bluuebunny/crossref_metadata_2025 huggingface dataset:
Longitudinal evaluation, acceptability and long-term retention of knowledge on a horizontally integrated organic and functional systems course
Authors: Palha Joana Almeida , Almeida Armando , Correia-Pinto Jorge , Costa Manuel João , Ferreira Maria Amélia , Sousa Nuno
Published: July 2015

Undergraduate medical education is moving from traditional disciplinary basic science courses into more integrated curricula. Integration models based on organ systems originated in the 1950s, but few longitudinal studies have evaluated their effectiveness. This article outlines the development and implementation of the Organic and Functional Systems (OFS) courses at the University of Minho in Portugal, using evidence collected over 10 years. It describes the organization of content, student academic performance and acceptability of the courses, the evaluation of preparedness for future courses and the retention of knowledge on basic sciences. Students consistently rated the OFS courses highly. Physician tutors in subsequent clinical attachments considered that students were appropriately prepared. Performance in the International Foundations of Medicine examination of a self-selected sample of students revealed similar performances in basic science items after the last OFS course and 4 years later, at the moment of graduation. In conclusion, the organizational and pedagogical approaches of the OFS courses achieve high acceptability by students and result in positive outcomes in terms of preparedness for subsequent training and long-term retention of basic science knowledge.
Impact of ToxigenicClostridium difficileColonization on the Risk of SubsequentC. difficileInfection in Intensive Care Unit Patients
Authors: Tschudin-Sutter Sarah , Carroll Karen C. , Tamma Pranita D. , Sudekum Madeleine L. , Frei Reno , Widmer Andreas F. , Ellis Brandon C. , Bartlett John , Perl Trish M.
Published: July 2015

BACKGROUND

Clostridium difficileinfection (CDI) in hospitalized patients is generally attributed to the current stay, but recent studies reveal highC. difficilecolonization rates on admission.

OBJECTIVE

To determine the rate of colonization with toxigenicC. difficileamong intensive care unit patients upon admission as well as acquired during hospitalization, and the risk of subsequent CDI.

METHODS

Prospective cohort study from April 15 through July 8, 2013. Adults admitted to an intensive care unit within 48 hours of admission to the Johns Hopkins Hospital, Baltimore, Maryland, were screened for colonization with toxigenicC. difficile. The primary outcome was risk of developing CDI.

RESULTS

Among 542 patients, 17 (3.1%) were colonized with toxigenicC. difficileon admission and an additional 3 patients were found to be colonized during hospitalization. Both colonization with toxigenicC. difficileon admission and colonization during hospitalization were associated with an increased risk for development of CDI (relative risk, 10.29 [95% CI, 2.24–47.40],P=.003; and 15.66 [4.01–61.08],P<.001, respectively). Using multivariable analysis, colonization on admission and colonization during hospitalization were independent predictors of CDI (relative risk, 8.62 [95% CI, 1.48–50.25],P=.017; and 10.93 [1.49–80.20],P=.019, respectively), while adjusting for potential confounders.

CONCLUSIONS

In intensive care unit patients, colonization with toxigenicC. difficileis an independent risk factor for development of subsequent CDI. Further studies are needed to identify populations with higher toxigenicC. difficilecolonization rates possibly benefiting from screening or avoidance of agents known to promote CDI.

Infect. Control Hosp. Epidemiol.2015;36(11):1324–1329
Stochastic analysis of steady seepage underneath a water-retaining wall through highly anisotropic porous media
Authors: Severino G. , De Bartolo S.
Published: July 2015

Steady seepage is determined by a head drop upstream/downstream of a water-retaining wall. Due to its erratic variations, hydraulic log-conductivity$Y=\ln K$is modelled as a stationary random space function (RSF). We deal with a highly anisotropic porous formation, i.e. an axisymmetric medium where the horizontal correlation integral scale of$Y$is much larger than the vertical one. The goal of computing the resulting flow field within a stochastic framework is complicated by non-uniformity of the mean flow. Simple (closed-form) expressions for the correlation functions of the flow variables as well as the mean head are derived. We use these results to quantify the impact of spatial variability of$Y$upon the probability that the exit volumetric flow rate downstream of the wall is greater than that obtained by regarding the formation as homogeneous (with constant hydraulic conductivity). In particular, we show that the spatial variability of$Y$may lead to predictions (and consequently to design choices) which significantly differ from those achieved by regarding the porous formation as homogeneous.
Triadic resonances in precessing rapidly rotating cylinder flows
Authors: Albrecht T. , Blackburn H. M. , Lopez J. M. , Manasseh R. , Meunier P.
Published: July 2015

Direct numerical simulations of flows in cylinders subjected to both rapid rotation and axial precession are presented and analysed in the context of a stability theory based on the triadic resonance of Kelvin modes. For a case that was chosen to provide a finely tuned resonant instability with a small nutation angle, the simulations are in good agreement with the theory and previous experiments in terms of mode shapes and dynamics, including long-time-scale regularization of the flow and recurrent collapses. Cases not tuned to the most unstable triad, but with the nutation angle still small, are also in quite good agreement with theoretical predictions, showing that the presence of viscosity makes the physics of the triadic-resonance model robust to detuning. Finally, for a case with $45^{\circ }$ nutation angle for which it has been suggested that resonance does not occur, the simulations show that a slowly growing triadic resonance predicted by theory is in fact observed if sufficient evolution time is allowed.
Knowledge sharing success and resistance in an engineering department: A case study
Authors: Gardiner Claire M
Published: July 2015

