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Sample records for variability improves expression

  1. Written emotional expression: effect sizes, outcome types, and moderating variables.

    Science.gov (United States)

    Smyth, J M

    1998-02-01

    A research synthesis was conducted to examine the relationship between a written emotional expression task and subsequent health. This writing task was found to lead to significantly improved health outcomes in healthy participants. Health was enhanced in 4 outcome types--reported physical health, psychological well-being, physiological functioning, and general functioning--but health behaviors were not influenced. Writing also increased immediate (pre- to postwriting) distress, which was unrelated to health outcomes. The relation between written emotional expression and health was moderated by a number of variables, including the use of college students as participants, gender, duration of the manipulation, publication status of the study, and specific writing content instructions.

  2. The role of art variables on the expression of drawing

    OpenAIRE

    Kosi, Tina

    2016-01-01

    The diploma thesis is dedicated to the art variables in conjunction with expression of drawings. In art - theoretical part of the thesis I address art on the conceptual level, which depends on each individual artist and, of course, also the viewer who is watching artwork. On the expression also affects the physical level, where the focus is primarily on the work and materials, which allow a certain type of expression. Then, I analyse the expression of drawings in terms of visual language, ...

  3. [Effects of situational and individual variables on critical thinking expression].

    Science.gov (United States)

    Tanaka, Yuko; Kusumi, Takashi

    2016-04-01

    The present study examined when people decide to choose an expression that is based on critical thinking, and how situational and individual variables affect such a decision process. Given a conversation scenario including overgeneralization with two friends, participants decided whether to follow the conversation by a critical-thinking expression or not. The authors controlled purpose and topic as situational variables, and measured critical-thinking ability, critical-thinking disposition, and self-monitoring as individual variables. We conducted an experiment in which the situational variables were counterbalanced in a within-subject design with 60 university students. The results of logistic regression analysis showed differences within individuals in the decision process whether to choose a critical-thinking expression, and that some situational factors and some subscales of the individual measurements were related to the differences.

  4. Capturing heterogeneity in gene expression studies by surrogate variable analysis.

    Directory of Open Access Journals (Sweden)

    Jeffrey T Leek

    2007-09-01

    Full Text Available It has unambiguously been shown that genetic, environmental, demographic, and technical factors may have substantial effects on gene expression levels. In addition to the measured variable(s of interest, there will tend to be sources of signal due to factors that are unknown, unmeasured, or too complicated to capture through simple models. We show that failing to incorporate these sources of heterogeneity into an analysis can have widespread and detrimental effects on the study. Not only can this reduce power or induce unwanted dependence across genes, but it can also introduce sources of spurious signal to many genes. This phenomenon is true even for well-designed, randomized studies. We introduce "surrogate variable analysis" (SVA to overcome the problems caused by heterogeneity in expression studies. SVA can be applied in conjunction with standard analysis techniques to accurately capture the relationship between expression and any modeled variables of interest. We apply SVA to disease class, time course, and genetics of gene expression studies. We show that SVA increases the biological accuracy and reproducibility of analyses in genome-wide expression studies.

  5. MicroRNA expression variability in human cervical tissues.

    Directory of Open Access Journals (Sweden)

    Patrícia M Pereira

    Full Text Available MicroRNAs (miRNAs are short (approximately 22 nt non-coding regulatory RNAs that control gene expression at the post-transcriptional level. Deregulation of miRNA expression has been discovered in a wide variety of tumours and it is now clear that they contribute to cancer development and progression. Cervical cancer is one of the most common cancers in women worldwide and there is a strong need for a non-invasive, fast and efficient method to diagnose the disease. We investigated miRNA expression profiles in cervical cancer using a microarray platform containing probes for mature miRNAs. We have evaluated miRNA expression profiles of a heterogeneous set of cervical tissues from 25 different patients. This set included 19 normal cervical tissues, 4 squamous cell carcinoma, 5 high-grade squamous intraepithelial lesion (HSIL and 9 low-grade squamous intraepithelial lesion (LSIL samples. We observed high variability in miRNA expression especially among normal cervical samples, which prevented us from obtaining a unique miRNA expression signature for this tumour type. However, deregulated miRNAs were identified in malignant and pre-malignant cervical tissues after tackling the high expression variability observed. We were also able to identify putative target genes of relevant candidate miRNAs. Our results show that miRNA expression shows natural variability among human samples, which complicates miRNA data profiling analysis. However, such expression noise can be filtered and does not prevent the identification of deregulated miRNAs that play a role in the malignant transformation of cervical squamous cells. Deregulated miRNAs highlight new candidate gene targets allowing for a better understanding of the molecular mechanism underlying the development of this tumour type.

