ALBERT

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: 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: 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: 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: 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: 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: 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: 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: 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.

Description: N. Aizawa, Z. Kuznetsova, and F. Toppan Inequivalent [script N]=2 supersymmetrizations of the [script-l]-conformal Galilei algebra in d-spatial dimensions are constructed from the chiral (2, 2) and the real (1, 2, 1) basic supermultiplets of the [script N]=2 supersymmetry. For non-negative integer and half-integer [script-l], both superal ... [J. Math. Phys. 54, 093506 (2013)] published Wed Sep 11, 2013.

Description: P. J. Saenz, P. Valluri, K. Sefiane, G. Karapetsas, and O. K. Matar A shallow planar layer of liquid bounded from above by gas is set into motion via the thermocapillary effect resulting from a thermal gradient applied along its interface. Depending on the physical properties of the liquid and the strength of the gradient, the system is prone to departure from its e ... [Phys. Fluids 25, 094101 (2013)] published Wed Sep 11, 2013.

Description: Alireza Paknezhad and Davoud Dorranian This article studies the nonlinear Raman shifted third harmonic backscattering of an intense extraordinary laser wave through a homogenous transversely magnetized cold plasma. Due to the relativistic nonlinearity, the plasma dynamic is modified in the presence of transversely magnetic field, and thi ... [Phys. Plasmas 20, 092108 (2013)] published Wed Sep 11, 2013.

Description: X. Xia and K. Mohseni Several previous experimental and theoretical studies have shown that a leading edge vortex (LEV) on an airfoil or wing can provide lift enhancement. In this paper, unsteady two-dimensional (2D) potential flow theory is employed to model the flow field of a pitching flat plate wing. A multi-vortices ... [Phys. Fluids 25, 091901 (2013)] published Wed Sep 11, 2013.

Description: H. B. Zhuo, X. H. Yang, C. T. Zhou, Y. Y. Ma, X. H. Li et al. The effect of resistivity gradient on laser-driven electron transport and ion acceleration is investigated using collisional particle-in-cell simulation. The study is motivated by recent proton acceleration experiments [Gizzi et al., Phys. Rev. ST Accel. Beams 14, 011301 (2011)], which showed signif ... [Phys. Plasmas 20, 093103 (2013)] published Wed Sep 11, 2013.

Description: Qing Zang, C. L. Hsieh, Junyu Zhao, Hui Chen, and Fengjuan Li The detector circuit is the core component of filter polychromator which is used for scattering light analysis in Thomson scattering diagnostic, and is responsible for the precision and stability of a system. High signal-to-noise and stability are primary requirements for the diagnostic. Recently, a ... [Rev. Sci. Instrum. 84, 093504 (2013)] published Wed Sep 11, 2013.

Description: Junku Liu, Qunqing Li, Mengxin Ren, Lihui Zhang, Mo Chen et al. Charging of insulating substrates is a common problem during Electron Beam lithography (EBL), which deflects the beam and distorts the pattern. A homogeneous, electrically conductive, and transparent graphene layer is used as a discharge layer for EBL processes on insulating substrates. The EBL reso ... [Appl. Phys. Lett. 103, 113107 (2013)] published Thu Sep 12, 2013.

Description: M. Vyshnepolsky, C. Klein, F. Klasing, A. Hanisch-Blicharski, and M. Horn-von Hoegen Using spot profile analysis low energy electron diffraction, we studied the growth mode and strain state of ultra-thin epitaxial BiSe(111) films grown by molecular beam epitaxy on Si(111). The first layer grows as complete quintuple layer and covers the Si substrate before the next layer nucleates. ... [Appl. Phys. Lett. 103, 111909 (2013)] published Thu Sep 12, 2013.

Description: Background: In cross breeding, it is important to choose a good parental combination that has high probability of generating offspring with desired characteristics. This study examines a method for predicting the segregation of target traits in a progeny population based on genome-wide markers and phenotype data of parental cultivars. Results: The proposed method combines segregation simulation and Bayesian modeling for genomic selection. Marker segregation in a progeny population was simulated based on parental genotypes. Posterior marker effects sampled via Markov Chain Monte Carlo were used to predict the segregation pattern of target traits. The posterior distribution of the proportion of progenies that fulfill selection criteria was calculated and used for determining a promising cross and the necessary size of the progeny population. We applied the proposed method to Japanese pear (Pyrus pyrifolia Nakai) data to demonstrate the method and to show how it works in the selection of a promising cross. Verification using an actual breeding population suggests that the segregation of target traits can be predicted with reasonable accuracy, especially in a highly heritable trait. The uncertainty in predictions was reflected on the posterior distribution of the proportion of progenies that fulfill selection criteria. A simulation study based on the real marker data of Japanese pear cultivars also suggests the potential of the method. Conclusions: The proposed method is useful to provide objective and quantitative criteria for choosing a parental combination and the breeding population size.