The centrality of knowledge sharing to organizations’ sustainability has been established. This research explores and illustrates the influences for individual professionals and paraprofessionals – specifically civil engineers and design drafters – to share their deep, personally constructed knowledge, in a public sector provider of railways infrastructure. It investigates the extent to which: (i) knowledge sharing will be positively influenced by the professional identity, values and knowledge culture to achieve organizational and project goals; and (ii) sharing of deep personal expertise will be influenced by the quality of relational capital among individuals and individual perspectives. It finds that knowledge sharing develops within frameworks established through the alignment among sector, profession and organization values. However, individual behavior is found to be most strongly influenced by the presence and quality of relational capital and individuals’ personal perspectives.
Modeling workplace contact networks: The effects of organizational structure, architecture, and reporting errors on epidemic predictions
Authors: POTTER GAIL E. , SMIESZEK TIMO , SAILER KERSTIN
Published: July 2015

Face-to-face social contacts are potentially important transmission routes for acute respiratory infections, and understanding the contact network can improve our ability to predict, contain, and control epidemics. Although workplaces are important settings for infectious disease transmission, few studies have collected workplace contact data and estimated workplace contact networks. We use contact diaries, architectural distance measures, and institutional structures to estimate social contact networks within a Swiss research institute. Some contact reports were inconsistent, indicating reporting errors. We adjust for this with a latent variable model, jointly estimating the true (unobserved) network of contacts and duration-specific reporting probabilities. We find that contact probability decreases with distance, and that research group membership, role, and shared projects are strongly predictive of contact patterns. Estimated reporting probabilities were low only for 0–5 min contacts. Adjusting for reporting error changed the estimate of the duration distribution, but did not change the estimates of covariate effects and had little effect on epidemic predictions. Our epidemic simulation study indicates that inclusion of network structure based on architectural and organizational structure data can improve the accuracy of epidemic forecasting models.
Reconstructing the Malaysian 370 Flight Trajectory by Optimal Search
Authors: Pleter Octavian Thor , Constantinescu Cristian Emil , Jakab Barna Istvan
Published: July 2015

In the aftermath of the disappearance of the Malaysian 370 (MH370) flight in March 2014, new positioning methods were employed to establish the search area. In the absence of all other positioning technologies (Transponder, Radio communications, Radar), these innovative methods are based on the handshake signals between an INMARSAT satellite and the satellite transceiver on board the aircraft. The log of these signals was made public in order for the scientific community to engage in solving the mystery of the MH370 trajectory. The log indicates the delay between the interrogation and response signals, as well as the relative velocity indications, based on the shift of the carrier frequency due to the Doppler-Fizeau effect. This paper puts forward an original, independent and accurate positioning method and allows the calculation of the MH370 trajectory considering the wind vector field that day, the accurate satellite orbit and an accurate model of the Earth (the WGS-84 ellipsoid). The results were compared to other results published, indicating a different final position of the aircraft from the locations of the published search area.
Some Realism About New Legal Realism: What's New, What's Legal, What's Real?
Authors: AUGSBERG INO
Published: July 2015

Current endeavours to develop a ‘realistic’ concept of international law should take into account that there is not only one reality. It does not suffice to admit that reality can be perceived from different angles. Rather, a realistic account of modern society has to acknowledge that we can no longer speak of the ‘world’ or ‘reality’ as a singular entity. Perspectives matter; they construct their own, distinct objects of cognition. A ‘New Legal Realism’ is deliberately new, legal, and realistic only insofar as it is conceived as an understanding of how (international) law creates its own realities.
Voltage and Dopant Concentration Measurements of Semiconductors using a Band-Pass Toroidal Energy Analyzer Inside a Scanning Electron Microscope
Authors: Srinivasan Avinash , Khursheed Anjam
Published: July 2015

This paper presents experimental results obtained from a scanning electron microscope (SEM) second-order focusing toroidal electron energy analyzer attachment. The results demonstrate that the analyzer can be used to obtain high signal-to-noise voltage and dopant concentration measurements on semiconductors in the presence of different electric field conditions at the sample. The experimentally calculated relative error of measurement typically varies from 31 to 63, corresponding to secondary electron (SE) signal mean shifts of 9–18 mV. The millivolt accuracy of these results is over one order of magnitude better than earlier quantitative dopant concentration measurements made by a retarding field analyzer.
Phylogenetic analysis of wheat cultivars in Kazakhstan based on the wheat 90 K single nucleotide polymorphism array
Authors: Turuspekov Yerlan , Plieske Joerg , Ganal Martin , Akhunov Eduard , Abugalieva Saule
Published: July 2015

The recent introduction of Illumina single nucleotide polymorphism (SNP) arrays is an important step towards comprehensive genome-wide studies of genetic diversity in wheat. In this study, 90 cultivars of hexaploid spring wheat growing in Kazakhstan were genotyped using the high-density wheat 90 K Illumina SNP array. The analysis allowed the identification of 30,288 polymorphic SNPs. A subset of 3541 high-quality SNPs were used for a comparison of 690 wheat accessions representing landraces and varieties, including those from Asia, Australia, Canada, Europe, Kazakhstan, USA and other parts of the world. Phylogenetic analysis showed a clear separation of wheat cultivars according to their geographic origin. In the phylogenetic tree, accessions from Kazakhstan and the USA formed two neighbouring clusters with a common node, and they were distinct from accessions from other regions of the world, including Europe. The results provide important new insights into the genetic relationships between diverse wheat accessions.
Psychometric validation of the Italian version of the Reported and Intended Behaviour Scale (RIBS)
Authors: Pingani L. , Evans-Lacko S. , Luciano M. , Del Vecchio V. , Ferrari S. , Sampogna G. , Croci I. , Del Fatto T. , Rigatelli M. , Fiorillo A.
Published: July 2015

Background.

