ALBERT

Description: A proper orthogonal decomposition (POD) method is used to interpolate the flow around an airfoil for various Mach numbers and angles of attack in the transonic regime. POD uses a few numerical simulations, called snapshots, to create eigenfunctions. These eigenfunctions are combined using weighting coefficients to create a new solution for different values of the input parameters. Since POD methods are linear, their interpolation capabilities are quite limited when dealing with flow presenting nonlinearities, such as shocks. In order to improve their performance for cases involving shocks, a new method is proposed using variable fidelity. The main idea is to use POD to interpolate the difference between the CFD solution obtained on two different grids, a coarse one and a fine one. Then, for any new input parameter value, a coarse grid solution is computed using CFD and the POD interpolated difference is added to predict the fine grid solution. This allows some nonlinearities associated with the flow to be introduced. Results for various Mach numbers and angles of attack are compared to full CFD results. The variable fidelity-based POD method shows good improvement over the classical approach.

Description: The preparation of carbon nanotube/metallic particle hybrids using pressed porous stainless steel pellets as a substrate is described. The catalytic growth of carbon nanotubes was carried out by CVD on a nickel catalyst obtained by impregnation of pellets with a highly dispersive colloidal solution of nickel acetate tetrahydrate in ethanol. Granular polyethylene was used as the carbon source. Metallic particles were deposited by thermal evaporation of Pt and Ag using pellets with grown carbon nanotubes as a base. The use of such composites as fuel cell electrodes is discussed.

Description: J. Tuma, O. Lyutakov, I. Huttel, P. Slepicka, and V. Svorcik Thin poly(methylmethacrylate) films doped by or covalently attached to disperse Red 1 acrylate (DR1) were patterned by laser scanning and simultaneous sample movement in confocal microscope. In both cases, periodical structure due to Marangoni effect is created. Modified polymers surfaces were analy ... [J. Appl. Phys. 114, 093104 (2013)] published Fri Sep 6, 2013.

Description: L. Kilanski, K. Szalowski, R. Szymczak, M. Gorska, E. Dynowska et al. We present the studies of electrical transport and magnetic interactions in ZnMnGeAs crystals with low Mn content 0

Description: G. Y. Gao, Z. B. Yang, W. Huang, H. Z. Zeng, Y. Wang et al. Epitaxial Mn-doped BiFeO (MBFO) thin films were grown on GaAs (001) substrate with SrTiO (STO) buffer layer by pulsed laser deposition. X-ray diffraction results demonstrate that the films show pure (00l) orientation, and MBFO (100)//STO(100), whereas STO (100)//GaAs (110). Piezoresponse force micro ... [J. Appl. Phys. 114, 094106 (2013)] published Fri Sep 6, 2013.

Description: Yanan Huang, Bangchuan Zhao, Shuai Lin, Wenhai Song, and Yuping Sun The effects of Ir doping on the low-temperature thermal and electrical transport properties of CaCoIrO (0

Description: P. Orlandi In this paper, it is demonstrated by DNS of turbulent rough channels that a proportionality between u-tilde| (the wall-normal Reynolds stress u-tilde= at the top of the roughness elements) and the roughness function does exist. This observation confirmed by experiments allows the derivation of a sim ... [Phys. Fluids 25, 110813 (2013)] published Fri Sep 6, 2013.

Description: Alessandra Adrover We investigate the effects of secondary (transverse) flows on convection-dominated dispersion of pressure driven, open column laminar flow in a conduit with rectangular cross-section. We show that secondary flows significantly reduce dispersion (enhancing transverse diffusion) in Taylor-Aris regime ... [Phys. Fluids 25, 093601 (2013)] published Fri Sep 6, 2013.

Description: Michael E. Mueller and Heinz Pitsch An integrated kinetics-based Large Eddy Simulation (LES) approach for soot evolution in turbulent reacting flows is applied to the simulation of a Pratt & Whitney aircraft gas turbine combustor, and the results are analyzed to provide insights into the complex interactions of the hydrodynamics, mixi ... [Phys. Fluids 25, 110812 (2013)] published Fri Sep 6, 2013.

Description: D. M. Valiev, V. Bychkov, V. Akkerman, L.-E. Eriksson, and C. K. Law The present paper addresses the phenomenon of spontaneous acceleration of a premixed flame front propagating in micro-channels, with subsequent deflagration-to-detonation transition. It has recently been shown experimentally [M. Wu, M. Burke, S. Son, and R. Yetter, Proc. Combust. Inst. 31, 2429 (200 ... [Phys. Fluids 25, 096101 (2013)] published Fri Sep 6, 2013.

Description: Young-Min Shin and Michael Church A deflecting mode cavity is the integral element for six-dimensional phase-space beam control in bunch compressors and emittance transformers at high energy beam test facilities. RF performance of a high-Q device is, however, highly sensitive to operational conditions, in particular in a cryo-coolin ... [Phys. Plasmas 20, 093101 (2013)] published Fri Sep 6, 2013.

Description: Marcus Weinwurm, Simon N. Bland, and Jeremy P. Chittenden Properties of degenerate hydrogen and deuterium (D) at pressures of the order of terapascals are of key interest to Planetary Science and Inertial Confinement Fusion. In order to recreate these conditions in the laboratory, we present a scheme, where a metal liner drives a cylindrically convergent q ... [Phys. Plasmas 20, 092701 (2013)] published Fri Sep 6, 2013.

Description: Jaetae Seo, Sangram Raut, Mahmoud Abdel-Fattah, Quinton Rice, Bagher Tabibi et al. Time-resolved and temperature-dependent photoluminescence (PL) spectroscopy of ternary compound copper indium disulfide (CuInS, or CIS) core materials, CIS/ZnS coreshells, and quaternary compound ZnCuInS (ZnCIS) revealed their optical properties with spectral, temporal, and thermal characteristics, ... [J. Appl. Phys. 114, 094310 (2013)] published Fri Sep 6, 2013.

Description: D. H. Feng, X. Q. Pan, X. Li, T. Q. Jia, and Z. R. Sun We report experiments of coherent acoustic phonon generations and detections using a two-color femtosecond pump-probe technique in [001] and [110] oriented ZnTe single crystals. The above-bandgap pump excitation initiates strain waves to yield coherent acoustic phonons. The generation and propagatio ... [J. Appl. Phys. 114, 093513 (2013)] published Fri Sep 6, 2013.

Description: Kun Gao, S. Prucnal, W. Skorupa, M. Helm, and Shengqiang Zhou GaAs and GaAs based materials have outstanding optoelectronic properties and are widely used as light emitting media in devices. Many approaches have been applied to GaAs to generate luminescence at 0.88, 1.30, and 1.55 [mu]m which are transmission windows of optical fibers. In this paper, we presen ... [J. Appl. Phys. 114, 093511 (2013)] published Fri Sep 6, 2013.

Description: Xinliang Gao, Quanming Lu, Xin Tao, Yufei Hao, and Shui Wang Alfven waves with a finite amplitude are found to be unstable to a parametric decay in low beta plasmas. In this paper, the parametric decay of a circularly polarized Alfven wave in a proton-electron-alpha plasma system is investigated with one-dimensional (1-D) hybrid simulations. In cases without ... [Phys. Plasmas 20, 092106 (2013)] published Fri Sep 6, 2013.

Description: Brian M. Haines, Fernando F. Grinstein, Leslie WelserSherrill, James R. Fincke, and Forrest W. Doss We perform an ensemble of simulations of a laser-driven shear experiment [L. Welser-Sherrill et al., Two laser-driven mix experiments to study reshock and shear, High Energy Density Phys. J. 9(3), 496499 (2013)] in the strong-shock high energy-density regime to better understand material mixing driv ... [Phys. Plasmas 20, 092301 (2013)] published Fri Sep 6, 2013.

Description: Anthony Ballandras, Guy Weber, Christian Paulin, Jean-Pierre Bellat, and Maud Rotger The adsorption of trichloroethylene, perchloroethylene, and p-xylene on a MFI (Mobile-FIve) zeolite is studied using in situ FTIR spectroscopy at 298 K. Spectra of self-supported zeolites in contact with increasing pressures of pure gas were recorded at equilibrium in the mid-infrared domain. Analys ... [J. Chem. Phys. 139, 091103 (2013)] published Fri Sep 6, 2013.

Description: Y. Zheng (郑轶) , L. N. Su (苏鲁宁) , M. Liu (刘梦) , B. C. Liu (刘必成) , Z. W. Shen (沈忠伟) et al. In typical laser-driven proton acceleration experiments Thomson parabola proton spectrometers are used to measure the proton spectra with very small acceptance angle in specific directions. Stacks composed of CR-39 nuclear track detectors, imaging plates, or radiochromic films are used to measure th ... [Rev. Sci. Instrum. 84, 096103 (2013)] published Fri Sep 6, 2013.

Description: E. K. Michailidou, M. J. Assael, M. L. Huber, and R. A. Perkins This paper contains new, representative reference equations for the viscosity of n-hexane. The equations are based in part upon a body of experimental data that has been critically assessed for internal consistency and for agreement with theory whenever possible. The correlations are valid from the ... [J. Phys. Chem. Ref. Data 42, 033104 (2013)] published Fri Sep 6, 2013.

Description: Hong-Biao Zhang, Lin Yang, and San-Xing Guo We construct so(3) algebra associated with the Morse potential and show that these operators obey so(3) commutation relations. A so(3) algebraic method is proposed in order to obtain the eigenvalues and eigenfunctions of the Morse potential. This method exhibits that Cartan operator J, the lowering ... [J. Math. Phys. 54, 092104 (2013)] published Fri Sep 6, 2013.