  6. Improving transition between power optimization and power limitation of variable speed/variable pitch wind turbines

    Energy Technology Data Exchange (ETDEWEB)

    Hansen, A.D.; Bindner, H. [Risoe National Lab., Wind Energy and Atmospheric Physics Dept., Roskilde (Denmark); Rebsdorf, A. [Vestas Wind Systems A/S, Lem (Denmark)

    1999-03-01

    The paper summarises and describes the main results of a recently performed study of improving the transition between power optimization and power limitation for variable speed/variable pitch wind turbines. The results show that the capability of varying the generator speed also can be exploited in the transition stage to improve the quality of the generated power. (au)

  7. Improving Cluster Analysis with Automatic Variable Selection Based on Trees

    Science.gov (United States)

    2014-12-01

    DATES COVERED Master’s Thesis 4. TITLE AND SUBTITLE IMPROVING CLUSTER ANALYSIS WITH AUTOMATIC VARIABLE SELECTION BASED ON TREES 5. FUNDING NUMBERS 6...BLANK iii Approved for public release; distribution is unlimited IMPROVING CLUSTER ANALYSIS WITH AUTOMATIC VARIABLE SELECTION BASED ON TREES Anton D...Cluster: Cluster analysis basics and extensions. (R Package Version, 1.15.2) R Core Team. (2014). R: A language and environment for statistical

  8. INTRINSIC REGULATION OF HEMOGLOBIN EXPRESSION BY VARIABLE SUBUNIT INTERFACE STRENGTHS

    Science.gov (United States)

    Manning, James M.; Popowicz, Anthony M.; Padovan, Julio C.; Chait, Brian T.; Manning, Lois R.

    2012-01-01

    SUMMARY The expression of the six types of human hemoglobin subunits over time is currently considered to be regulated mainly by transcription factors that bind to upstream control regions of the gene (the “extrinsic” component of regulation). Here we describe how subunit pairing and further assembly to tetramers in the liganded state is influenced by the affinity of subunits for one another (the “intrinsic” component of regulation). The adult hemoglobin dimers have the strongest subunit interfaces and the embryonic hemoglobins are the weakest with fetal hemoglobins of intermediate strength, corresponding to the temporal order of their expression. These variable subunit binding strengths and the attenuating effects of acetylation contribute to the differences with which these hemoglobin types form functional O2-binding tetramers consistent with gene switching. PMID:22129306

  9. MAR elements and transposons for improved transgene integration and expression.

    Directory of Open Access Journals (Sweden)

    Déborah Ley

    Full Text Available Reliable and long-term expression of transgenes remain significant challenges for gene therapy and biotechnology applications, especially when antibiotic selection procedures are not applicable. In this context, transposons represent attractive gene transfer vectors because of their ability to promote efficient genomic integration in a variety of mammalian cell types. However, expression from genome-integrating vectors may be inhibited by variable gene transcription and/or silencing events. In this study, we assessed whether inclusion of two epigenetic control elements, the human Matrix Attachment Region (MAR 1-68 and X-29, in a piggyBac transposon vector, may lead to more reliable and efficient expression in CHO cells. We found that addition of the MAR 1-68 at the center of the transposon did not interfere with transposition frequency, and transgene expressing cells could be readily detected from the total cell population without antibiotic selection. Inclusion of the MAR led to higher transgene expression per integrated copy, and reliable expression could be obtained from as few as 2-4 genomic copies of the MAR-containing transposon vector. The MAR X-29-containing transposons was found to mediate elevated expression of therapeutic proteins in polyclonal or monoclonal CHO cell populations using a transposable vector devoid of selection gene. Overall, we conclude that MAR and transposable vectors can be used to improve transgene expression from few genomic transposition events, which may be useful when expression from a low number of integrated transgene copies must be obtained and/or when antibiotic selection cannot be applied.