Many instruments have been developed and validated to assess the stigma associated with mental disorders and its various domains across different populations. To our knowledge, the Reported and Intended Behaviour Scale (RIBS) is the only validated questionnaire to analyse the presence of reported and intended stigmatising/discriminatory behaviours towards people with mental health problems in the general population. The aims of the study presented herein are to translate and validate the RIBS in Italian language and to adapt it to the Italian socio-cultural background (RIBS-I).

Method.

The RIBS considers reported and intended behaviours across four different domains: (1) living with, (2) working with, (3) living nearby and (4) continuing a relationship with someone with a mental health problem. The validation process included four phases: (1) translation/back translation of the questionnaire from English to Italian and vice versa; (2,3) face validity and reliability of RIBS-I; (4) description of model fit through confirmatory factor analysis. The questionnaire was administered to a sample of the general public via distribution in public places such as shopping centres, markets, squares, cinemas and other gathering places. Questionnaires were administered by trained mental health professionals.

Results.

A total of 447 lay respondents were recruited. The mean age was 38.08 (s.d. = ±14.74) years. Fifty-seven per cent of the sample (n = 257) were female. The Cronbach alpha of RIBS-I was 0.83. All indices of model fit were above the reference values: Goodness of Fit Index (GFI) = 0.987 (GFI > 0.9); Adjusted Goodness of Fit Index (AGFI) = 0.975 (AGFI > 0.9); Comparative Fit Index (CFI) = 0.994 (CFI > 0.9); and Root-Mean-Square Error of Approximation (RMSEA) = 0.023 (RMSEA < 0.05). The χ2 = 23.60 (df = 19; p = 0.21) and χ2/df = 1.24 supported the model.

Conclusions.

The RIBS-I demonstrated good psychometric properties and it can be considered a useful tool to: (1) assess stigmatising (actual or potential) behaviours in the general population; (2) test the efficacy of anti-stigma campaigns and actions; (3) design further studies to better understand the relationship between the three different components of stigmatisation: knowledge, attitudes and behaviours.
Actin nucleation by WH2 domains at the autophagosome
Authors: Coutts Amanda S. , La Thangue Nicholas B.
Published: July 2015

Autophagy is a catabolic process whereby cytosolic components and organelles are degraded to recycle key cellular materials. It is a constitutive process required for proper tissue homoeostasis but can be rapidly regulated by a variety of stimuli (for example, nutrient starvation and chemotherapeutic agents). JMY is a DNA damage-responsive p53 cofactor and actin nucleator important for cell survival and motility. Here we show that JMY regulates autophagy through its actin nucleation activity. JMY contains an LC3-interacting region, which is necessary to target JMY to the autophagosome where it enhances the autophagy maturation process. In autophagosomes, the integrity of the WH2 domains allows JMY to promote actin nucleation, which is required for efficient autophagosome formation. Thus our results establish a direct role for actin nucleation mediated by WH2 domain proteins that reside at the autophagosome.
A Model based Survey of Colour Deconvolution in Diagnostic Brightfield Microscopy: Error Estimation and Spectral Consideration
Authors: Haub Peter , Meckel Tobias
Published: July 2015

Colour deconvolution is a method used in diagnostic brightfield microscopy to transform colour images of multiple stained biological samples into images representing the stain concentrations. It is applied by decomposing the absorbance values of stain mixtures into absorbance values of single stains. The method assumes a linear relation between stain concentration and absorbance, which is only valid under monochromatic conditions. Diagnostic applications, in turn, are often performed under polychromatic conditions, for which an accurate deconvolution result cannot be achieved. To show this, we establish a mathematical model to calculate non-monochromatic absorbance values based on imaging equipment typically used in histology and use this simulated data as the ground truth to evaluate the accuracy of colour deconvolution. We show the non-linear characteristics of the absorbance formation and demonstrate how it leads to significant deconvolution errors. In particular, our calculations reveal that polychromatic illumination causes 10-times higher deconvolution errors than sequential monochromatic LED illumination. In conclusion, our model can be used for a quantitative assessment of system components - and also to assess and compare colour deconvolution methods.
Identification of a novel lymphoid population in the murine epidermis
Authors: Almeida Francisca F. , Tenno Mari , Brzostek Joanna , Li Jackson LiangYao , Allies Gabriele , Hoeffel Guillaume , See Peter , Ng Lai Guan , Fehling Hans Jörg , Gascoigne Nicholas R. J. , Taniuchi Ichiro , Ginhoux Florent
Published: July 2015