Description: Publication date: Available online 7 September 2013 Source: FEBS Open Bio Author(s): Veronika Temml , Susanne Kuehnl , Daniela Schuster , Stefan Schwaiger , Hermann Stuppner , Dietmar Fuchs Mediterranean Carthamus tinctorius (Safflower) is used for treatment of inflammatory conditions and neuropsychiatric disorders. Recently C. tinctorius lignans arctigenin and trachelogenin but not matairesinol were described to interfere with the activity of tryptophan-degrading enzyme indoleamine 2,3-dioxygenase (IDO) in peripheral blood mononuclear cells in vitro . We examined a potential direct influence of compounds on IDO enzyme activity applying computational calculations based on 3D geometry of the compounds. The interaction pattern analysis and force field-based minimization was performed within LigandScout 3.03, the docking simulation with MOE 2011.10 using the X-ray crystal structure of IDO. Results confirm the possibility of an intense interaction of arctigenin and trachelogenin with the binding site of the enzyme, while matairesinol had no such effect.

Description: Publication date: Available online 7 September 2013 Source: FEBS Open Bio Author(s): Mitsuru Ishikawa , Jun Shiota , Yuta Ishibashi , Tomoyuki Hakamata , Shizuku Shoji , Mamoru Fukuchi , Masaaki Tsuda , Tomoaki Shirao , Yuko Sekino , Toshihisa Ohtsuka , Jay M. Baraban , Akiko Tabuchi Megakaryoblastic leukemia 1 (MKL1) is a member of the MKL family of serum response factor (SRF) coactivators. Here we have identified three rat MKL1 transcripts: two are homologues of mouse MKL1 transcripts, full-length MKL1 (FLMKL1) and basic, SAP, and coiled-coil domains (BSAC), the third is a novel transcript, M KL1- elo ngated d erivative of y ield (MELODY). These rat MKL1 transcripts are differentially expressed in a wide variety of tissues with highest levels in testis and brain. During brain development, these transcripts display differential patterns of expression. The FLMKL1 transcript encodes two isoforms that utilize distinct translation start sites. The longer form possesses three actin-binding RPXXXEL (RPEL) motifs and the shorter form, MKL1met only has two RPEL motifs. All four rat MKL1 isoforms, FLMKL1, BSAC, MKL1met and MELODY increased SRF-mediated transcription, but not CREB-mediated transcription. Accordingly, the differential expression of MKL1 isoforms may help fine-tune gene expression during brain development.

Description: Background: The process of creating and designing Virtual Patients for teaching students of medicine is an expensive and time-consuming task. In order to explore potential methods of mitigating these costs, our group began exploring the possibility of creating Virtual Patients based on electronic health records. This review assesses the usage of electronic health records in the creation of interactive Virtual Patients for teaching clinical decision-making. Methods: The PubMed database was accessed programmatically to find papers relating to Virtual Patients. The returned citations were classified and the relevant full text articles were reviewed to find Virtual Patient systems that used electronic health records to create learning modalities. Results: A total of n = 362 citations were found on PubMed and subsequently classified, of which n = 28 full-text articles were reviewed. Few articles used unformatted electronic health records other than patient CT or MRI scans. The use of patient data, extracted from electronic health records or otherwise, is widespread. The use of unformatted electronic health records in their raw form is less frequent. Patient data use is broad and spans several areas, such as teaching, training, 3D visualisation, and assessment. Conclusions: Virtual Patients that are based on real patient data are widespread, yet the use of unformatted electronic health records, abundant in hospital information systems, is reported less often. The majority of teaching systems use reformatted patient data gathered from electronic health records, and do not use these electronic health records directly. Furthermore, many systems were found that used patient data in the form of CT or MRI scans. Much potential research exists regarding the use of unformatted electronic health records for the creation of Virtual Patients.

Description: Background: Despite their widespread use, the biological mechanisms underlying the efficacy of psychotropic drugs are still incompletely known; improved understanding of these is essential for development of novel more effective drugs and rational design of therapy. Given the large number of psychotropic drugs available and their differential pharmacological effects, it would be important to establish specific predictors of response to various classes of drugs. Results: To identify the molecular mechanisms that may initiate therapeutic effects, whole-genome expression profiling (using 324 Illumina Mouse WG-6 microarrays) of drug-induced alterations in the mouse brain was undertaken, with a focus on the time-course (1, 2, 4 and 8 h) of gene expression changes produced by eighteen major psychotropic drugs: antidepressants, antipsychotics, anxiolytics, psychostimulants and opioids. The resulting database is freely accessible at www.genes2mind.org. Bioinformatics approaches led to the identification of three main drug-responsive genomic networks and indicated neurobiological pathways that mediate the alterations in transcription. Each tested psychotropic drug was characterized by a unique gene network expression profile related to its neuropharmacological properties. Functional links that connect expression of the networks to the development of neuronal adaptations (MAPK signaling pathway), control of brain metabolism (adipocytokine pathway), and organization of cell projections (mTOR pathway) were found. Conclusions: The comparison of gene expression alterations between various drugs opened a new means to classify the different psychoactive compounds and to predict their cellular targets; this is well exemplified in the case of tianeptine, an antidepressant with unknown mechanisms of action. This work represents the first proof-of-concept study of a molecular classification of psychoactive drugs.

Description: Phage PhiC31 integrase integrates attB-containing plasmid into pseudo attP site in eukaryotic genomes in a unidirectional site-specific manner and maintains robust transgene expression. Few studies, however, explore its potential in livestock. This study aims to discover the molecular basis of PhiC31 integrase-mediated site-specific recombination in pig cells. We show that PhiC31 integrase can mediate site-specific transgene integration into the genome of pig kidney PK15 cells. Intramolecular recombination in pig PK15 cell line occurred at maximum frequency of 82% with transiently transfected attB- and attP-containing plasmids. An optimal molar ratio of pCMV-Int to pEGFP-N1-attB at 5:1 was observed for maximum number of cell clones under drug selection. Four candidate pseudo attP sites were identified by TAIL-PCR from those cell clones with single-copy transgene integration. Two of them gave rise to higher integration frequency occurred at 33%. 5[prime]and 3[prime]junction PCR showed that transgene integration mediated by PhiC31 integrase was mono-allelic. Micro- deletion and insertion were observed by sequencing the integration border, indicating that double strand break was induced by the recombination. We then constructed rescue reporter plasmids by ABI-REC cloning of the four pseudo attP sites into pBCPB + plasmid. Transfection of these rescue plasmids and pCMV-Int resulted in expected intramolecular recombination between attB and pseudo attP sites. This proved that the endogenous pseudo attP sites were functional substrates for PhiC31 integrase-mediated site-specific recombination. Two pseudo attP sites maintained robust extracellular and intracellular EGFP expression. Alamar blue assay showed that transgene integration into these specific sites had little effect on cell proliferation. This is the first report to document the potential use of PhiC31 integrase to mediate site-specific recombination in pig cells. Our work established an ideal model to study the position effect of identical transgene located in diverse chromosomal contexts. These findings also form the basis for targeted pig genome engineering and may be used to produce genetically modified pigs for agricultural and biomedical uses.

Description: Background: The molecular epidemiology of C. jejuni and C. coli clinical strains isolated from children with gastroenteritis, was investigated using the multilocus sequence typing method (MLST). This analysis establishes for the first time in Greece and constitutes an important tool for the epidemiological surveillance and control of Campylobacter infection in our country. Methods: The MLST genotypes were compared with those gained by other typing methods (HS-typing, PFGE and FlaA typing) and were also phylogenetically analyzed, in order to uncover genetic relationships. Results: Among 68 C. jejuni strains, 41 different MLST-Sequence Types (MLST-STs) were found. Fifty six strains or 34 MLST-STs could be sorted into 15 different MLST-Sequence Type Complexes (MLST-STCs), while twelve strains or seven MLST-STs did not match any of the MLST-STCs of the database. Twenty C. coli strains belonged to 14 different MLST-STs. Eleven MLST-STs were classified in the same MLST-STC (828), and three were unclassifiable. There was no significant association between the MLST-STs and the results of the other typing methods.Phylogenetic analysis revealed that some strains, classified to the species of C. jejuni, formed a separate, phylogenetically distinct group. In eight strains some alleles belonging to the taxonomic cluster of C. jejuni, were also detected in C. coli and vice versa, a phenomenon caused by the genetic mosaic encountered inside the genus Campylobacter. Conclusions: The MLST-ST determination proved to be a very useful tool for the typing as well as the identification of Campylobacter on the species level.

Description: Background: Opsins have been found in the majority of animals and their most apparent functions are related to vision and light-guided behaviour. As an increasing number of sequences have become available it has become clear that many opsin-like transcripts are expressed in tissues other than the eyes. Opsins can be divided into three main groups: rhabdomeric opsins (r-opsins), ciliary opsins (c-opsins) and group 4 opsins. In arthropods, the main focus has been on the r-opsins involved in vision. However, with increased sequencing it is becoming clear that arthropods also possess opsins of the c-type, group 4 opsins and the newly discovered arthropsins but the functions of these opsins are unknown in arthropods and data on their localisation is limited or absent. Results: We identified opsins from the spider Cupiennius salei and the onychophoran Euperipatoides kanangrensis and characterised the phylogeny and localisation of these transcripts. We recovered all known visual opsins in C. salei, and in addition found a peropsin, a c-opsin and an opsin resembling Daphnia pulex arthropsin. The peropsin was expressed in all eye types except the anterior median eyes. The arthropsin and the c-opsin were expressed in the central nervous system but not the eyes. In E. kanangrensis we found: a c-opsin; an opsin resembling D. pulex arthropsins; and an r-opsin with high sequence similarity to previously published onychophoran onychopsins. The E. kanangrensis c-opsin and onychopsin were expressed in both the eyes and the brain but the arthropsin only in the brain. Conclusion: Our novel finding that opsins of both the ciliary and rhabdomeric type are present in the onychophoran and a spider suggests that these two types of opsins were present in the last common ancestor of the Onychophora and Euarthropoda. The expression of the c-opsin in the eye of an onychophoran indicates that c-opsins may originally have been involved in vision in the arthropod clade. The lack of c-opsin expression in the spider retina suggests that the role for c-opsin in vision was lost in the euarthropods. Our discovery of arthropsin in onychophorans and spiders dates the emergence of arthropsin to the common ancestor of Onychophora and Euarthropoda and their expression in the brain suggests a non-visual function.