  10. PROCESS VARIABILITY REDUCTION THROUGH STATISTICAL PROCESS CONTROL FOR QUALITY IMPROVEMENT

    Directory of Open Access Journals (Sweden)

    B.P. Mahesh

    2010-09-01

    Full Text Available Quality has become one of the most important customer decision factors in the selection among the competing product and services. Consequently, understanding and improving quality is a key factor leading to business success, growth and an enhanced competitive position. Hence quality improvement program should be an integral part of the overall business strategy. According to TQM, the effective way to improve the Quality of the product or service is to improve the process used to build the product. Hence, TQM focuses on process, rather than results as the results are driven by the processes. Many techniques are available for quality improvement. Statistical Process Control (SPC is one such TQM technique which is widely accepted for analyzing quality problems and improving the performance of the production process. This article illustrates the step by step procedure adopted at a soap manufacturing company to improve the Quality by reducing process variability using Statistical Process Control.

  11. [Analysing heart rate variability to improve the monitoring of pain].

    Science.gov (United States)

    Butruille, Laura; De Jonckheere, Julien; Jeanne, Mathieu; Tavernier, Benoît; Logier, Régis

    2016-12-01

    An innovative technique based on the analysis of instantaneous heart rate variability helps to improve the prevention and management of pain and discomfort. Simple to implement, this non-invasive technique is based on the continuous recording of the electrocardiograph signal. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  12. Facial expression recognition based on improved deep belief networks

    Science.gov (United States)

    Wu, Yao; Qiu, Weigen

    2017-08-01

    In order to improve the robustness of facial expression recognition, a method of face expression recognition based on Local Binary Pattern (LBP) combined with improved deep belief networks (DBNs) is proposed. This method uses LBP to extract the feature, and then uses the improved deep belief networks as the detector and classifier to extract the LBP feature. The combination of LBP and improved deep belief networks is realized in facial expression recognition. In the JAFFE (Japanese Female Facial Expression) database on the recognition rate has improved significantly.

  13. Gene Expression Variability in Human Hepatic Drug Metabolizing Enzymes and Transporters

    Science.gov (United States)

    Yang, Lun; Price, Elvin T.; Chang, Ching-Wei; Li, Yan; Huang, Ying; Guo, Li-Wu; Guo, Yongli; Kaput, Jim; Shi, Leming; Ning, Baitang

    2013-01-01

    Interindividual variability in the expression of drug-metabolizing enzymes and transporters (DMETs) in human liver may contribute to interindividual differences in drug efficacy and adverse reactions. Published studies that analyzed variability in the expression of DMET genes were limited by sample sizes and the number of genes profiled. We systematically analyzed the expression of 374 DMETs from a microarray data set consisting of gene expression profiles derived from 427 human liver samples. The standard deviation of interindividual expression for DMET genes was much higher than that for non-DMET genes. The 20 DMET genes with the largest variability in the expression provided examples of the interindividual variation. Gene expression data were also analyzed using network analysis methods, which delineates the similarities of biological functionalities and regulation mechanisms for these highly variable DMET genes. Expression variability of human hepatic DMET genes may affect drug-gene interactions and disease susceptibility, with concomitant clinical implications. PMID:23637747

  14. svapls: an R package to correct for hidden factors of variability in gene expression studies.

    Science.gov (United States)

    Chakraborty, Sutirtha; Datta, Somnath; Datta, Susmita

    2013-07-24

    Hidden variability is a fundamentally important issue in the context of gene expression studies. Collected tissue samples may have a wide variety of hidden effects that may alter their transcriptional landscape significantly. As a result their actual differential expression pattern can be potentially distorted, leading to inaccurate results from a genome-wide testing for the important transcripts. We present an R package svapls that can be used to identify several types of unknown sample-specific sources of heterogeneity in a gene expression study and adjust for them in order to provide a more accurate inference on the original expression pattern of the genes over different varieties of samples. The proposed method implements Partial Least Squares regression to extract the hidden signals of sample-specific heterogeneity in the data and uses them to find the genes that are actually correlated with the phenotype of interest. We also compare our package with three other popular softwares for testing differential gene expression along with a detailed illustration on the widely popular Golub dataset. Results from the sensitivity analyes on simulated data with widely different hidden variation patterns reveal the improved detection power of our R package compared to the other softwares along with reasonably smaller error rates. Application on the real-life dataset exhibits the efficacy of the R package in detecting potential batch effects from the dataset. Overall, Our R package provides the user with a simplified framework for analyzing gene expression data with a wide range of hidden variation patterns and delivering a differential gene expression analysis with substantially improved power and accuracy.The R package svapls is freely available at http://cran.r-project.org/web/packages/svapls/index.html.