T cell progenitors are known to arise from the foetal liver in embryos and the bone marrow in adults; however different studies have shown that a pool of T cell progenitors may also exist in the periphery. Here, we identified a lymphoid population resembling peripheral T cell progenitors which transiently seed the epidermis during late embryogenesis in both wild-type and T cell-deficient mice. We named these cells ELCs (Epidermal Lymphoid Cells). ELCs expressed Thy1 and CD2, but lacked CD3 and TCRαβ/γδ at their surface, reminiscent of the phenotype of extra- or intra- thymic T cell progenitors. Similarly to Dendritic Epidermal T Cells (DETCs), ELCs were radioresistant and capable of self-renewal. However, despite their progenitor-like phenotype and expression of T cell lineage markers within the population, ELCs did not differentiate into conventional T cells or DETCs in in vitro, ex vivo or in vivo differentiation assays. Finally, we show that ELC expressed NK markers and secreted IFN-γ upon stimulation. Therefore we report the discovery of a unique population of lymphoid cells within the murine epidermis that appears related to NK cells with as-yet-unidentified functions.
Selective Generation of Dopaminergic Precursors from Mouse Fibroblasts by Direct Lineage Conversion
Authors: Tian Changhai , Li Yuju , Huang Yunlong , Wang Yongxiang , Chen Dapeng , Liu Jinxu , Deng Xiaobei , Sun Lijun , Anderson Kristi , Qi Xinrui , Li Yulong , Lee Mosley R. , Chen Xiangmei , Huang Jian , Zheng Jialin C.
Published: July 2015

Degeneration of midbrain dopaminergic (DA) neurons is a key pathological event of Parkinson’s disease (PD). Limited adult dopaminergic neurogenesis has led to novel therapeutic strategies such as transplantation of dopaminergic precursors (DPs). However, this strategy is currently restrained by a lack of cell source, the tendency for the DPs to become a glial-restricted state and the tumor formation after transplantation. Here, we demonstrate the direct conversion of mouse fibroblasts into induced DPs (iDPs) by ectopic expression of Brn2, Sox2 and Foxa2. Besides expression with neural progenitor markers and midbrain genes including Corin, Otx2 and Lmx1a, the iDPs were restricted to dopaminergic neuronal lineage upon differentiation. After transplantation into MPTP-lesioned mice, iDPs differentiated into DA neurons, functionally alleviated the motor deficits and reduced the loss of striatal DA neuronal axonal termini. Importantly, no iDPs-derived astroctyes and neoplasia were detected in mouse brains after transplantation. We propose that the iDPs from direct reprogramming provides a safe and efficient cell source for PD treatment.
An iodine(iii) mediated oxidative rearrangement of enamines: efficient synthesis of α-amino ketones
Authors: Yadagiri Dongari , Anbarasan Pazhamalai
Published: July 2015

An iodine(iii) mediated chemoselective oxidative rearrangement of β,β-diarylenamines to α-amino ketones has been accomplished with excellent yield.
Diarylamino-substituted tetraarylethene (TAE) as an efficient and robust hole transport material for 11% methyl ammonium lead iodide perovskite solar cells
Authors: Cabau Lydia , Garcia-Benito Ines , Molina-Ontoria Agustin , Montcada Nuria F. , Martin Nazario , Vidal-Ferran Anton , Palomares Emilio
Published: July 2015

We report the synthesis and characterisation of tetra{4-[N,N-(4,4′-dimethoxydiphenylamino)]phenyl}ethene (TAE-1) as an efficient and robust hole transport material for its application in methyl ammonium lead iodide (MAPI) perovskite solar cells.
A furosemide–isonicotinamide cocrystal: an investigation of properties and extensive structural disorder
Authors: Kerr Hannah E. , Softley Lorna K. , Suresh Kuthuru , Nangia Ashwini , Hodgkinson Paul , Evans Ivana Radosavljevic
Published: July 2015

Multi-nuclear variable temperature solid state NMR, supported by DFT calculations, elucidates the nature of structural disorder in furosemide–isonicotinamide cocrystals.
Fullerene-based materials for solar cell applications: design of novel acceptors for efficient polymer solar cells – a DFT study
Authors: Mohajeri Afshan , Omidvar Akbar
Published: July 2015

DFT calculations have been performed to design novel fullerene-based acceptors for the high performance P3HT:fullerene solar cells.
Dependence of photoinduced bending behavior of diarylethene crystals on irradiation wavelength of ultraviolet light
Authors: Kitagawa Daichi , Tanaka Rika , Kobatake Seiya
Published: July 2015

A comprehensive mechanism for different photoresponsive bending behavior of diarylethene crystals depending on irradiation wavelength of ultraviolet light has been proposed.
A trimetallic strategy towards ZnII4DyIII2CrIII2 and ZnII4DyIII2CoIII2 single-ion magnets
Authors: Hu Kong-Qiu , Jiang Xiang , Wu Shu-Qi , Liu Cai-Ming , Cui Ai-Li , Kou Hui-Zhong
Published: July 2015

Two cyano- and phenoxo-bridged ZnIIDyIIICoIII/CrIII trimetallic cyclic complexes display single-ion magnet behavior with the high energy barrier of 85.9 K and 100.9 K, respectively.
Palladium(ii) complexes with chelating N-phosphanyl acyclic diaminocarbenes: synthesis, characterization and catalytic performance in Suzuki couplings
Authors: Marchenko Anatoliy , Koidan Georgyi , Hurieva Anastasiya , Vlasenko Yurii , Kostyuk Aleksandr , Biffis Andrea
Published: July 2015