Description: H. Perez, T. Cordova-Fraga, S. Lopez-Briones, J. C. Martinez-Espinosa, E. F. Rosas et al. A device's instrumentation for magnetic stimulation on human lymphocytes is presented. This is a new procedure to stimulate growing cells with ferrofluid in vortices of magnetic field. The stimulation of magnetic vortices was provided at five different frequencies, from 100 to 2500 Hz and intensitie ... [Rev. Sci. Instrum. 84, 094701 (2013)] published Mon Sep 9, 2013.

Description: Kui Wang, Jianchun Jiang, Zhan Si, and Xinyu Liang A solid acid catalyst SO/TiO/La was prepared via sol-gel method using tetrabutyl titanate as TiO precursor. The catalyst simultaneously catalyzed esterification and transesterification resulting in the synthesis of biodiesel from waste cooking oil with high content of free fatty acids as feedstock. ... [J. Renewable Sustainable Energy 5, 052001 (2013)] published Mon Sep 9, 2013.

Description: This work provides a distributed fault-tolerant event region detection algorithm for wireless sensor networks. The proposed algorithm can identify faulty and fault-free sensors and ignore the abnormal readings to avoid false alarm. Moreover, every event region can also be detected and identified. Simulation results show that fault detection accuracy (FDA) is greater than 92%, false alarm rate (FAR) is near 0%, and event detection accuracy (EDA) is greater than 99% under uniform distribution. FDA is greater than 92%, FAR is less than 1.2%, and EDA is greater than 88% under random distribution when sensor fault probability is less than 0.3.

Description: Background: Statin-fibrate combination therapy has been used to treat patients with acute coronary syndrome (ACS) complicated by elevated triglycerides (TG) and decreased high density lipoprotein cholesterol (HDL-C). The purpose of this study was to evaluate the influence of the combination therapy on lipids profile and apolipoprotein A5 (apoA5) level in patients with ACS. Methods: One hundred and four patients with ACS were recruited and randomly assigned into two groups: one was statin group (n = 52), given atorvastatin (20 mg QN) or other statins with equivalent dosages; the other was combination group (n = 52), given the same dose of statin plus bezafibrate (200 mg BID). Follow-up visits were scheduled at the end of 6 and 12 weeks post treatment. Serum apoA5 levels were determined using a commercial available ELISA kit. Results: (1) Compared with that of statin monotherapy, statin-bezafibrate combination treatment not only resulted in a significant reduction of TG, TC and LDL-C levels , (all p 〈 0.05), but also led to increases in HDL-C and apoA5 levels (p 〈 0.05).(2) The percentage changes of TC, TG, LDL-C and apoA5 levels in both groups were even bigger at 12 weeks after treatment than that at 6 weeks.(all p 〈 0.05). Similarly, the rates of achieving lipid-control target were higher in statin-bezafibrate combination treatment group than those in statin monotherapy group (all p 〈 0.05).(3) Spearman rank correlation analysis showed that the pre-treatment apoA5 level was positively correlated with TG (r = 0.359, p = 0.009). However, a negative correlation was observed between apoA5 and TG (r = -0.329, p = 0.017) after 12 weeks treatment. Conclusions: Statin and fibrate combination therapy is more effective than statin alone in achieving a comprehensive lipid control for ACS patients. Serum apoA5 elevation after statin and fibrate combination treatment could be due to the synergistic effect of both drugs on hypertriglyceridemia control.

Description: Pupylation, one of the most important posttranslational modifications of proteins, typically takes place when prokaryotic ubiquitin-like protein (Pup) is attached to specific lysine residues on a target protein. Identification of pupylation substrates and their corresponding sites will facilitate the understanding of the molecular mechanism of pupylation. Comparing with the labor-intensive and time-consuming experiment approaches, computational prediction of pupylation sites is much desirable for their convenience and fast speed. In this study, a new bioinformatics tool named EnsemblePup was developed that used an ensemble of support vector machine classifiers to predict pupylation sites. The highlight of EnsemblePup was to utilize the Bi-profile Bayes feature extraction as the encoding scheme. The performance of EnsemblePup was measured with a sensitivity of 79.49%, a specificity of 82.35%, an accuracy of 85.43%, and a Matthews correlation coefficient of 0.617 using the 5-fold cross validation on the training dataset. When compared with other existing methods on a benchmark dataset, the EnsemblePup provided better predictive performance, with a sensitivity of 80.00%, a specificity of 83.33%, an accuracy of 82.00%, and a Matthews correlation coefficient of 0.629. The experimental results suggested that EnsemblePup presented here might be useful to identify and annotate potential pupylation sites in proteins of interest. A web server for predicting pupylation sites was developed.

Description: Background: The geographic distribution of evolutionary lineages and the patterns of gene flow upon secondary contact provide insight into the process of divergence and speciation. We explore the evolutionary history of the common lizard Zootoca vivipara (= Lacerta vivipara) in the Iberian Peninsula and test the role of the Pyrenees and the Cantabrian Mountains in restricting gene flow and driving lineage isolation and divergence. We also assess patterns of introgression among lineages upon secondary contact, and test for the role of high-elevation trans-mountain colonisations in explaining spatial patterns of genetic diversity. We use mtDNA sequence data and genome-wide AFLP loci to reconstruct phylogenetic relationships among lineages, and measure genetic structure Results: The main genetic split in mtDNA corresponds generally to the French and Spanish sides of the Pyrenees as previously reported, in contrast to genome-wide AFLP data, which show a major division between NW Spain and the rest. Both types of markers support the existence of four distinct and geographically congruent genetic groups, which are consistent with major topographic barriers. Both datasets reveal the presence of three independent contact zones between lineages in the Pyrenean region, one in the Basque lowlands, one in the low-elevation mountains of the western Pyrenees, and one in the French side of the central Pyrenees. The latter shows genetic evidence of a recent, high-altitude trans-Pyrenean incursion from Spain into France. Conclusions: The distribution and age of major lineages is consistent with a Pleistocene origin and a role for both the Pyrenees and the Cantabrian Mountains in driving isolation and differentiation of Z. vivipara lineages at large geographic scales. However, mountain ranges are not always effective barriers to dispersal, and have not prevented a recent high-elevation trans-Pyrenean incursion that has led to asymmetrical introgression among divergent lineages. Cytonuclear discordance in patterns of genetic structure and introgression at contact zones suggests selection may be involved at various scales. Suture zones are important areas for the study of lineage formation and speciation, and our results show that biogeographic barriers can yield markedly different phylogeographic patterns in different vertebrate and invertebrate taxa.

Description: Background: Loss of CpG dinucleotides in genomic DNA through methylation-induced mutation is characteristic of vertebrates and plants. However, these and other eukaryotic phyla show a range of other dinucleotide frequency biases with currently uncharacterized underlying mutational or selection mechanisms. We developed a parameterized Markov process to identify what neighbour context-dependent mutations best accounted for patterns of dinucleotide frequency biases in genomic and cytoplasmically expressed mRNA sequences of different vertebrates, other eukaryotic groups and RNA viruses that infect them. Results: Consistently, 11- to 14-fold greater frequencies of the methylation-association mutation of C to T upstream of G (depicted C[rightwards arrow]T,G) than other transitions best modelled dinucleotide frequencies in mammalian genomic DNA. However, further mutations such as G[rightwards arrow]T,T (5-fold greater than the default transversion rate) were required to account for the full spectrum of dinucleotide frequencies in mammalian sequence datasets. Consistent with modeling predictions for these two mutations, instability of both CpG and CpT dinucleotides was identified through SNP frequency analysis of human DNA sequences. Different sets of context-dependent mutations were modelled in other eukaryotes with non-methylated genomic DNA. In contrast to genomic DNA, best-fit models of dinucleotide frequencies in transcribed RNA sequences expressed in the cytoplasm from all organisms were dominated by mutations that eliminated UpA dinucleotides, observations consistent with cytoplasmically driven selection for mRNA stability. Surprisingly, mRNA sequences from organisms with methylated genomes showed evidence for additional selection against CpG through further context-dependent mutations (eg. C[rightwards arrow]A,G). Similar mutation or selection processes were identified among single-stranded mammalian RNA viruses; these potentially account for their previously described but unexplained under-representations of CpG and UpA dinucleotides. Conclusions: Methods we have developed identify mutational processes and selection pressures in organisms provide new insights into nucleotide compositional constraints and a wealth of biochemical and evolutionarily testable predictions for the future.

Description: Background: Human resources are an important building block of the health system. During the last decade, enormous investment has gone into the information systems to manage human resources, but due to the lack of a clear vision, policy, and strategy, the results of these efforts have not been very visible. No reliable information portal captures the actual state of human resources in Pakistan's health sector. The World Health Organization (WHO) has provided technical support for the assessment of the existing system and development of a comprehensive Human Resource Information System (HRIS) in Pakistan. Methods: The questions in the WHO-HRIS Assessment tool were distributed into five thematic groups. Purposively selected (n=65) representatives from the government, private sector, and development partners participated in this cross sectional study, based on their programmatic affiliations. Results: Fifty-five percent of organizations and departments have an independent Human Resources (HR) section managed by an establishment branch and are fully equipped with functional computers. Forty-five organizations (70%) had HR rules, regulations and coordination mechanisms, yet these are not implemented. Data reporting is mainly in paper form, on prescribed forms (51%), registers (3%) or even plain papers (20%). Data analysis does not give inputs to the decision making process and dissemination of information is quite erratic. Most of the organizations had no feedback mechanism for cross checking the HR data, rendering it unreliable. Conclusion: Pakistan is lacking appropriate HRIS management. The current HRIS indeed has a multitude of problems. In the wake of 2011 reforms within the health sector, provinces are even in a greater need for planning their respective health department services and must work on the deficiencies and inefficiencies of their HRIS so that the gaps and HR needs are better aligned for reaching the 2015 UN Millennium Development Goals (MDGs) targets.