  15. Engineering cells to improve protein expression.

    Science.gov (United States)

    Xiao, Su; Shiloach, Joseph; Betenbaugh, Michael J

    2014-06-01

    Cellular engineering of bacteria, fungi, insect cells and mammalian cells is a promising methodology to improve recombinant protein production for structural, biochemical, and commercial applications. Increased understanding of the host organism biology has suggested engineering strategies targeting bottlenecks in transcription, translation, protein processing and secretory pathways, as well as cell growth and survival. A combination of metabolic engineering and synthetic biology has been used to improve the properties of cells for protein production, which has resulted in enhanced yields of multiple protein classes. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Model for expressing leaf photosynthesis in terms of weather variables

    African Journals Online (AJOL)

    A theoretical mathematical model for describing photosynthesis in individual leaves in terms of weather variables is proposed. The model utilizes a series of efficiency parameters, each of which reflect the fraction of potential photosynthetic rate permitted by the different environmental elements. These parameters are useful ...

  17. Variable patterns of expression of luciferase in transgenic tobacco leaves.

    Science.gov (United States)

    Barnes, W M

    1990-01-01

    A carboxyl-terminally modified firefly luciferase, encoded as a gene fusion to the neomycin phosphotransferase gene (which confers kanamycin resistance), was found to be enzymatically active for both enzymes when expressed in bacteria and in transgenic plants. A military-type starlight vision system was used to conveniently analyze the pattern of gene expression in transgenic tobacco plant leaves. Transgenic tobacco plants which expressed luciferase uniformly in all areas of the leaf, and assays for luciferin, demonstrated that luciferin rapidly penetrates all regions of a tobacco leaf in at least two dimensions. Depending on the test gene structure or, presumably, on the transferred DNA (T-DNA) insertional context, other transgenic plants were obtained that expressed luciferase with a wide range of nonuniform patterns from nominally the same cauliflower mosaic virus 35S promoter. For instance, the veins can be dark, while only the interveinal regions of the leaf lamina glow, or only the small capillary veins glow, or only the major veins glow. Local and/or systemic induction in response to wounding was also demonstrated. Images PMID:2251262

  18. View-constrained latent variable model for multi-view facial expression classification

    NARCIS (Netherlands)

    Eleftheriadis, Stefanos; Rudovic, Ognjen; Pantic, Maja

    2014-01-01

    We propose a view-constrained latent variable model for multi-view facial expression classification. In this model, we first learn a discriminative manifold shared by multiple views of facial expressions, followed by the expression classification in the shared manifold. For learning, we use the

  19. Combining SNPs in latent variables to improve genomic prediction

    DEFF Research Database (Denmark)

    Heuven, Henri C M; Rosa, G J M; Janss, Luc

    The objective of this study was to develop and test hierarchical genomic models with latent variables that represent parts of the genomic values. An interaction model and a chromosome model were compared with a model based on variable selection in a simulated and real dataset. The program Bayz......: Hierarchical genetic model; Predictive value; Gibbs sampling; Variable selection....

  20. Lineage variability in surface components expression within Porphyromonas gingivalis.

    Science.gov (United States)

    Teixeira, Silvia Regina Loureiro; D'Epiro, Talyta Thereza Soares; Pinheiro, Ericka Tavares; Simionato, Maria Regina L; Taniwaki, Noemi Nosomi; Kisielius, Jonas José; Mayer, Marcia Pinto Alves

    2014-12-01

    The periodontopathogen Porphyromonas gingivalis is represented by a spectrum of phenotypes ranging from commensals to pathogenic lineages. Capsule and fimbriae are considered key virulence factors in this specie, involved in colonization and host defenses evasion. Since these virulence traits may not be expressed by certain strains, we aimed to test the hypothesis that certain clusters or genotypes of P. gingivalis correlate with the production of capsule and fimbriae. Sixteen P. gingivalis isolates were evaluated. Capsule (K) was detected by optical microscopy of negatively stained cells. The presence of fimbriae (F) was determined by TEM. Genotypes were determined by NotI macrorestriction fragments analysis through Pulsed-Field Gel Electrophoresis (PFGE) and Multi-locus sequence typing (MLST) based on seven house-keeping genes. The phenotypes included F(+)K(+) (n = 4), F(-)K(+) (n = 5), F(+)K(-) (n = 5) and F(-)K(-) (n = 2). The analysis of whole genome macrorestriction fragments revealed 14 different clusters. MLST data also revealed extensive genetic diversity; however, PFGE and MLST profiles showed evident differences. There was no association between P. gingivalis clusters and encapsulated and/or fimbriated phenotypes. Genotyping methods were not able to discriminate isolates according to the production of virulence factors such as capsule and major fimbriae, indicating that recombination played a key role in the expression of capsule and fimbriae in P. gingivalis. Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. [TSA improve transgenic porcine cloned embryo development and transgene expression].