Novel palladium(ii) complexes with the title ligands have been prepared and tested as precatalysts in Suzuki couplings of aryl chlorides.
Rejection of trace organic chemicals by a nanofiltration membrane: the role of molecular properties and effects of caustic cleaning
Authors: Fujioka Takahiro , Khan Stuart J. , McDonald James A. , Nghiem Long D.
Published: July 2015

The aim of this study was to provide further insights to the rejection mechanisms of trace organic chemicals (TrOCs) by nanofiltration (NF).
Correction: Microfluidic pumping, routing and metering by contactless metal-based electro-osmosis
Authors: Fu Xiaotong , Mavrogiannis Nicholas , Doria Steven , Gagnon Zachary
Published: July 2015

Correction for ‘Microfluidic pumping, routing and metering by contactless metal-based electro-osmosis’ by Xiaotong Fu et al., Lab Chip, 2015, DOI: 10.1039/c5lc00504c.
Experimental design, modeling and optimization of polyplex formation between DNA oligonucleotides and branched polyethylenimine
Authors: Clima Lilia , Ursu Elena L. , Cojocaru Corneliu , Rotaru Alexandru , Barboiu Mihail , Pinteala Mariana
Published: July 2015

The complexes formed by DNA and polycations have received great attention owing to their potential application in gene therapy.
Dual-axis vapor cell for simultaneous laser frequency stabilization on disparate optical transitions
Authors: Jayakumar Anupriya , Plotkin-Swing Benjamin , Jamison Alan O. , Gupta Subhadeep
Published: July 2015

We have developed a dual-axis ytterbium (Yb) vapor cell and used it to simultaneously address the two laser cooling transitions in Yb at wavelengths 399 nm and 556 nm, featuring the disparate linewidths of 2π × 29 MHz and 2π × 182 KHz, respectively. By utilizing different optical paths for the two wavelengths, we simultaneously obtain comparable optical densities suitable for saturated absorption spectroscopy for both the transitions and keep both the lasers frequency stabilized over several hours. We demonstrate that by appropriate control of the cell temperature profile, two atomic transitions differing in relative strength across a large range of over three orders of magnitude can be simultaneously addressed, making the device adaptable to a variety of spectroscopic needs. We also show that our observations can be understood with a simple theoretical model of the Yb vapor.
Pasted type distributed two-dimensional fiber Bragg grating vibration sensor
Authors: Li Tianliang , Tan Yuegang , Zhou Zude , Wei Qin
Published: July 2015

A pasted type distributed two-dimensional fiber Bragg grating (FBG) vibration sensor has been proposed and studied in this paper. The optical fiber is directly considered as an elastomer. The two-dimensional vibration can be separated by subtraction/addition of two FBGs’ center wavelength shift. The principle of the sensor as well as numerical simulation and experimental analyses are presented. Experimental results show that the resonant frequencies of the sensor x/y main vibration direction are separately 1300/20.51 Hz, which are consistent with the numerical simulation analysis result. The flat frequency range resides in 10-750 Hz and 3-12 Hz, respectively; dynamic range is 28.63 dB; in the x main vibration direction, the sensor’s sensitivity is 32.84 pm/g, with linearity 3.91% in the range of 10-60 m/s2, while in the y main vibration direction, the sensor’s sensitivity is 451.3 pm/g, with linearity 1.92% in the range of 1.5-8 m/s2. The cross sensitivity is 3.91%. Benefitting from the two dimensional sensing properties, it can be used in distributed two-dimensional vibration measurement.
Nonlinear Alfvén wave dynamics in plasmas
Authors: Sarkar Anwesa , Chakrabarti Nikhil , Schamel Hans
Published: July 2015

Nonlinear Alfvén wave dynamics is presented using Lagrangian fluid approach in a compressible collisional magnetized plasma. In the framework of two fluid dynamics, finite electron inertia is shown to serve as a dispersive effect acting against the convective nonlinearity. In a moving frame, the Alfvén wave can, therefore, form an arbitrarily strong amplitude solitary wave structure due to the balance between nonlinearity and dispersion. Weak amplitude Alfvén waves are shown to be governed by a modified KdV equation, which extends for finite dissipation to a mKdV-Burgers equation. These equations have well known solutions. Next, we have analyzed the fourth order nonlinear Alfvén wave system of equations both numerically and by approximation method. The results indicate a collapse of the density and magnetic field irrespective of the presence of dispersion. The wave magnetic field, however, appears to be less singular showing collapse only when the dispersive effects are negligible. These results may contribute to our understanding of the generation of strongly localized magnetic fields (and currents) in plasmas and are expected to be of special importance in the astrophysical context of magnetic star formation.
High electron mobility in epitaxial SnO2−x in semiconducting regime
Authors: Mun Hyosik , Yang Hyeonseok , Park Jisung , Ju Chanjong , Char Kookrin
Published: July 2015

