less to 3,4′/4,3′/3,3′-substituted XBAYs, while Y group contributes more to them. Additionally, it was observed that either para-substituted XBAYs or meta-substituted XBAYs, the substituent effects of X are larger than those of Y on the E(Red) of substituted XBAYs.
Spiritual leadership and organizational citizenship behavior: relationship with Confucian values
Authors: Hunsaker William D.
Published: May 2016

Spiritual leadership is achieving universal recognition as an effective tool to measure the interactive relationship between leaders, followers, and organizational performance. However, the construct needs robust investigation of the relationship to positive organizational behaviors in diverse country contexts. This study examined the relationship of spiritual leadership on organizational citizenship behavior (OCB) through the well-being of workers and the impact of Korean Confucian values with results fully supporting the relationship of employee well-being on OCBs. Furthermore, Confucian values, operationalized as Confucian mindset, also influenced and partially mediated the relationship between spiritual leadership and OCBs. The results of this study lend support to the enabling influence of spiritual leadership on positive organizational behavior such as OCB. Moreover, the study increases our understanding of the emic manifestations, like Confucian values, of leadership theory in generalizing western leadership theories to outside cultures.
Spirituality and Ubuntu as the foundation for building African institutions, organizations and leaders
Authors: Mamman Aminu , Zakaria Hamza B.
Published: May 2016

It is widely argued that institutions and organizations are the building blocks of modern societies. However, African nations are characterized by an institutional void and ineffective organizations. In fact, even the effectiveness of informal institutions such as customs and traditions is now debatable. Therefore, this paper sets out to provide a novel approach for building effective organizations, leaders and people based on the foundation of spirituality and the African philosophy of Ubuntu. We coupled the concepts of spirituality and Ubuntu and advanced a framework and techniques to guide the development of African organizations and its people. We have provided theoretical and practical rationale for the use of spirituality and Ubuntu to augment the Western-based modern approach to managing organizations and their people.
Spatiotemporal strategies that facilitate recruitment in a habitat specialist tree species
Authors: Krishna Shivani , Somanathan Hema
Published: May 2016

Our understanding of processes underlying plant recruitment emerges from species and habitats that are widely distributed at regional and global scales. However, the applicability of dispersal-recruitment models and the role of dispersal limitation versus microsite limitation have not been examined for specialized habitats. In patchy, freshwater Myristica swamp forests (Western Ghats, India), we examine the roles of primary seed dispersal, secondary seed removal and microsite suitability for the establishment of a swamp specialist tree, Myristica fatua . We estimated primary seed shadows, performed secondary removal experiments and enumerated recruits in swamp sites. Steady-state fruiting was observed with the extended production (>7 months) of small numbers of fruits. Frugivores dropped most of the large and heavy seeds under parent crowns, while a few seeds were transported over short distances by hornbills. Seed placement experiments indicated that removal, germination and establishment were similar within swamp microsites, while seeds failed to survive in matrix habitats surrounding the swamp. Crabs, which were major secondary removers of M. fatua , did not alter the initial seed dispersal patterns substantially, which led to the retention of seeds within the swamp. Distribution of saplings and adults from previous seasons also suggest that dispersal-recruitment dynamics in the swamp specialist M. fatua did not strictly follow predictions of Janzen-Connell model while abiotic effects were significant. Large seeds, steady-state fruiting and small crop sizes may be significant selective forces facilitating escape from density and distance-dependent effects in space and time in specialist plant species such as M. fatua .
Calculating and scoring high quality multiple flexible protein structure alignments
Authors: Ritchie David W.
Published: May 2016

Motivation: Calculating multiple protein structure alignments (MSAs) is important for understanding functional and evolutionary relationships between protein families, and for modeling protein structures by homology. While incorporating backbone flexibility promises to circumvent many of the limitations of rigid MSA algorithms, very few flexible MSA algorithms exist today. This article describes several novel improvements to the Kpax algorithm which allow high quality flexible MSAs to be calculated. This article also introduces a new Gaussian-based MSA quality measure called ‘M-score’, which circumvents the pitfalls of RMSD-based quality measures.

Results: As well as calculating flexible MSAs, the new version of Kpax can also score MSAs from other aligners and from previously aligned reference datasets. Results are presented for a large-scale evaluation of the Homstrad, SABmark and SISY benchmark sets using Kpax and Matt as examples of state-of-the-art flexible aligners and 3DCOMB as an example of a state-of-the-art rigid aligner. These results demonstrate the utility of the M-score as a measure of MSA quality and show that high quality MSAs may be achieved when structural flexibility is properly taken into account.

Availability and Implementation: Kpax 5.0 may be downloaded for academic use at http://kpax.loria.fr/ .

Contact:  dave.ritchie@inria.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
PRESS: PRotEin S-Sulfenylation server
Authors: Sakka Marianna , Tzortzis Grigorios , Mantzaris Michalis D. , Bekas Nick , Kellici Tahsin F. , Likas Aristidis , Galaris Dimitrios , Gerothanassis Ioannis P. , Tzakos Andreas G.
Published: May 2016

Motivation: Transient S-sulfenylation of cysteine thiols mediated by reactive oxygen species plays a critical role in pathology, physiology and cell signaling. Therefore, discovery of new S-sulfenylated sites in proteins is of great importance towards understanding how protein function is regulated upon redox conditions.

Results: We developed PRESS (PRotEin S-Sulfenylation) web server, a server which can effectively predict the cysteine thiols of a protein that could undergo S-sulfenylation under redox conditions. We envisage that this server will boost and facilitate the discovery of new and currently unknown functions of proteins triggered upon redox conditions, signal regulation and transduction, thus uncovering the role of S-sulfenylation in human health and disease.