Description: Background: Gene reshuffling, point mutations and horizontal gene transfer contribute to bacterial genome variation, but require the genome to rewire its transcriptional circuitry to ensure that inserted, mutated or reshuffled genes are transcribed at appropriate levels. The genomes of Epsilonproteobacteria display very low synteny, due to high levels of reshuffling and reorganisation of gene order, but still share a significant number of gene orthologs allowing comparison. Here we present the primary transcriptome of the pathogenic Epsilonproteobacterium Campylobacter jejuni, and have used this for comparative and predictive transcriptomics in the Epsilonproteobacteria. Results: Differential RNA-sequencing using 454 sequencing technology was used to determine the primary transcriptome of C. jejuni NCTC 11168, which consists of 992 transcription start sites (TSS), which included 29 putative non-coding and stable RNAs, 266 intragenic (internal) TSS, and 206 antisense TSS. Several previously unknown features were identified in the C. jejuni transcriptional landscape, like leaderless mRNAs and potential leader peptides upstream of amino acid biosynthesis genes. A cross-species comparison of the primary transcriptomes of C. jejuni and the related Epsilonproteobacterium Helicobacter pylori highlighted a lack of conservation of operon organisation, position of intragenic and antisense promoters or leaderless mRNAs. Predictive comparisons using 40 other Epsilonproteobacterial genomes suggests that this lack of conservation of transcriptional features is common to all Epsilonproteobacterial genomes, and is associated with the absence of genome synteny in this subdivision of the Proteobacteria. Conclusions: Both the genomes and transcriptomes of Epsilonproteobacteria are highly variable, both at the genome level by combining and division of multicistronic operons, but also on the gene level by generation or deletion of promoter sequences and 5[prime] untranslated regions. Regulatory features may have evolved after these species split from a common ancestor, with transcriptome rewiring compensating for changes introduced by genomic reshuffling and horizontal gene transfer.

Description: N. Ortega, Ashok Kumar, Oscar Resto, O. A. Maslova, Yu. I. Yuzyuk et al. Epitaxial strain is one of the major factors influencing physical properties of artificial superlattice (SL) structures. One way to control the local stress in epitaxial films is altering the lattice parameters by doping. Superlattices of BT/BaSrTiO (BT/BST) with x = (0, 0.3, 0.4, 0.5, 0.6, 0.7, 1) ... [J. Appl. Phys. 114, 104102 (2013)] published Thu Sep 12, 2013.

Description: B. Brennan, R. V. Galatage, K. Thomas, E. Pelucchi, P. K. Hurley et al. InAlAs has the potential to be used as a barrier layer in buried channel quantum well field effect transistor devices due to favorable lattice-matching and carrier confinement properties with InGaAs. Field effect device structures of this nature may also require a high-k oxide deposited on the InAlA ... [J. Appl. Phys. 114, 104103 (2013)] published Thu Sep 12, 2013.

Description: Pooja Srivastava, B. J. Nagare, Dilip G. Kanhere, and Prasenjit Sen First-principles electronic structure calculations are performed for the pure and Co-doped PbPdO using plane wave density functional method using different exchange-correlation functionals. These calculations indicate the 25% Co-doped PbPdO to be a spin gapless semiconductor, as proposed earlier [X. ... [J. Appl. Phys. 114, 103709 (2013)] published Thu Sep 12, 2013.

Description: M. N. Shneider and M. Pekker A non-thermal mechanism of weak microwave field impact on a nerve fiber is proposed. It is shown that in the range of about 30300 GHz, there are strongly pronounced resonances associated with the excitation of ultrasonic vibrations in the membrane as a result of interaction with electromagnetic radi ... [J. Appl. Phys. 114, 104701 (2013)] published Thu Sep 12, 2013.

Description: K. Simeonidis, C. Martinez-Boubeta, Ll. Balcells, C. Monty, G. Stavropoulos et al. Magnetic hyperthermia, an alternative anticancer modality, is influenced by the composition, size, magnetic properties, and degree of aggregation of the corresponding nanoparticle heating agents. Here, we attempt to evaluate the AC magnetic field heating response of Fe-based nanoparticles prepared b ... [J. Appl. Phys. 114, 103904 (2013)] published Thu Sep 12, 2013.