We investigated the electronic transport properties of epitaxial SnO2−x thin films on r-plane sapphire substrates. The films were grown by pulsed laser deposition technique and its epitaxial growth direction was [101] and the in-plane alignment was of SnO2−x [010]//Al2O3[12̄10]. When the SnO2−x films were grown in the oxygen pressure of 30 mTorr, we have found the electron mobility of the 30 nm thick SnO2−x thin films strongly dependent on the thicknesses of the fully oxidized insulating SnO2 buffer layer. When the buffer layer thickness increased from 100 nm to 700 nm, the electron mobility of values increased from 23 cm2 V−1 s−1 to 106 cm2 V−1 s−1 and the carrier density increased from 9 × 1017 cm−3 to 3 × 1018 cm−3, which we attribute to reduction of large density of dislocations as the buffer layer thickness increases. In addition, we studied the doping dependence of the electron mobility of SnO2−x thin films grown on top of 500 nm thick insulating SnO2 buffer layers. The oxygen vacancy doping level was controlled by the oxygen pressure during deposition. As the oxygen pressure increased to 47.5 mTorr, the carrier density was found to decrease to 9.1 × 1016 cm−3 and the electron mobility values to 13 cm2 V−1 s−1, which is consistent with the dislocation limited transport properties. We also checked the conductance change of the SnO2−x during thermal annealing cycles, demonstrating unusual stability of its oxygen. The correlation between the electronic transport properties and microstructural defects investigated by the transmission electron microscopy was drawn. The excellent oxygen stability and high electron mobility of low carrier density SnO2−x films demonstrate its potential as a transparent oxide semiconductor.
Dynamics of rising bubble inside a viscosity-stratified medium
Authors: Premlata A. R. , Tripathi Manoj Kumar , Sahu Kirti Chandra
Published: July 2015

The rising bubble dynamics in an unconfined quiescent viscosity-stratified medium has been numerically investigated. This is frequently encountered in industrial as well as natural phenomena. In spite of the large number of studies carried out on bubbles and drops, very few studies have examined the influence of viscosity stratification on bubble rise dynamics. To the best of our knowledge, none of them have isolated the effects of viscosity-stratification alone, even though it is known to influence the dynamics extensively, which is the main objective of the present study. By conducting time-dependent simulations, we present a library of bubble shapes in the Galilei and the Eötvös numbers plane. Our results demonstrate some counter-intuitive phenomena for certain range of parameters due to the presence of viscosity stratification in the surrounding fluid. We found that in a linearly increasing viscosity medium, for certain values of parameters, bubble undergoes large deformation by forming an elongated skirt, while the skirt tends to physically separate the wake region from the rest of the surrounding fluid. This peculiar dynamics is attributed to the migration of less viscous fluid that is carried in the wake of the bubble as it rises, and thereby creating an increasingly larger viscosity contrast between the fluid occupied in the wake region and the surrounding fluid, unlike that observed in a constant viscosity medium. It is also observed that the effect of viscosity stratification is qualitatively different for different regimes of the dimensionless parameters. In future, it will be interesting to investigate this problem in three-dimensions.
Free energy of ion hydration: Interface susceptibility and scaling with the ion size
Authors: Dinpajooh Mohammadhasan , Matyushov Dmitry V.
Published: July 2015

Free energy of solvation of a spherical ion in a force-field water is studied by numerical simulations. The focus is on the linear solvation susceptibility connecting the linear response solvation free energy to the squared ion charge. Spherical hard-sphere solutes, hard-sphere ions, and Kihara solutes (Lennard-Jones modified hard-sphere core) are studied here. The scaling of the solvation susceptibility with the solute size significantly deviates from the Born equation. Using empirical offset corrections of the solute size (or the position of the first peak of the solute-solvent distribution function) do not improve the agreement with simulations. We advance a new perspective on the problem by deriving an exact relation for the radial susceptibility function of the interface. This function yields an effective cavity radius in the Born equation calculated from the solute-solvent radial distribution function. We find that the perspective of the local response, assuming significant alteration of the solvent structure by the solute, is preferable compared to the homogeneous approximation assuming intact solvent structure around the solute. The model finds a simple explanation of the asymmetry of hydration between anions and cations in denser water shells around anions and smaller cavity radii arising from the solute-solvent density profiles.
Stress relaxation in vanadium under shock and shockless dynamic compression
Authors: Kanel G. I. , Razorenov S. V. , Garkushin G. V. , Savinykh A. S. , Zaretsky E. B.
Published: July 2015

Evolutions of elastic-plastic waves have been recorded in three series of plate impact experiments with annealed vanadium samples under conditions of shockless and combined ramp and shock dynamic compression. The shaping of incident wave profiles was realized using intermediate base plates made of different silicate glasses through which the compression waves were entered into the samples. Measurements of the free surface velocity histories revealed an apparent growth of the Hugoniot elastic limit with decreasing average rate of compression. The growth was explained by “freezing” of the elastic precursor decay in the area of interaction of the incident and reflected waves. A set of obtained data show that the current value of the Hugoniot elastic limit and plastic strain rate is rather associated with the rate of the elastic precursor decay than with the local rate of compression. The study has revealed the contributions of dislocation multiplications in elastic waves. It has been shown that independently of the compression history the material arrives at the minimum point between the elastic and plastic waves with the same density of mobile dislocations.
Current-direction dependence of the transport properties in single-crystalline face-centered-cubic cobalt films
Authors: Xiao X. , Liang J. H. , Chen B. L. , Li J. X. , Ma D. H. , Ding Z. , Wu Y. Z.
Published: July 2015

Face-centered-cubic cobalt films are epitaxially grown on insulating LaAlO3(001) substrates by molecular beam epitaxy. Transport measurements are conducted in different current directions relative to the crystal axes. We find that the temperature dependent anisotropic magnetoresistance ratio strongly depends on the current direction. However, the anomalous Hall effect shows isotropic behavior independent of the current direction. Our results demonstrate the interplay between the current direction and the crystalline lattice in single-crystalline ferromagnetic films. A phenomenological analysis is presented to interpret the experimental data.
Characterization of ultrafast laser-ablation plasma plumes at various Ar ambient pressures
Authors: Diwakar P. K. , Harilal S. S. , Phillips M. C. , Hassanein A.
Published: July 2015