Availability and implementation: The PRESS web server is freely available at http://press-sulfenylation.cse.uoi.gr/

Contacts:  agtzakos@gmail.com or gtzortzi@cs.uoi.gr

Supplementary information:  Supplementary data are available at Bioinformatics online.
A simple yet accurate correction for winner's curse can predict signals discovered in much larger genome scans
Authors: Bigdeli T. Bernard , Lee Donghyung , Webb Bradley Todd , Riley Brien P. , Vladimirov Vladimir I. , Fanous Ayman H. , Kendler Kenneth S. , Bacanu Silviu-Alin
Published: May 2016

Motivation: For genetic studies, statistically significant variants explain far less trait variance than ‘sub-threshold’ association signals. To dimension follow-up studies, researchers need to accurately estimate ‘true’ effect sizes at each SNP, e.g. the true mean of odds ratios (ORs)/regression coefficients (RRs) or Z -score noncentralities. Naïve estimates of effect sizes incur winner’s curse biases, which are reduced only by laborious winner’s curse adjustments (WCAs). Given that Z -scores estimates can be theoretically translated on other scales, we propose a simple method to compute WCA for Z -scores, i.e. their true means/noncentralities.

Results: WCA of Z -scores shrinks these towards zero while, on P -value scale, multiple testing adjustment (MTA) shrinks P -values toward one, which corresponds to the zero Z -score value. Thus, WCA on Z -scores scale is a proxy for MTA on P -value scale. Therefore, to estimate Z -score noncentralities for all SNPs in genome scans, we propose F DR I nverse Q uantile T ransformation (FIQT). It (i) performs the simpler MTA of P -values using FDR and (ii) obtains noncentralities by back-transforming MTA P -values on Z -score scale. When compared to competitors, realistic simulations suggest that FIQT is more (i) accurate and (ii) computationally efficient by orders of magnitude. Practical application of FIQT to Psychiatric Genetic Consortium schizophrenia cohort predicts a non-trivial fraction of sub-threshold signals which become significant in much larger supersamples.

Conclusions : FIQT is a simple, yet accurate, WCA method for Z -scores (and ORs/RRs, via simple transformations).

Availability and Implementation: A 10 lines R function implementation is available at https://github.com/bacanusa/FIQT .

Contact:  sabacanu@vcu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
seqlm: an MDL based method for identifying differentially methylated regions in high density methylation array data
Authors: Kolde Raivo , Märtens Kaspar , Lokk Kaie , Laur Sven , Vilo Jaak
Published: May 2016

Motivation : One of the main goals of large scale methylation studies is to detect differentially methylated loci. One way is to approach this problem sitewise, i.e. to find differentially methylated positions (DMPs). However, it has been shown that methylation is regulated in longer genomic regions. So it is more desirable to identify differentially methylated regions (DMRs) instead of DMPs. The new high coverage arrays, like Illuminas 450k platform, make it possible at a reasonable cost. Few tools exist for DMR identification from this type of data, but there is no standard approach.

Results : We propose a novel method for DMR identification that detects the region boundaries according to the minimum description length (MDL) principle, essentially solving the problem of model selection. The significance of the regions is established using linear mixed models. Using both simulated and large publicly available methylation datasets, we compare seqlm performance to alternative approaches. We demonstrate that it is both more sensitive and specific than competing methods. This is achieved with minimal parameter tuning and, surprisingly, quickest running time of all the tried methods. Finally, we show that the regional differential methylation patterns identified on sparse array data are confirmed by higher resolution sequencing approaches.

Availability and Implementation : The methods have been implemented in R package seqlm that is available through Github: https://github.com/raivokolde/seqlm

Contact:  rkolde@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
The impact of alternative rebuilding strategies to rebuild overfished stocks
Authors: Wetzel Chantel R. , Punt André E. ,   Handling editor: Emory Anderson
Published: May 2016

Ending overfishing and rebuilding fish stocks to levels that provide for optimum sustainable yield is a concern for fisheries management worldwide. In the United States, fisheries managers are legally mandated to end overfishing and to implement rebuilding plans for fish stocks that fall below minimum stock size thresholds. Rebuilding plans should lead to recovery to target stock sizes within 10 years, except in situations where the life history of the stock or environmental conditions dictate otherwise. Federally managed groundfish species along the US West Coast have diverse life histories where some are able to rebuild quickly from overfished status, while others, specifically rockfish (Sebastes spp.), may require decades for rebuilding. A management strategy evaluation which assumed limited estimation error was conducted to evaluate the performance of alternative strategies for rebuilding overfished stocks for these alternative US West Coast life histories. Generally, the results highlight the trade-off between the reduction of catches during rebuilding vs. the length of rebuilding. The most precautionary rebuilding plans requiring the greatest harvest reduction resulted in higher average catches over the entire projection period compared with strategies that required a longer rebuilding period with less of a reduction in rebuilding catch. Attempting to maintain a 50% probability of rebuilding was the poorest performing rebuilding strategy for all life histories, resulting in a large number of changes to the rebuilding plan, increased frequency of failing to meet rebuilding targets, and higher variation in catch. The rebuilding plans that implemented a higher initial rebuilding probability (≥60%) for determining rebuilding fishing mortality and targets generally resulted in fewer changes to the rebuilding plans and rebuilt by the target rebuilding year, particularly for stocks with the longer rebuilding plans (e.g. rockfishes).