Description: Background: Ramie fiber extracted from stem bark is one of the most important natural fibers. Drought is a main environment stress which severely inhibits the stem growth of ramie and leads to a decrease of the fiber yield. The drought stress-regulatory mechanism of ramie is poorly understood.Result: Using Illumina sequencing, approximately 4.8 and 4.7 million (M) 21-nt cDNA tags were respectively sequenced in the cDNA libraries derived from the drought-stressed ramie (DS) and the control ramie under well water condition (CO). The tags generated from the two libraries were aligned with ramie transcriptome to annotate their function and a total of 23,912 and 22,826 ramie genes were matched by these tags of DS and CO library, respectively. Comparison of gene expression level between CO and DS ramie based on the differences of tag frequencies appearing in the two libraries revealed that there were 1516 potential drought stress-responsive genes, in which 24 genes function as transcription factor (TF). Among these 24 TFs, the unigene19721 encoding the DELLA protein which is a key negative regulator in gibberellins (GAs) signal pathway was probably markedly up-regulated under water stress for a increase of tag abundance in DS library, which is possibly responsible for the inhibition of the growth of drought-stressed ramie. In order to validate the change of expression of these potential stress-responsive TFs under water deficit condition, the unigene19721 and another eleven potential stress-responsive TFs were chosen for further expression analysis in well-watered and drought-stressed ramie by real-time quantitative PCR (qRT-PCR) and the result showed that all 12 TFs were authentically involved in the response of drought stress. Conclusion: In this study, twelve TFs involving in the response of drought stress were first found by Illumina tag-sequencing and qRT-PCR in ramie. The discovery of these drought stress-responsive TFs will be helpful for further understanding the drought stress-regulatory mechanism of ramie and improving the drought tolerance ability of ramie.

Description: Hanping Hu, Jun Xu, Xiang Xia, Shaobin Wu, Yanlong Liu et al. A singular resonance is discovered in investigating the features of high-frequency photoacoustic (PA) effect with multilayers. Theoretical analysis of its formation is carried out and reveals that it is a result of interaction between the resonance of gas-heat and that of solid-heat, while they happ ... [J. Appl. Phys. 114, 104902 (2013)] published Tue Sep 10, 2013.

Description: Punam Silwal, Ludi Miao, Jin Hu, Leonard Spinu, Dae Ho Kim et al. We present the thickness dependent structural, magnetic, and transport properties of transparent conducting spinel NiCoO thin films on MgAlO (001) substrates. The structural examination of the films reveals that the epitaxial stain is independent of the films' thickness. Electric and magnetic measur ... [J. Appl. Phys. 114, 103704 (2013)] published Tue Sep 10, 2013.

Description: Junbo Guo, Zhanghua Gan, Zhihong Lu, Jing Liu, Jingjing Xi et al. Low visible light absorption and high charge carrier recombination rate are two main disadvantages of TiO as a photocatalyst which severely limit its practical applications. To overcome the problems, Fe mono-doped and (Fe+Mo) co-doped TiO were synthesized and studied. It was found that (Fe+Mo) co-do ... [J. Appl. Phys. 114, 104903 (2013)] published Tue Sep 10, 2013.

Description: We used a one-dimensional simulation program Solar Cell Capacitance Simulator in 1 Dimension (SCAPS-1D) to investigate Copper-Indium-Gallium-Diselenide- (CIGS-) based solar cells properties. Starting with a conventional ZnO-B/i-ZnO/CdS/CIGS structure, we simulated the parameters of current-voltage characteristics and showed how the absorber layer thickness, hole density, and band gap influence the short-circuit current density (), open-circuit voltage (), fill factor (FF), and efficiency of solar cell. Our simulation results showed that all electrical parameters are greatly affected by the absorber thickness (w) below 1000 nm, due to the increase of back-contact recombination and very poor absorption. Increasing hole density (p) or absorber band gap () improves and leads to high efficiency, which equals value of 16.1% when p = 1016 cm−3 and  eV. In order to reduce back-contact recombination, the effect of a very thin layer with high band gap inserted near the back contact and acting as electrons reflector, the so-called back-electron reflector (EBR), has been investigated. The performances of the solar cells are significantly improved, when ultrathin absorbers (w 〈 500 nm) are used; the corresponding gain of due to the EBR is 3 mA/cm2. Our results are in good agreement with those reported in the literature from experiments.

Description: The work presents comparisons of the flame stabilization characteristics of axisymmetric disk and 2D slender bluff-body burner configurations, operating with inlet mixture stratification, under ultralean conditions. A double cavity propane air premixer formed along three concentric disks, supplied with a radial equivalence ratio gradient the afterbody disk recirculation, where the first flame configuration is stabilized. Planar fuel injection along the center plane of the leading face of a slender square cylinder against the approach cross-flow results in a stratified flame configuration stabilized alongside the wake formation region in the second setup. Measurements of velocities, temperatures, and chemiluminescence, local extinction criteria, and large-eddy simulations are employed to examine a range of ultralean and close to extinction flame conditions. The variations of the reacting front disposition within these diverse reacting wake topologies, the effect of the successive suppression of heat release on the near flame region characteristics, and the reemergence of large-scale vortical activity on approach to lean blowoff (LBO) are investigated. The cross-correlation of the performance of these two popular flame holders that are at the opposite ends of current applications might offer helpful insights into more effective control measures for expanding the operational margin of a wider range of stabilization configurations.

Description: Background: The great majority of afferent neurons of insect legs project into their segmental ganglion. Intersegmental projections are rare and are only formed by sense organs associated with the basal joints of the legs. Such intersegmental projections never ascend as far as the brain and they form extensive ramifications within thoracic ganglia. A few afferents of chordotonal organs of the subcoxal joints ascend as far as the suboesophageal ganglion. Results: We describe novel afferent neurons in distal segments of locust legs that project directly into the brain without forming ramifications in other ganglia. In the brain, the fibres terminate with characteristic terminals in a small neuropile previously named the superficial ventral inferior protocerebrum. The somata of these neurons are located in the tibiae and tarsi of all legs and they are located within branches of peripheral nerves, or closely associated with such branches. They are not associated with any accessory structures such as tendons or connective tissue strands as typical for insect internal mechanoreceptors such as chordotonal organs or stretch receptors. Morphologically they show great similarity to certain insect infrared receptors.We could not observe projections into the superficial ventral inferior protocerebrum after staining mandibular or labial nerves, but we confirm previous studies that showed projections into the same brain neuropile after staining maxillary and antennal nerves, indicating that most likely similar neurons are present in these appendages also. Conclusion: Because of their location deep within the lumen of appendages the function of these neurons as infrared receptors is unlikely. Their projection pattern and other morphological features indicate that the neurons convey information about an internal physiological parameter directly into a special brain neuropile. We discuss their possible function as thermoreceptors.

Description: This review covers methods for modifying the structures of polysaccharides. The introduction of hydrophobic, acidic, basic, or other functionality into polysaccharide structures can alter the properties of materials based on these substances. The development of chemical methods to achieve this aim is an ongoing area of research that is expected to become more important as the emphasis on using renewable starting materials and sustainable processes increases in the future. The methods covered in this review include ester and ether formation using saccharide oxygen nucleophiles, including enzymatic reactions and aspects of regioselectivity; the introduction of heteroatomic nucleophiles into polysaccharide chains; the oxidation of polysaccharides, including oxidative glycol cleavage, chemical oxidation of primary alcohols to carboxylic acids, and enzymatic oxidation of primary alcohols to aldehydes; reactions of uronic-acid-based polysaccharides; nucleophilic reactions of the amines of chitosan; and the formation of unsaturated polysaccharide derivatives.

Description: The electroreduction behaviour and determination of cefoperazone using a hanging mercury drop electrode were investigated. Cyclic voltammograms of cefoperazone recorded in universal Britton-Robinson buffers pH 3–6 exhibited a single irreversible cathodic peak. The process was adsorption-controlled. Britton-Robinson buffer 0.04 M pH 4.0 was selected as a supporting electrolyte for quantitative purposes by differential pulse and square wave adsorptive cathodic stripping voltammetry. The experimental voltammetric conditions were optimized using Central Composite Face design. A reduction wave was seen in the range from −0.7 to −0.8 V. These voltammetric techniques were successfully validated as per ICH guidelines and applied for the determination of cefoperazone in its single and sulbactam containing powders for injection and statistically comparable to USP-HPLC. They were further extended to determine cefoperazone in spiked human urine with no matrix effect.

Description: L. Li, A. Nikiforov, Q. Xiong, N. Britun, R. Snyders et al. Recently, plasma jet systems found numerous applications in the field of biomedicine and treatment of temperature-sensitive materials. OH radicals are one of the main active species produced by these plasmas. Present study deals with the investigation of RF atmospheric pressure plasma jet in terms o ... [Phys. Plasmas 20, 093502 (2013)] published Tue Sep 10, 2013.

Description: H. Comişel, D. Verscharen, Y. Narita, and U. Motschmann We present a method for studying the evolution of plasma turbulence by tracking dispersion relations in the energy spectrum in the wavenumber-frequency domain. We apply hybrid plasma simulations in a simplified two-dimensional geometry to demonstrate our method and its applicability to plasma turbul ... [Phys. Plasmas 20, 090701 (2013)] published Tue Sep 10, 2013.

Description: Yi Zhang, Hayaki Murata, Yoshimi Hatsukade, and Saburo Tanaka We introduce a method to improve the detection sensitivity for the magnetization M of superparamagnetic nanoparticles (MNP). The M response of MNP to an applied magnetic field H (MH characteristics) could be divided into a linear region and a saturation region, which are separated at a transition po ... [Rev. Sci. Instrum. 84, 094702 (2013)] published Tue Sep 10, 2013.

Description: J. M. Gao, Y. Liu, W. Li, J. Lu, Y. B. Dong et al. An infrared imaging bolometer diagnostic has been developed recently for the HL-2A tokamak to measure the temporal and spatial distribution of plasma radiation. The three-dimensional tomography, reduced to a two-dimensional problem by the assumption of plasma radiation toroidal symmetry, has been pe ... [Rev. Sci. Instrum. 84, 093503 (2013)] published Tue Sep 10, 2013.

Description: G. C. Schmidt, D. Hoft, M. Bhuie, K. Haase, M. Bellmann et al. The influence of post-press treatment on the modification of printed source/drain electrodes made of poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) with ethylene glycol is presented. Beside changes of the geometry and the conductivity of these mass printed structures, the work f ... [Appl. Phys. Lett. 103, 113302 (2013)] published Wed Sep 11, 2013.