Recently, we reported morphological changes in ultrafast laser ablation plumes in varying ambient pressures [Diwakar et al., J. Appl. Phys. 116, 133301 (2014)]. In this paper, we report the emission features of fs laser ablated brass plasma plumes at various Ar background pressure levels ranging from vacuum to atmospheric conditions and correlated to changes in plume morphology. Spatially resolved wavelength dispersed images of the plume were recorded for characterizing the spectral features at various pressure levels and also used for obtaining spatial distribution of Cu I and Zn I species in the plume, signal-to-noise ratios, and fundamental parameters of the plasma, specifically temperature and density. The spatial evolution of plasma temperature and density showed significant changes at various ambient pressure levels; these results were correlated to morphological changes seen in the plume images. Optical time-of-flight profiles were used to study time evolution of various species in the plume and indicated oscillations of ablation plumes at intermediate pressure levels. Possible mechanisms for observed changes in plume shape, optical emission intensity, and dual peak structures in time-of-flight profiles are discussed.
Periodicity in bimodal atomic force microscopy
Authors: Lai Chia-Yun , Barcons Victor , Santos Sergio , Chiesa Matteo
Published: July 2015

Periodicity is fundamental for quantification and the application of conservation principles of many important systems. Here, we discuss periodicity in the context of bimodal atomic force microscopy (AFM). The relationship between the excited frequencies is shown to affect and control both experimental observables and the main expressions quantified via these observables, i.e., virial and energy transfer expressions, which form the basis of the bimodal AFM theory. The presence of a fundamental frequency further simplifies the theory and leads to close form solutions. Predictions are verified via numerical integration of the equation of motion and experimentally on a mica surface.
Optical properties of amorphous and polycrystalline Sb2Se3 thin films prepared by thermal evaporation
Authors: Chen Chao , Li Weiqi , Zhou Ying , Chen Cheng , Luo Miao , Liu Xinsheng , Zeng Kai , Yang Bo , Zhang Chuanwei , Han Junbo , Tang Jiang
Published: July 2015

Sb2Se3 is a very promising photovoltaic material because of its attractive material, optical and electrical properties. Very recently, we reported a superstrate CdS/Sb2Se3 solar cell with 5.6% certified efficiency. In this letter, we focused on the optical properties of amorphous and polycrystalline Sb2Se3 thin films prepared by thermal evaporation. Using temperature dependent transmission spectrum and temperature dependent photoluminescence, the indirect optical transition nature and bandgap values as functions of temperature were acquired. Using ellipsometry measurements and Swanepoel's envelope method, the refractive indices as well as the dielectric constant in a wide wavelength range of 193–2615 nm were obtained. These works would lay the foundation for the further development of Sb2Se3 thin film solar cells.
Fabrication of thermoelectric devices using precisely Fermi level-tuned semiconducting single-wall carbon nanotubes
Authors: Oshima Yuki , Kitamura Yoshimasa , Maniwa Yutaka , Yanagi Kazuhiro
Published: July 2015

Precisely Fermi level-tuned one-dimensional materials have great potential for highly efficient thermoelectric devices. Here, we report continuous control of thermoelectric power using precisely Fermi level-tuned thermoelectric devices, in which P-type and N-type single-wall carbon nanotube networks are connected electrically in series and thermally in parallel. We fabricated thermoelectric devices with two channels using semiconducting single-wall carbon nanotubes and tuned the Seebeck polarity of one side to the N-type using electric double-layer carrier injections and then enhanced the thermoelectric power of the device by tuning the gate voltage.
Carrier lifetimes and interface recombination velocities in CdTe/MgxCd1−xTe double heterostructures with different Mg compositions grown by molecular beam epitaxy
Authors: Liu Shi , Zhao Xin-Hao , Campbell Calli M. , Lassise Maxwell B. , Zhao Yuan , Zhang Yong-Hang
Published: July 2015

The interface recombination velocities of CdTe/MgxCd1−xTe double heterostructure (DH) samples with different CdTe layer thicknesses and Mg compositions are studied using time-resolved photoluminescence measurements. A lowest interface recombination velocity of 30 ± 10 cm/s has been measured for the CdTe/Mg0.46Cd0.54Te interface, and a longest carrier lifetime of 0.83 μs has been observed for the studied DHs. These values are very close to the best reported numbers for GaAs/AlGaAs DHs. The impact of carrier escape through thermionic emission over the MgCdTe barrier on the recombination process in the DHs is also studied.
Impacts of repeated wildfire on long-unburned plant communities of the southern Appalachian Mountains
Authors: Hagan Donald L. , Waldrop Thomas A. , Reilly Matthew , Shearman Timothy M.
Published: July 2015