    Science.gov (United States)

    Kong, Qing-Ran; Zhu, Jiang; Huang, Bo; Huan, Yan-Jun; Wang, Feng; Shi, Yong-Qian; Liu, Zhong-Feng; Wu, Mei-Ling; Liu, Zhong-Hua

    2011-07-01

    Uncompleted epigenetic reprogramming is attributed to the low efficiency of producing transgenic cloned animals. Histone modification associated with epigenetics can directly influence the embryo development and transgene expression. Trichostatin A (TSA), as an inhibitor of histone deacetylase, can change the status of histone acetylation, improve somatic cell reprogramming, and enhance cloning efficiency. TSA prevents the chromatin structure from being condensed, so that transcription factor could binds to DNA sequence easily and enhance transgene expression. Our study established the optimal TSA treatment on porcine donor cells and cloned embryos, 250 nmol/L, 24 h and 40 nmol/L, 24 h, respectively. Furthermore, we found that both the cloned embryo and the donor cell treated by TSA resulted in the highest development efficiency. Meanwhile, TSA can improve transgene expression in donor cell and cloned embryo. In summary, TSA can significantly improve porcine reconstructed embryo development and transgene expression.

  2. Gene Expression Variability as a Unifying Element of the Pluripotency Network

    Directory of Open Access Journals (Sweden)

    Elizabeth A. Mason

    2014-08-01

    Full Text Available Heterogeneity is a hallmark of stem cell populations, in part due to the molecular differences between cells undergoing self-renewal and those poised to differentiate. We examined phenotypic and molecular heterogeneity in pluripotent stem cell populations, using public gene expression data sets. A high degree of concordance was observed between global gene expression variability and the reported heterogeneity of different human pluripotent lines. Network analysis demonstrated that low-variability genes were the most highly connected, suggesting that these are the most stable elements of the gene regulatory network and are under the highest regulatory constraints. Known drivers of pluripotency were among these, with lowest expression variability of POU5F1 in cells with the highest capacity for self-renewal. Variability of gene expression provides a reliable measure of phenotypic and molecular heterogeneity and predicts those genes with the highest degree of regulatory constraint within the pluripotency network.

  3. Genetic analysis of reaction time variability : room for improvement?

    NARCIS (Netherlands)

    Kuntsi, J.; Frazier-Wood, A. C.; Banaschewski, T.; Gill, M.; Miranda, A.; Oades, R. D.; Roeyers, H.; Rothenberger, A.; Steinhausen, H. -C.; van der Meere, J. J.; Faraone, S. V.; Asherson, P.; Rijsdijk, F.

    Background. Increased reaction time variability (RTV) on cognitive tasks requiring a speeded response is characteristic of several psychiatric disorders. In attention deficit hyperactivity disorder (ADHD), the association with RTV is strong phenotypically and genetically, yet high RTV is not a

  4. Variability of chromosome number and morphology and gymnosperm improvement

    OpenAIRE

    Tucović Aleksandar; Šijačić-Nikolić Mirjana; Vilotić Dragica

    2004-01-01

    The causes of monotypic and polytypic variability of the gymnosperm chromosome complex were studied. The development of karyogram and idiograms of the species should be applied in the aim of upgrading the breeding method and technique. The study of the chromosome variability depends on the knowledge on gene function at the level of chromosome and at the level of genome, i.e. at the supra-chromosome level.

  5. Expression and production of llama variable heavy-chain antibody fragments (VHHs) by Aspergillus awamori

    NARCIS (Netherlands)

    Joosten, V.; Gouka, R.J.; Hondel, C.A.M.J.J. van den; Verrips, C.T.; Lokman, B.C.