Description: Hideki Gotoh, Haruki Sanada, Hiroshi Yamaguchi, and Tetsuomi Sogawa The distinctive effects of coherent phonons (groups of phase-matched phonons) on exciton states are reported by using single dot photoluminescence (PL) spectroscopy in semiconductor quantum dots (QDs). Coherent phonons that were induced with titanium thin metal films close to QDs by irradiating ultr ... [Appl. Phys. Lett. 103, 112104 (2013)] published Wed Sep 11, 2013.

Description: O. V. Bilousov, H. Geaney, J. J. Carvajal, V. Z. Zubialevich, P. J. Parbrook et al. Porous GaN layers are grown on silicon from gold or platinum catalyst seed layers, and self-catalyzed on epitaxial GaN films on sapphire. Using a Mg-based precursor, we demonstrate p-type doping of the porous GaN. Electrical measurements for p-type GaN on Si show Ohmic and Schottky behavior from gol ... [Appl. Phys. Lett. 103, 112103 (2013)] published Wed Sep 11, 2013.

Description: Roberto Rosati and Fausto Rossi In spite of their intrinsic validity limits, a number of Boltzmann-like simulation schemes are extensively employed in the investigation of semiconductor nanomaterials and nanodevices. Such modeling strategies, based on the neglect of carrier phase coherence, are definitely unable to describe space- ... [Appl. Phys. Lett. 103, 113105 (2013)] published Wed Sep 11, 2013.

Description: The problem of exponential stability for the uncertain neutral Markovian jump systems with interval time-varying delays and nonlinear perturbations is investigated in this paper. This study starts from the corresponding nominal systems with known and partially unknown transition rates, respectively. By constructing a novel augmented Lyapunov functional which contains triple-integral terms and fully utilizes the bound of the delay, the delay-range-dependent and rate-dependent exponential stability criteria are developed by the Lyapunov theory, reciprocally convex lemma, and free weighting matrices. Then, the results about nominal systems are extended to the uncertain case. Finally, numerical examples are given to demonstrate the effectiveness of the proposed methods.

Description: The local fractional Schrödinger equations in the one-dimensional Cantorian system are investigated. The approximations solutions are obtained by using the local fractional series expansion method. The obtained solutions show that the present method is an efficient and simple tool for solving the linear partial differentiable equations within the local fractional derivative.

Description: Background: Decision support systems for differential diagnosis have traditionally been evaluated on the basis of criteria how sensitively and specifically they are able to identify the correct diagnosis established by expert clinicians.DiscussionThis article questions whether evaluation criteria pertaining to identifying the correct diagnosis are most appropriate or useful. Instead it advocates evaluation of decision support systems for differential diagnosis based on the criterion of maximizing value of information.SummaryThis approach quantitatively and systematically integrates several important clinical management priorities, including avoiding serious diagnostic errors of omission and avoiding harmful or expensive tests.

Description: Background: Multidrug-resistant (MDR) Salmonella isolates are associated with increased morbidity compared to antibiotic-sensitive strains and are an important health and safety concern in both humans and animals. Salmonella enterica serovar Typhimurium is a prevalent cause of foodborne disease, and a considerable number of S. Typhimurium isolates from humans and livestock are resistant to three or more antibiotics. The majority of these MDR S. Typhimurium isolates are resistant to tetracycline, a commonly used and clinically and agriculturally relevant antibiotic. Because exposure of drug-resistant bacteria to antibiotics can affect cellular processes associated with virulence, such as invasion, we investigated the effect tetracycline had on the invasiveness of tetracycline-resistant MDR S. Typhimurium isolates. Results: The isolates selected and tested were from two common definitive phage types of S. Typhimurium, DT104 and DT193, and were resistant to tetracycline and at least three other antibiotics. Although Salmonella invasiveness is temporally regulated and normally occurs during late-log growth phase, tetracycline exposure induced the full invasive phenotype in a cell culture assay during early-log growth in several DT193 isolates. No changes in invasiveness due to tetracycline exposure occurred in the DT104 isolates during early-log growth or in any of the isolates during late-log growth. Real-time PCR was used to test expression of the virulence genes hilA, prgH, and invF, and these genes were significantly up-regulated during early-log growth in most isolates due to tetracycline exposure; however, increased virulence gene expression did not always correspond with increased invasion, and therefore was not an accurate indicator of elevated invasiveness. This is the first report to assess DT193 isolates, as well as the early-log growth phase, in response to tetracycline exposure, and it was the combination of both parameters that was necessary to observe the induced invasion phenotype. Conclusions: In this report, we demonstrate that the invasiveness of MDR S. Typhimurium can be modulated in the presence of tetracycline, and this effect is dependent on growth phase, antibiotic concentration, and strain background. Identifying the conditions necessary to establish an invasive phenotype is important to elucidate the underlying factors associated with increased virulence of MDR Salmonella.

Description: Background: Mutations in the PTRF gene, coding for cavin-1, cause congenital generalized lipodystrophy type 4 (CGL4) associated with myopathy. In CGL4, symptoms are variable comprising, in addition to myopathy, smooth and skeletal muscle hypertrophy, cardiac arrhythmias, and skeletal abnormalities. Secondary features are atlantoaxial instability, acanthosis nigricans, hepatomegaly, umbilical prominence and metabolic abnormalities related to insulin resistance, such as diabetes mellitus, hyperlipidemia and hepatic steatosis.Case presentationWe describe a 3 year-old child of Moroccan origin with mild muscle phenotype, mainly characterized by mounding, muscle pain, hyperCKemia and mild caveolin 3 reduction on muscle biopsy. No CAV3 gene mutation was detected; instead we found a novel mutation, a homozygous single base pair deletion, in the PTRF gene. Only after detection of this mutation a mild generalized loss of subcutaneous fat, at first underestimated, was noticed and the diagnosis of lipodystrophy inferred. Conclusions: The PTRF gene should be investigated in patients with hyperCKemia, mild myopathy associated with spontaneous or percussion-induced muscle contractions like rippling or mounding, and no CAV3 mutation. The analysis should be performed even if cardiac or metabolic alterations are absent, particularly in young patients in whom lipodystrophy may be difficult to ascertain.

Description: Background: Magnetotactic bacteria produce membrane-enveloped magnetite crystals (magnetosomes) whose formation is controlled primarily by a gene island termed the magnetosome island (MAI). Characterization of single gene and operon function in MAI has elucidated in part the genetic basis of magnetosome formation. The mamX gene, located in the mamXY operon, is highly conserved in the MAI of all Magnetospirillum strains studied to date. Little is known regarding the function of mamX in the process of biomineralization. Results: A mamX deletion mutant ([increment]mamX) and its complemented strain (CmamX) by conjugation in M. gryphiswaldense strain MSR-1 were constructed. There were no striking differences in cell growth among [increment]mamX, CmamX, and wild-type strain (WT). [increment]mamX displayed a much weaker magnetic response than WT. Transmission electron microscopy revealed the presence of irregular, superparamagnetic magnetite particles in [increment]mamX, in contrast to regular, single-domain particles in WT and CmamX. The phenotype of [increment]mamX was similar to that of an ftsZ-like deleted mutant and mamXY operon deleted mutant reported previously. Quantitative real-time RT-PCR (qPCR) results indicated that the deletion of mamX had differential effects on the transcription levels of the other three genes in the operon. Conclusions: The MamX protein plays an important role in controlling magnetosome size, maturation, and crystal form. The four MamXY proteins appear to have redundant functions involved in magnetosome formation. Our findings provide new insights into the coordinated function of MAI genes and operons in magnetosome formation.

Description: Background: Host plant roots, mycorrhizal mycelium and microbes are important and potentially interacting factors shaping the performance of mycorrhization helper bacteria (MHB). We investigated the impact of a soil microbial community on the interaction between the extraradical mycelium of the ectomycorrhizal fungus Piloderma croceum and the MHB Streptomyces sp. AcH 505 in both the presence and the absence of pedunculate oak microcuttings. Results: Specific primers were designed to target the internal transcribed spacer of the rDNA and an intergenic region between two protein encoding genes of P. croceum and the intergenic region between the gyrA and gyrB genes of AcH 505. These primers were used to perform real-time PCR with DNA extracted from soil samples. With a sensitivity of 10 genome copies and a linear range of 6 orders of magnitude, these real-time PCR assays enabled the quantification of purified DNA from P. croceum and AcH 505, respectively. In soil microcosms, the fungal PCR signal was not affected by AcH 505 in the absence of the host plant. However, the fungal signal became weaker in the presence of the plant. This decrease was only observed in microbial filtrate amended microcosms. In contrast, the PCR signal of AcH 505 increased in the presence of P. croceum. The increase was not significant in sterile microcosms that contained plant roots. Conclusions: Real-time quantitative PCR assays provide a method for directly detecting and quantifying MHB and mycorrhizal fungi in plant microcosms. Our study indicates that the presence of microorganisms and plant roots can both affect the nature of MHB-fungus interactions, and that mycorrhizal fungi may enhance MHB growth.

Description: Background: Little is known about the Phasmatodea gut microbial community, including whether phasmids have symbiotic bacteria aiding in their digestion. While symbionts are near ubiquitous in herbivorous insects, the Phasmatodea's distinctively thin body shape precludes the gut enlargements needed for microbial fermentation. High-throughput sequencing was used to characterize the entire microbiota of the fat bodies, salivary glands, and anterior and posterior midguts of two species of walking stick. Results: Most bacterial sequences belonged to a strain of Spiroplasma (Tenericutes) found primarily in the posterior midgut of the parthenogenetic species Ramulus artemis (Phasmatidae). Beyond this, no significant differences were found between the R. artemis midgut sections or between that species and Peruphasma schultei (Pseudophasmatidae). Histological analysis further indicated a lack of bacteriocytes. Conclusions: Phasmids are unlikely to depend on bacteria for digestion, suggesting they produce enzymes endogenously that most other herbivorous insects obtain from symbionts. This conclusion matches predictions based on phasmid anatomy. The role of Spiroplasma in insects warrants further study.