Description: Souheil Mouetsi and Abdelillah El Hdiy The 1/f noise is investigated in an epitaxial AlGaAs/GaAs/AlGaAs heterostructure in the temperature range of [4300 K]. The sample is biased at very low voltage to avoid velocity saturation at low temperature. Hooge parameters are determined at very low frequency assuming the absence of correlation b ... [J. Appl. Phys. 114, 104507 (2013)] published Thu Sep 12, 2013.

Description: V. R. Singh, V. K. Verma, K. Ishigami, G. Shibata, Y. Yamazaki et al. BiFeO (BFO) shows both ferroelectricity and magnetic ordering at room temperature, but its ferromagnetic component, which is due to spin canting, is negligible. Substitution of transition-metal atoms such as Co for Fe is known to enhance the ferromagnetic component in BFO. In order to reveal the ori ... [J. Appl. Phys. 114, 103905 (2013)] published Thu Sep 12, 2013.

Description: N. Kotsina, S. Kaziannis, S. Danakas, and C. Kosmidis We report on the selective ionization of oriented nitrous oxide (NO) molecules in gas phase by the use of an intense asymmetric two-color omega/2omega 40 fs laser field. By means of a time-of-flight mass spectrometer the induced NO mass spectra have been recorded as a function of the relative phase ... [J. Chem. Phys. 139, 104313 (2013)] published Thu Sep 12, 2013.

Description: Bryan Nichols and Vitaly A. Rassolov The electron correlation energy in a chemical system is defined as a difference between the energy of an exact energy for a given Hamiltonian, and a mean-field, or single determinant, approximation to it. A promising way to model electron correlation is through the expectation value of a linear two- ... [J. Chem. Phys. 139, 104111 (2013)] published Thu Sep 12, 2013.

Description: Scott Habershon We introduce a new approach for calculating quantum time-correlation functions and time-dependent expectation values in many-body thermal systems; both electronically adiabatic and non-adiabatic cases can be treated. Our approach uses a path integral simulation to sample an initial thermal density m ... [J. Chem. Phys. 139, 104107 (2013)] published Thu Sep 12, 2013.

Description: Gustavo E. Scuseria, Thomas M. Henderson, and Ireneusz W. Bulik We establish a formal connection between the particle-particle (pp) random phase approximation (RPA) and the ladder channel of the coupled cluster doubles (CCD) equations. The relationship between RPA and CCD is best understood within a Bogoliubov quasiparticle (qp) RPA formalism. This work is a fol ... [J. Chem. Phys. 139, 104113 (2013)] published Thu Sep 12, 2013.

Description: Liangguo He, Chengliang Pan, Hongbo Wang, and Zhihua Feng We develop a novel approach to match harmonics and vibration modes based on the mechanism of multiple tuning fork structure (MTFS), through which it is promising to realize arbitrary periodical vibrations in the resonant state. A prototype three-layer MTFS with first three harmonics is presented to ... [Rev. Sci. Instrum. 84, 096104 (2013)] published Thu Sep 12, 2013.

Description: Yue Lin, Yong Zhang, Zhiqiang Liu, Liqin Su, Jihong Zhang et al. Abstract not available. [Appl. Phys. Lett. 103, 119902 (2013)] published Fri Sep 13, 2013.

Description: D. Haasmann and S. Dimitrijev Based on the insight that the Fermi level in a metaloxidesemiconductor field-effect transistor (MOSFET) channel is set in the conduction band, due to the quantum confinement of the channel electrons, this letter provides an experimental demonstration that the near-interface traps responsible for deg ... [Appl. Phys. Lett. 103, 113506 (2013)] published Fri Sep 13, 2013.

Description: Akira Nagaoka, Hideto Miyake, Tomoyasu Taniyama, Koichi Kakimoto, and Kenji Yoshino Temperature dependent Hall effect measurements from 20 to 300 K have been performed on the quaternary compounds CuZnSnS (CZTS) single crystals. The conductivity mechanisms can be described by a two-path system using Mott variable range hopping and typical thermal activation conduction. The center le ... [Appl. Phys. Lett. 103, 112107 (2013)] published Fri Sep 13, 2013.