The infrequent occurrence of large wildfires in the southern Appalachian Mountains over the last several decades has offered few opportunities to study their impacts. From 2000 to 2008, five wildfires burned a large portion of the area in and surrounding the Linville Gorge Wilderness in North Carolina. Areas were burned either once or twice. The response of acid cove and thermic oak plant communities (structure, cover, richness, diversity) was measured in 78 vegetation monitoring plots, established in 1992 and remeasured in 2010–11. Fire altered forest structure in both communities, resulting in the mortality of larger trees and increases in the abundance of smaller (<5 cm diameter at breast height (DBH)) stems. Burning twice decreased stem counts for mountain laurel (Kalmia latifolia) in both communities, whereas oaks (Quercus spp.) responded positively to burning twice in the thermic oak community. Table Mountain pine stem counts increased in acid cove and thermic oak communities burned once. Fire appears to promote princesstree (Paulownia tomentosa) invasion. Herbaceous species cover responded positively to fire (once or twice; both communities), with concurrent increases in woody species richness and diversity. Tree species composition in acid cove plots was not affected by burning, although some slight changes occurred in thermic oak plots burned twice.
SIMULATED PHOTOEVAPORATIVE MASS LOSS FROM HOT JUPITERS IN 3D
Authors: Tripathi Anjali , Kratter Kaitlin M. , Murray-Clay Ruth A. , Krumholz Mark R.
Published: July 2015

Ionizing stellar photons heat the upper regions of planetary atmospheres, driving atmospheric mass loss. Gas escaping from several hot, hydrogen-rich planets has been detected using UV and X-ray transmission spectroscopy. Because these planets are tidally locked, and thus asymmetrically irradiated, escaping gas is unlikely to be spherically symmetric. In this paper, we focus on the effects of asymmetric heating on local outflow structure. We use the Athena code for hydrodynamics to produce 3D simulations of hot Jupiter mass loss that jointly model wind launching and stellar heating via photoionization. Our fiducial planet is an inflated, hot Jupiter with radius

and mass

. We irradiate the initially neutral, atomic hydrogen atmosphere with 13.6 eV photons and compute the outflow’s ionization structure. There are clear asymmetries in the atmospheric outflow, including a neutral shadow on the planet’s nightside. Given an incident ionizing UV flux comparable to that of the Sun, we find a steady-state mass loss rate of

g s−1. The total mass loss rate and the outflow substructure along the substellar ray show good agreement with earlier 1D models, for two different fluxes. Our 3D data cube can be used to generate the outflow’s extinction spectrum during transit. As a proof of concept, we find absorption of stellar Lyα at Doppler-shifted velocities of up to ±50 km s−1. Our work provides a starting point for further 3D models that can be used to predict observable signatures of hot Jupiter mass loss.
Metabolic Syndrome and Cardiovascular Risk in Elderly Treated
Hypertensive Patients
Authors: Pierdomenico Sante D. , Pierdomenico Anna M. , Di Tommaso Roberta , Coccina Francesca , Di Carlo Silvio , Cuccurullo Franco , Porreca Ettore
Published: July 2015

BACKGROUND

The independent prognostic significance of the metabolic syndrome (MetS) in the elderly is not yet clear. We investigated the association between MetS and cardiovascular risk (composite endpoint of stroke and coronary events) in elderly treated hypertensive patients.

METHODS

Cardiovascular outcome was evaluated in 1,191 elderly treated hypertensive patients (≥60 years). Among them, 578 (48.5%) had MetS according to a modified joint interim statement definition (body mass index in place of waist circumference).

RESULTS

During the follow-up (9.1±4.9 years, range 0.4–20 years), 139 strokes and 120 coronary events occurred. In univariate analysis, patients with MetS had higher risk of the composite endpoint (hazard ratio (HR) 1.322, 95% confidence interval (CI) 1.035–1.688, P < 0.05). Among the single components of MetS, only blood pressure (BP) level and impaired fasting glucose/diabetes were significantly associated with increased cardiovascular risk. After adjustment for age, previous events, estimated glomerular filtration rate (eGFR), left ventricular (LV) hypertrophy and left atrial (LA) enlargement, the prognostic relevance of MetS was attenuated (HR 1.245, 95% CI 0.974–1.591, P = 0.08). After further adjustment for the above-mentioned variables and ambulatory BP parameters and impaired fasting glucose/diabetes, Cox regression analysis showed that MetS was not independently associated with increased cardiovascular risk (HR 1.090, 95% CI 0.805–1.475, P = 0.58).

CONCLUSIONS

In elderly treated hypertensive patients, MetS is associated with increased cardiovascular risk, but not independently of BP and glucose levels and of organ damage.
SNPGenie: estimating evolutionary parameters to detect natural selection using pooled next-generation sequencing data
Authors: Nelson Chase W. , Moncla Louise H. , Hughes Austin L.
Published: July 2015

Summary: New applications of next-generation sequencing technologies use pools of DNA from multiple individuals to estimate population genetic parameters. However, no publicly available tools exist to analyse single-nucleotide polymorphism (SNP) calling results directly for evolutionary parameters important in detecting natural selection, including nucleotide diversity and gene diversity. We have developed SNPGenie to fill this gap. The user submits a FASTA reference sequence(s), a Gene Transfer Format (.GTF) file with CDS information and a SNP report(s) in an increasing selection of formats. The program estimates nucleotide diversity, distance from the reference and gene diversity. Sites are flagged for multiple overlapping reading frames, and are categorized by polymorphism type: nonsynonymous, synonymous, or ambiguous. The results allow single nucleotide, single codon, sliding window, whole gene and whole genome/population analyses that aid in the detection of positive and purifying natural selection in the source population.

Availability and implementation: SNPGenie version 1.2 is a Perl program with no additional dependencies. It is free, open-source, and available for download at https://github.com/hugheslab/snpgenie.

Contact:  nelsoncw@email.sc.edu or austin@biol.sc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.