Description: Background: High-throughput sequencing technologies are improving in quality, capacity and costs, providing versatile applications in DNA and RNA research. For small genomes or fraction of larger genomes, DNA samples can be mixed and loaded together on the same sequencing track. This so-called multiplexing approach relies on a specific DNA tag or barcode that is attached to the sequencing or amplification primer and hence appears at the beginning of the sequence in every read. After sequencing, each sample read is identified on the basis of the respective barcode sequence.Alterations of DNA barcodes during synthesis, primer ligation, DNA amplification, or sequencing may lead to incorrect sample identification unless the error is revealed and corrected. This can be accomplished by implementing error correcting algorithms and codes. This barcoding strategy increases the total number of correctly identified samples, thus improving overall sequencing efficiency. Two popular sets of error-correcting codes are Hamming codes and Levenshtein codes.ResultLevenshtein codes operate only on words of known length. Since a DNA sequence with an embedded barcode is essentially one continuous long word, application of the classical Levenshtein algorithm is problematic. In this paper we demonstrate the decreased error correction capability of Levenshtein codes in a DNA context and suggest an adaptation of Levenshtein codes that is proven of efficiently correcting nucleotide errors in DNA sequences. In our adaption we take the DNA context into account and redefine the word length whenever an insertion or deletion is revealed. In simulations we show the superior error correction capability of the new method compared to traditional Levenshtein and Hamming based codes in the presence of multiple errors. Conclusion: We present an adaptation of Levenshtein codes to DNA contexts capable of correction of a pre-defined number of insertion, deletion, and substitution mutations. Our improved method is additionally capable of recovering the new length of the corrupted codeword and of correcting on average more random mutations than traditional Levenshtein or Hamming codes.As part of this work we prepared software for the flexible generation of DNA codes based on our new approach. To adapt codes to specific experimental conditions, the user can customize sequence filtering, the number of correctable mutations and barcode length for highest performance.

Description: Background: Angiogenesis is the main therapeutic mechanism of cell therapy for cardiovascular diseases, but diabetes is reported to reduce the function and number of progenitor cells. Therefore, we studied the effect of streptozotocin-induced diabetes on the bone marrow-mesenchymal stem cell (MSC) function, and examined whether diabetes-impaired MSC could be rescued by pretreatment with oxytocin. Results: MSCs were isolated and cultured from diabetic (DM) or non-diabetic (non-DM) rat, and proliferation rate was compared. DM-MSC was pretreated with oxytocin and compared with non-DM-MSC. Angiogenic capacity was estimated by tube formation and Matrigel plug assay, and therapeutic efficacy was studied in rat myocardial infarction (MI) model.The proliferation and angiogenic activity of DM-MSC were severely impaired but significantly improved by pretreatment with oxytocin. Kruppel-like factor 2 (KLF2), a critical angiogenic factor, was dramatically reduced in DM-MSC and significantly restored by oxytocin. In the Matrigel plug assay, vessel formation of DM-BMSCs was attenuated but was recovered by oxytocin. In rat MI model, DM-MSC injection did not ameliorate cardiac injury, whereas oxytocin-pretreated DM-MSC improved cardiac function and reduced fibrosis. Conclusions: Our results show that diabetes influenced MSC by reducing angiogenic capacity and therapeutic potential. We demonstrate the striking effect of oxytocin on stem cell dysfunction and suggest the use of oxytocin as a priming reagent in autologous stem cell therapy.

Description: Background: Temperature is one of key environmental parameters that affect the whole life of fishes and an increasing number of studies have been directed towards understanding the mechanisms of cold acclimation in fish. However, the adaptation of larvae to cold stress and the cold-specific transcriptional alterations in fish larvae remain largely unknown. In this study, we characterized the development of cold-tolerance in zebrafish larvae and investigated the transcriptional profiles under cold stress using RNA-seq. Results: Pre-exposure of 96hpf zebrafish larvae to cold stress (16[degree sign]C) for 24 h significantly increased their survival rates under severe cold stress (12[degree sign]C). RNA-seq generated 272 million raw reads from six sequencing libraries and about 92% of the processed reads were mapped to the reference genome of zebrafish. Differential expression analysis identified 1,431 up- and 399 down-regulated genes. Gene ontology enrichment analysis of cold-induced genes revealed that RNA splicing, ribosome biogenesis and protein catabolic process were the most highly overrepresented biological processes. Spliceosome, proteasome, eukaryotic ribosome biogenesis and RNA transport were the most highly enriched pathways for genes up-regulated by cold stress. Moreover, alternative splicing of 197 genes and promoter switching of 64 genes were found to be regulated by cold stress. A shorter isoform of stk16 that lacks 67 amino acids at the N-terminus was specifically generated by skipping the second exon in cold-treated larvae. Alternative promoter usage was detected for per3 gene under cold stress, which leading to a highly up-regulated transcript encoding a truncated protein lacking the C-terminal domains. Conclusions: These findings indicate that zebrafish larvae possess the ability to build cold-tolerance under mild low temperature and transcriptional and post-transcriptional regulations are extensively involved in this acclimation process.

Description: Background: Apoptosis is a highly controlled process of cell death that can be induced by periodontopathogens. The present study aimed to investigate the expression of Fas and Bcl-2 proteins by CD3+ T cells in vitro under stimulation by total Porphyromonas gingivalis antigens and purified recombinant P. gingivalis HmuY protein. Results: CD3+ T cells derived from CP patients and stimulated with HmuY expressed higher levels of Bcl-2 compared to identical cells stimulated with P. gingivalis crude extract or cells derived from NP control subjects (p = 0.043). Conclusion: The authors hypothesize that P. gingivalis HmuY plays a role in the pathogenesis of chronic periodontitis, possibly by reducing or delaying apoptosis in T cells through a pathway involving the Bcl-2 protein.

Description: Background: It is increasingly recognized that the bacteria that live in and on the human body (the microbiome) can play an important role in health and disease. The composition of the microbiome is potentially influenced by both internal factors (such as phylogeny and host physiology) and external factors (such as diet and local environment), and interspecific comparisons can aid in understanding the importance of these factors. Results: To gain insights into the relative importance of these factors on saliva microbiome diversity, we here analyze the saliva microbiomes of chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) from two sanctuaries in Africa, and from human workers at each sanctuary. The saliva microbiomes of the two Pan species are more similar to one another, and the saliva microbiomes of the two human groups are more similar to one another, than are the saliva microbiomes of human workers and apes from the same sanctuary. We also looked for the existence of a core microbiome and find no evidence for a taxon-based core saliva microbiome for Homo or Pan. In addition, we studied the saliva microbiome from apes from the Leipzig Zoo, and found an extraordinary diversity in the zoo ape saliva microbiomes that is not found in the saliva microbiomes of the sanctuary animals. Conclusions: The greater similarity of the saliva microbiomes of the two Pan species to one another, and of the two human groups to one another, are in accordance with both the phylogenetic relationships of the hosts as well as with host physiology. Moreover, the results from the zoo animals suggest that novel environments can have a large impact on the microbiome, and that microbiome analyses based on captive animals should be viewed with caution as they may not reflect the microbiome of animals in the wild.

Description: Background: The choice of variable selection methods to identify important variables for binary classification modeling is critical to produce stable models that are interpretable, that generate accurate predictions and have minimum bias. This work is motivated by data on clinical and laboratory features of severe dengue infections (dengue hemorrhagic fever, DHF) obtained from 51 individuals enrolled in a prospective observational study of acute human dengue infections. Results: We carry out a comprehensive performance comparison using several classification models for DHF over the dengue data set. We compared variable selection results by Multivariate Adaptive Regression Splines, Learning Ensemble, Random Forest, Bayesian Moving Averaging, Stochastic Search Variable Selection, and Generalized Regularized Logistics Regression. Model averaging methods (bagging, boosting and ensemble learners) have higher accuracy, but the generalized regularized regression model has the highest predictive power because the linearity assumptions of candidate predictors are strongly satisfied via deviance chi-square testing procedures. Bootstrapping applications for evaluating predictive regression coefficients in regularized regression model are performed. Conclusions: Feature reduction methods introduce inherent biases and therefore are data-type dependent. We propose that these limitations can be overcome using an exhaustive approach for searching feature space. Using this approach, we results suggest that IL-10, platelet and lymphocyte counts are the major features for predicting dengue DHF on the basis of blood chemistries and cytokine measurements.

Description: Background: Sjogren's syndrome is characterized by lymphocytic infiltration of the exocrine glands, together with polyclonal B-cell activation, and lung diseases are well-known complications of the disease. Therefore, in most cases associated with Sjogren's syndrome, infiltrating lymphocytes in the lung specimen exhibit the features of B-cells. We herein report an atypical case of lymphoproliferative pulmonary involvement in a patient with Sjogren's syndrome.Case presentationA 46-year-old female was admitted to our hospital because of an abnormal chest roentgenogram finding on a medical checkup. Chest computed tomography showed randomly-distributed micronodules and patchy ground-glass opacities. A surgical biopsied specimen showed an atypical pattern of interstitial pneumonia with numerous lymphoid follicles. Among the infiltrating lymphocytes in the lung, only the monoclonality of the T-cells was proven by a gene rearrangement analysis, but there was no cytological atypicality or genetic disorder revealed by testing the bone marrow aspirate. A diagnosis of Sjogren's syndrome was made based on the patient's other symptoms and these negative findings. The patient's pulmonary lesions have been successfully treated and remission has been maintained for over three years with corticosteroid treatment alone. Conclusion: The present patient was an atypical case of lymphoproliferative pulmonary involvement in a patient with Sjogren's syndrome. Although monoclonality of the infiltrating T-cells was proven, the clinical course and the findings of the imaging and laboratory examinations were inconsistent with the previously-reported cases of primary pulmonary T-cell lymphoma. This suggests that the monoclonality of lymphocytes does not always define malignancy. The diagnosis of malignant lymphoma or lymphoproliferative diseases should be made clinically, pathologically and cytogenetically to rule out other similar diseases.