Description: Manesh Gopinadhan, Zhen Shao, Yanhui Liu, Sundeep Mukherjee, Ryan C. Sekol et al. We explore finite size effects in the crystallization of a bulk metallic glass with nm-scale dimensions. Nanorods of PtCuNiP are produced by thermoplastic extrusion of supercooled liquid through a nanoporous template. The nanorods exhibit remarkable differences in their crystallization behavior abov ... [Appl. Phys. Lett. 103, 111912 (2013)] published Fri Sep 13, 2013.

Description: A. Bojovschi, J. Scott, and K. Ghorbani An investigation of the interaction between guided electromagnetic waves and carbon fibre reinforced polymer waveguide short circuits is presented. To determine the electromagnetic response of the composite waveguide short circuit, its anisotropic characteristics are considered. The reflection coeff ... [Appl. Phys. Lett. 103, 111910 (2013)] published Fri Sep 13, 2013.

Description: E. Pagounis, R. Chulist, T. Lippmann, M. Laufenberg, and W. Skrotzki Mechanical and synchrotron diffraction experiments were performed to investigate the temperature dependent structural changes in a Ni-Mn-Ga single crystal. The initial sample exhibits a mixture of seven-layered (7M) and non-modulated (NM) martensites at room temperature. Compression along resulted ... [Appl. Phys. Lett. 103, 111911 (2013)] published Fri Sep 13, 2013.

Description: Background: Hypersensitivity pneumonitis is defined as an allergic lung disease that occurs in response to inhalation of fungal antigens, bacterial antigens, chemicals, dusts, or animal proteins. The incidence of summer-type hypersensitivity pneumonitis is higher in the summer season, especially in Japan, due to the influence of the hot and humid environment and the common style of wood house or old concrete condominiums.Case presentationThe present report describes a case of a middle-aged married couple who lived in the same house and who simultaneously suffered from summer-type hypersensitivity pneumonitis. This report analyzes these two cases in terms of environmental research and its microbiological, radiological, and pathological aspects. This case report is followed by a review of family occurrences of summer-type hypersensitivity pneumonitis from 22 studies with a total of 49 patients (including the two present cases) in Japan. Conclusion: Summer-type hypersensitivity pneumonitis may be unrecognized and misdiagnosed as pneumonia or other respiratory diseases. A greater understanding of the clinical, pathologic, and environmental features of summer-type hypersensitivity pneumonitis might help improve diagnosis and delivery of appropriate management for this condition.

Description: Background: Cell migration is a fundamental biological process and has an important role in the developing brain by regulating a highly specific pattern of connections between nerve cells. Cell migration is required for axonal guidance and neurite outgrowth and involves a series of highly co-ordinated and overlapping signalling pathways. The non-receptor tyrosine kinase, Focal Adhesion Kinase (FAK) has an essential role in development and is the most highly expressed kinase in the developing CNS. FAK activity is essential for neuronal cell adhesion and migration. Results: The objective of this study was to optimise a protocol for the differentiation of the neuroblastoma cell line, SH-SY5Y. We determined the optimal extracellular matrix proteins and growth factor combinations required for the optimal differentiation of SH-SY5Y cells into neuronal-like cells and determined those conditions that induce the expression of FAK. It was confirmed that the cells were morphologically and biochemically differentiated when compared to undifferentiated cells. This is in direct contrast to commonly used differentiation methods that induce morphological differentiation but not biochemical differentiation. Conclusions: We conclude that we have optimised a protocol for the differentiation of SH-SY5Y cells that results in a cell population that is both morphologically and biochemically distinct from undifferentiated SH-SY5Y cells and has a distinct adhesion and spreading pattern and display extensive neurite outgrowth. This protocol will provide a neuronal model system for studying FAK activity during cell adhesion and migration events.

Description: I. Tsioutsios, J. Moser, J. A. Plaza, and A. Bachtold We report on the fabrication and operation of a multi-element vibrational structure consisting of two graphene mechanical resonators coupled by a nanotube beam. The whole structure is suspended. Each graphene resonator is clamped by two metal electrodes. The structure is fabricated using a combinati ... [J. Appl. Phys. 114, 104310 (2013)] published Fri Sep 13, 2013.

Description: Marcela F. Silva, Luiz A. S. de Oliveira, Mariani A. Ciciliati, Lais T. Silva, Bruna S. Pereira et al. FeO nanoparticles with sizes ranging from 15 to 53 nm were synthesized by a modified sol-gel method. Maghemite particles as well as particles with admixture of maghemite and hematite were obtained and characterized by XRD, FTIR, UV-Vis photoacoustic and Mossbauer spectroscopy, TEM, and magnetic meas ... [J. Appl. Phys. 114, 104311 (2013)] published Fri Sep 13, 2013.