Description: Publication date: Available online 11 September 2013 Source: FEBS Open Bio Author(s): Gisele Castro , Maria Fernanda C. Areias , Lais Weissmann , Paula G.F. Quaresma , Carlos K. Katashima , Mario J.A. Saad , Patricia O. Prada Insulin acts in the hypothalamus, decreasing food intake (FI) by the IR/PI3K/Akt pathway. This pathway is impaired in obese animals and endoplasmic reticulum (ER) stress and low-grade inflammation are possible mechanisms involved in this impairment. Here, we highlighted the amygdala as an important brain region for FI regulation in response to insulin. This regulation was dependent on PI3K/AKT pathway similar to the hypothalamus. Insulin was able to decrease neuropeptide Y (NPY) and increase oxytocin mRNA levels in the amygdala via PI3K, which may contribute to hypophagia. Additionally, obese rats did not reduce FI in response to insulin and AKT phosphorylation was decreased in the amygdala, suggesting insulin resistance. Insulin resistance was associated with ER stress and low-grade inflammation in this brain region. The inhibition of ER stress with PBA reverses insulin action/signaling, decreases NPY and increases oxytocin mRNA levels in the amygdala from obese rats, suggesting that ER stress is probably one of the mechanisms that induce insulin resistance in the amygdala.

Description: An experiment of hydrogen preparation from steam-carbon reaction catalyzed by K2CO3 was carried out at 700°C, which was driven by the solar reaction system simulated with Xenon lamp. It can be found that the rate of reaction with catalyst is 10 times more than that without catalyst. However, for the catalytic reaction, there is no obvious change for the rate of hydrogen generation with catalyst content range from 10% to 20%. Besides, the conversion efficiency of solar energy to chemical energy is more than 13.1% over that by photovoltaic-electrolysis route. An analysis to the mechanism of catalytic steam-carbon reaction with K2CO3 is given, and an explanation to the nonbalanced [H2]/[CO + 2CO2] is presented, which is a phenomenon usually observed in experiment.

Description: Concentrations of Cd, Co, Pb, and Zn in riverbed sediments from six sampling stations along the Sungai Kilim, Langkawi, Malaysia, were determined by using the Teflon Bomb Digestion. From this study, the concentrations of heavy metals in riverbed sediments were found ranging between 6.10 and 8.87 μg/g dry weight for Co, 0.03 and 0.45 μg/g dry weight for Cd, 59.8 and 74.9 μg/g dry weight for Zn, and 1.06 and 11.69 μg/g dry weight for Pb. From the observation, these areas were polluted by domestic waste, aquaculture, and tourism activities. For clarity, enrichment factor index was used to determine the level of sediment contamination in the study area. From this study, the average EF value is a bit high for Cd () followed by Zn (), Pb (), and lastly, Co (). Based on the contamination categories, Cd was categorised as moderately enriched, while the rest of the metals studied were in deficient-to-minimally enriched by the anthropogenic sources.

Description: A catalytic adsorptive cathodic stripping voltammetric method on an improved bismuth film electrode (BiFE) for the determination of trace germanium in the presence of pyrogallol has been investigated. A well-defined and sensitive stripping peak of Ge(IV)-pyrogallol complex was observed at −0.79 V (versus SCE) in a 0.1 M acetate buffer solution (pH 4.8) at a deposition potential of −0.34 V. The reduction current is catalytically enhanced by adding KBrO3. The experimental variables and potential interference were studied. Compared with the BiFE plated in the solution prepared based on HAc-NaAc without trisodium citrate, the improved BiFE electrodeposited in the solution of HAc-NaAc containing trisodium citrate displayed a better electroanalytical performance for the determination of germanium(IV). Under the optimized conditions, the detection limit of Ge(IV) was 60 ng L−1, and the relative standard deviation (RSD) was 3.73% at 5 μg L−1 level (). This method was successfully applied to determine the total germanium in several Chinese herbal remedies.

Description: Changes of antioxidant properties of -lipoic acid (LA) after UV irradiation were studied. LA is the typical drug used in diabetic neuropathy. Quenching of free radicals is an important factor of therapy by using this substance. -Lipoic acid is exposed to UV irradiation during the storage. The aim of our studies was to examine the effect of UV irradiation on the interactions of LA with free radicals. The -lipoic acid was irradiated by UVA 315–400 nm light during 10 to 110 minutes by intervals of 10 minutes. The electron paramagnetic resonance spectroscopy was used as the experimental technique. The antioxidant properties of LA were spectroscopically confirmed. The strong effect of UV irradiation on interactions of -lipoic acid with free radicals was observed. It was pointed out that interactions of LA with free radicals decrease after its exposition on UV. The interactions of LA with free radicals were higher after the sample irradiation during 10 minutes than for the samples irradiated longer (20–110 minutes). The results are important for problems connected with photomedicine; they pointed out that -lipoic acid should not be stored on UV exposition. Application of electron paramagnetic resonance spectroscopy to characterize interactions of pharmacological substance with free radicals was confirmed.

Description: Copper antimony sulfide (CAS) is a relatively new class of sustainable absorber material, utilizing cost effective and abundant elements. Band gap engineered, modified CAS thin films were synthesized using electrodeposition and elevated temperature sulfurization approach. A testing analog of copper zinc antimony sulfide (CZAS) film-electrolyte interface was created in order to evaluate photoelectrochemical performance of the thin film of absorber materials. Eu3+/Eu2+ redox couple was selected for this purpose, based on its relative band offset with copper antimony sulfide. It was observed that zinc has a significant effect on CAS film properties. An enhanced photocurrent was observed for CAS film, modified with zinc addition. A detailed investigation has been carried out by changing stoichiometry, and corresponding surface and optical characterization results have been evaluated. A summary of favorable processing parameters of the films showing enhanced photoelectrochemical response is presented.

Description: Tidal influence and local morphology on circulation and salt transport are investigated in the Caeté river estuary, a well-mixed estuary along the north coast of Brazil. Velocity, temperature, and salinity data were collected in three different locations along the estuary’s main channel, over three single, 13 h tidal cycles. The aim of this study was to investigate the relationship between tidal distortion and salinity by using classical methods of comparison of three cross-channel circulation characteristics, as well as computation of salt flux and vertical mixing. Findings indicate a flood-ebb asymmetry in currents, due to the distinct funneling morphology of the estuary, with shallow marginal areas being dominant towards the estuary head, while both stratification and shear dominate near the estuary mouth. The tidal currents enhanced vertical diffusion in the mid- and lower reaches, explaining the prevailing weakly stratified conditions, while the dominant well-mixed conditions in the upper estuary are a result of a combination of stronger flood currents and negligible vertical saline gradient. The predominant downstream salt transport supports the conclusion that there is little accumulation of salt in the Caeté river estuary. In addition, findings indicate that tidal correlation and Stokes drift are important components in the upper estuary, while tidal correlation played an important role in the middle estuary, with fluvial discharge most important in the lower estuary.

Description: The present paper investigates the reliability analysis of industrial systems by using vague lambda-tau methodology in which information related to system components is uncertain and imprecise in nature. The uncertainties in the data are handled with the help of intuitionistic fuzzy set (IFS) theory rather than fuzzy set theory. Various reliability parameters are addressed for strengthening the analysis in terms of degree of acceptance and rejection of IFS. Performance as well as sensitivity analysis of the system parameter has been investigated for accessing the impact of taking wrong combinations on its performance. Finally results are compared with the existing traditional crisp and fuzzy methodologies results. The technique has been demonstrated through a case study of bleaching unit of a paper mill.

Description: A new stability-indicating reversed-phase high-performance thin-layer chromatographic (RP-HPTLC) method for densitometric analysis of thiocolchicoside was developed and validated. The chromatograms were developed using aluminum plates pre-coated with silica gel 60 RP-18 F254S as a stationary phase and methanol : water (70 : 30 ) as a mobile phase. The compact band for thiocolchicoside was observed at value of at an absorption wavelength of 377 nm. The linear regression data for the calibration plots () was found with respect to peak area in the concentration range of 100–600 ng per band. The limit of detection (LOD) and limit of quantification (LOQ) were 9.77 ng and 29.63 ng, respectively. The drug was exposed to acidic and alkaline hydrolysis, oxidation, photo degradation, and dry heat conditions. The peaks of degradation products were well-resolved from the peak of the standard drug with significantly different values. Statistical analysis proved that the established RP-HPTLC method is reproducible, selective, and accurate for the determination of thiocolchicoside in its formulations. The method can effectively separate the drug from its degradation products, and it can be considered as stability-indicating assay.

Description: In CdS/CdTe solar cells, chemical interdiffusion at the interface gives rise to the formation of an interlayer of the ternary compound . In this work, we evaluate the effects of this interlayer in CdS/CdTe photovoltaic cells in order to improve theoretical results describing experimental - (capacitance versus voltage) characteristics. We extended our previous theoretical methodology developed on the basis of three cardinal equations (Castillo-Alvarado et al., 2010). The present results provide a better fit to experimental data obtained from CdS/CdTe solar cells grown in our laboratory by the chemical bath deposition (for CdS film) and the close-spaced vapor transport (for CdTe film) techniques.

Description: Mohammad Arif Ishtiaque Shuvo, Tzu-Liang (Bill) Tseng, Md. Ashiqur Rahaman Khan, Hasanul Karim, Philip Morton et al. The study of electrochemical super-capacitors has become one of the most attractive topics in both academia and industry as energy storage devices because of their high power density, long life cycles, and high charge/discharge efficiency. Recently, there has been increasing interest in the developm ... [J. Appl. Phys. 114, 104306 (2013)] published Wed Sep 11, 2013.

Description: A relationship between sea surface temperature (SST) and surface nitrate concentrations has been obtained for the first time based on in situ datasets retrieved from U.S. JGOFS (1991–96) and Indian cruises (2000–2006) in the Arabian Sea, Bay of Bengal and Indian Ocean region around the southern Indian tip. The dataset includes 1537 points. A sigmoid relationship obtained with

Description: The ice floe speed variations were monitored at the research camp North Pole 35 established on the Arctic ice pack in 2008. A three-month time series of measured speed values was used for determining changes in the kinetic energy of the drifting ice floe. The constructed energy distributions were analyzed by methods of nonextensive statistical mechanics based on the Tsallis statistics for open nonequilibrium systems, such as tectonic formations and drifting sea ice. The nonextensivity means the nonadditivity of externally induced energy changes in multicomponent systems due to dynamic interrelation of components having no structural links. The Tsallis formalism gives one an opportunity to assess the correlation between ice floe motions through a specific parameter, the so-called parameter of nonextensivity. This formalistic assessment of the actual state of drifting pack allows one to forecast some important trends in sea ice behavior, because the level of correlated dynamics determines conditions for extended mechanical perturbations in ice pack. In this work, we revealed temporal fluctuations of the parameter of nonextensivity and observed its maximum value before a large-scale sea ice fragmentation (faulting) of consolidated sea ice. The correlation was not detected in fragmented sea ice where long-range interactions are weakened.

Description: Symbiotic diatom-diazotrophic cyanobacteria association (DDA) of Rhizosolenia hebetata and Rhizosolenia formosa with endosymbiotic cyanobacteria Richelia intracellularis was noticed and documented for the first time during a bloom of the cyanobacterium Trichodesmium erythraeum in the oligotrophic shelf waters along Kochi and Mangalore transects, southeastern Arabian Sea (SEAS), during spring intermonsoon (April 2012). Although the host is frequently seen, the symbiont is rarely reported in the Indian EEZ. The presence of nitrogen-fixing symbiotic association of Rhizosolenia-Richelia along with Trichodesmium erythraeum highlights the significance of DDAs on the nutrient and energy budgets of phytoplankton in the oligotrophic environments of the Arabian Sea during spring intermonsoon.

Description: Recent studies on the diazotrophic cyanobacterium Trichodesmium showed that increasing CO2 partial pressure (pCO2) enhances N2 fixation and growth. We studied the in situ and satellite-derived environmental parameters within and outside a Trichodesmium bloom in the western coastal Bay of Bengal (BoB) during the spring intermonsoon 2009. Here we show that the single most important nitrogen fixer in today’s ocean, Trichodesmium erythraeum, is strongly abundant in high (≥300 μatm) pCO2 concentrations. N : P ratios almost doubled (~10) at high pCO2 region. This could enhance the productivity of N-limited BoB and increase the biological carbon sequestration. We also report presence of an oxygen minimum zone at Thamnapatnam. Earlier studies have been carried out using lab cultures, showing the increase in growth rate of T. erythraeum under elevated pCO2 conditions, but to our knowledge, this study is the first to report that in natural environment also T. erythraeum prefers blooming in high pCO2 concentrations. The observed CO2 sensitivity of T. erythraeum could thereby provide a strong negative feedback to rising atmospheric CO2 but would also drive towards phosphorus limitation in a future high CO2 world.

Description: In a silicon wafer-based photovoltaic (PV) module, significant power is lost due to current transport through the ribbons interconnecting neighbour cells. Using halved cells in PV modules is an effective method to reduce the resistive power loss which has already been applied by some major PV manufacturers (Mitsubishi, BP Solar) in their commercial available PV modules. As a consequence, quantitative analysis of PV modules using halved cells is needed. In this paper we investigate theoretically and experimentally the difference between modules made with halved and full-size solar cells. Theoretically, we find an improvement in fill factor of 1.8% absolute and output power of 90 mW for the halved cell minimodule. Experimentally, we find an improvement in fill factor of 1.3% absolute and output power of 60 mW for the halved cell module. Also, we investigate theoretically how this effect confers to the case of large-size modules. It is found that the performance increment of halved cell PV modules is even higher for high-efficiency solar cells. After that, the resistive loss of large-size modules with different interconnection schemes is analysed. Finally, factors influencing the performance and cost of industrial halved cell PV modules are discussed.

Description: In three-phase photovoltaic (PV) system, three-phase filter inductors are important part for the output electrical power quality. The comparison analyses of three-phase discrete filter inductors and two kinds of three-phase integrated filter inductors in three-phase PV inverter are proposed. Firstly, the three-phase PV inverter operation with discrete filter inductors is analyzed, and the design of discrete filter inductors is given; then operation of the three-phase PV inverter with three-phase integrated five-limb magnetic core filter inductors is analyzed, the design of integrated filter inductors with five-limb magnetic core is given, then the operation of three-phase PV inverter with three-phase integrated three-limb magnetic core filter inductors is analyzed, and the design of integrated filter inductors with three limbs magnetic core is given. The conclusion of comparison between three-phase discrete filter inductors and two kinds of three-phase integrated filter inductors is done; it means that the three-phase discrete filter inductors can achieve better output electrical power quality with lower power density and three-phase integrated filter inductors can achieve higher power density with lower output electrical power quality. Finally, the experiment results are given to compare the volume and filter effect of three kinds of filter inductors in three-phase PV inverter.

Description: A classical issue in many applied fields is to obtain an approximating surface to a given set of data points. This problem arises in Computer-Aided Design and Manufacturing (CAD/CAM), virtual reality, medical imaging, computer graphics, computer animation, and many others. Very often, the preferred approximating surface is polynomial, usually described in parametric form. This leads to the problem of determining suitable parametric values for the data points, the so-called surface parameterization. In real-world settings, data points are generally irregularly sampled and subjected to measurement noise, leading to a very difficult nonlinear continuous optimization problem, unsolvable with standard optimization techniques. This paper solves the parameterization problem for polynomial Bézier surfaces by applying the firefly algorithm, a powerful nature-inspired metaheuristic algorithm introduced recently to address difficult optimization problems. The method has been successfully applied to some illustrative examples of open and closed surfaces, including shapes with singularities. Our results show that the method performs very well, being able to yield the best approximating surface with a high degree of accuracy.

Description: Atreyee Banerjee, Suman Chakrabarty, and Sarika Maitra Bhattacharyya In this work we explore the interplay between crystallization and glass transition in different binary mixtures by changing their inter-species interaction length and also the composition. We find that only those systems which form bcc crystal in the equimolar mixture and whose global structure for ... [J. Chem. Phys. 139, 104501 (2013)] published Wed Sep 11, 2013.

Description: S. Vigne, S. Delprat, M. Chaker, and J. Margot It is found that in specific Cl plasma conditions, using a nickel hard mask over calcium barium niobate, CBN (a material particularly difficult to etch) significantly improves both sidewall angles and etching selectivity. This mask hardening is due to the competition between NiCl growth and etching ... [J. Appl. Phys. 114, 103303 (2013)] published Wed Sep 11, 2013.

Description: S. Agnello, D. Di Francesca, A. Alessi, G. Iovino, M. Cannas et al. The O content and emission properties in silica nanoparticles after thermal treatments in oxygen rich atmosphere have been investigated by Raman and photoluminescence measurements. The nanoparticles have different sizes with average diameter ranging from 7 up to 40 nm. It is found that O concentrati ... [J. Appl. Phys. 114, 104305 (2013)] published Wed Sep 11, 2013.

Description: S. Maidul Haque, A. Biswas, Debarati Bhattacharya, R. B. Tokas, D. Bhattacharyya et al. Using an indigenously built r.f. magnetron sputtering system, several single layer Ti and Ni films have been deposited at varying deposition conditions. All the samples have been characterized by Grazing Incidence X-ray Reflectivity (GIXR) and Atomic Force Microscopy to estimate their thickness, den ... [J. Appl. Phys. 114, 103508 (2013)] published Wed Sep 11, 2013.

Description: Larisa V. Arapkina and Vladimir A. Yuryev Structural models of growing Ge hut clusterspyramids and wedgesare proposed on the basis of data of recent STM investigations of nucleation and growth of Ge huts on the Si(001) surface in the process of molecular beam epitaxy. It is shown that extension of a hut base along directions goes non-unifo ... [J. Appl. Phys. 114, 104304 (2013)] published Wed Sep 11, 2013.

Description: Jorg Schormann, Pascal Hille, Markus Schafer, Jan Mussener, Pascal Becker et al. Germanium doping of GaN nanowires grown by plasma-assisted molecular beam epitaxy on Si(111) substrates is studied. Time of flight secondary ion mass spectrometry measurements reveal a constant Ge-concentration along the growth axis. A linear relationship between the applied Ge-flux and the resultin ... [J. Appl. Phys. 114, 103505 (2013)] published Wed Sep 11, 2013.

Description: Younes Achaoui, Vincent Laude, Sarah Benchabane, and Abdelkrim Khelif The propagation of surface acoustic waves in two-dimensional phononic crystals of pillars on a surface is investigated experimentally for hexagonal and honeycomb lattice symmetries. A random array of pillars is also compared to the periodic phononic crystals. Taking into account that the geometrical ... [J. Appl. Phys. 114, 104503 (2013)] published Wed Sep 11, 2013.

Description: Yating Chai, Howard C. Wikle, Zhenyu Wang, Shin Horikawa, Steve Best et al. The real-time, in-situ bacteria detection on food surfaces was achieved by using a magnetoelastic biosensor combined with a surface-scanning coil detector. This paper focuses on the coil design for signal optimization. The coil was used to excite the sensor's vibration and detect its resonant freque ... [J. Appl. Phys. 114, 104504 (2013)] published Wed Sep 11, 2013.

Description: Frederik Westergaard Osterberg, Anders Dahl Henriksen, Giovanni Rizzi, and Mikkel Fougt Hansen Abstract not available. [J. Appl. Phys. 114, 106101 (2013)] published Wed Sep 11, 2013.

Description: Tomas Zimmermann and Jiri VaniCek We analyze how the choice of the sampling weight affects efficiency of the Monte Carlo evaluation of classical time autocorrelation functions. Assuming uncorrelated sampling or sampling with constant correlation length, we propose a sampling weight for which the number of trajectories needed for con ... [J. Chem. Phys. 139, 104105 (2013)] published Wed Sep 11, 2013.

Description: Y. V. Kalyuzhnyi and P. T. Cummings We propose a second-order thermodynamic perturbation theory for a hard-sphere patchy colloidal model with two doubly bondable patches of type A and B. AB bonding results in the formation of a three-dimensional network of the particles and AA and BB bonding promotes chain formation. The theory is app ... [J. Chem. Phys. 139, 104905 (2013)] published Wed Sep 11, 2013.