    2005-01-01

    We report the expression and production of llama variable heavy-chain antibody fragments (VHHs) by Aspergillus awamori. Fragments encoding VHHs were cloned in a suitable Aspergillus expression vector and transformants secreting VHH fragments were analysed for integrated gene copy-numbers, mRNA

  6. Regulation of cell-to-cell variability in divergent gene expression.

    Science.gov (United States)

    Yan, Chao; Wu, Shuyang; Pocetti, Christopher; Bai, Lu

    2016-03-24

    Cell-to-cell variability (noise) is an important feature of gene expression that impacts cell fitness and development. The regulatory mechanism of this variability is not fully understood. Here we investigate the effect on gene expression noise in divergent gene pairs (DGPs). We generated reporters driven by divergent promoters, rearranged their gene order, and probed their expressions using time-lapse fluorescence microscopy and single-molecule fluorescence in situ hybridization (smFISH). We show that two genes in a co-regulated DGP have higher expression covariance compared with the separate, tandem and convergent configurations, and this higher covariance is caused by more synchronized firing of the divergent transcriptions. For differentially regulated DGPs, the regulatory signal of one gene can stochastically 'leak' to the other, causing increased gene expression noise. We propose that the DGPs' function in limiting or promoting gene expression noise may enhance or compromise cell fitness, providing an explanation for the conservation pattern of DGPs.

  7. Modeling bi-modality improves characterization of cell cycle on gene expression in single cells.

    Science.gov (United States)

    McDavid, Andrew; Dennis, Lucas; Danaher, Patrick; Finak, Greg; Krouse, Michael; Wang, Alice; Webster, Philippa; Beechem, Joseph; Gottardo, Raphael

    2014-07-01

    Advances in high-throughput, single cell gene expression are allowing interrogation of cell heterogeneity. However, there is concern that the cell cycle phase of a cell might bias characterizations of gene expression at the single-cell level. We assess the effect of cell cycle phase on gene expression in single cells by measuring 333 genes in 930 cells across three phases and three cell lines. We determine each cell's phase non-invasively without chemical arrest and use it as a covariate in tests of differential expression. We observe bi-modal gene expression, a previously-described phenomenon, wherein the expression of otherwise abundant genes is either strongly positive, or undetectable within individual cells. This bi-modality is likely both biologically and technically driven. Irrespective of its source, we show that it should be modeled to draw accurate inferences from single cell expression experiments. To this end, we propose a semi-continuous modeling framework based on the generalized linear model, and use it to characterize genes with consistent cell cycle effects across three cell lines. Our new computational framework improves the detection of previously characterized cell-cycle genes compared to approaches that do not account for the bi-modality of single-cell data. We use our semi-continuous modelling framework to estimate single cell gene co-expression networks. These networks suggest that in addition to having phase-dependent shifts in expression (when averaged over many cells), some, but not all, canonical cell cycle genes tend to be co-expressed in groups in single cells. We estimate the amount of single cell expression variability attributable to the cell cycle. We find that the cell cycle explains only 5%-17% of expression variability, suggesting that the cell cycle will not tend to be a large nuisance factor in analysis of the single cell transcriptome.

  8. Genomic variability and protein species - Improving sequence coverage for proteogenomics

    NARCIS (Netherlands)

    Bischoff, Rainer; Permentier, Hjalmar; Guryev, Victor; Horvatovich, Peter

    2016-01-01

    Protein heterogeneity may result from many factors often closely related to the regulation of biological mechanisms. This review addresses one source of protein heterogeneity, the translation of genetic variability and transcriptional modulation to the protein level. We provide an overview how

  9. Improving uncertainty estimates: Inter-annual variability in Ireland

    Science.gov (United States)

    Pullinger, D.; Zhang, M.; Hill, N.; Crutchley, T.

    2017-11-01

    This paper addresses the uncertainty associated with inter-annual variability used within wind resource assessments for Ireland in order to more accurately represent the uncertainties within wind resource and energy yield assessments. The study was undertaken using a total of 16 ground stations (Met Eireann) and corresponding reanalysis datasets to provide an update to previous work on this topic undertaken nearly 20 years ago. The results of the work demonstrate that the previously reported 5.4% of wind speed inter-annual variability is considered to be appropriate, guidance is given on how to provide a robust assessment of IAV using available sources of data including ground stations, MERRA-2 and ERA-Interim.

  10. Improving Space Project Cost Estimating with Engineering Management Variables

    Science.gov (United States)

    Hamaker, Joseph W.; Roth, Axel (Technical Monitor)

    2001-01-01

    Current space project cost models attempt to predict space flight project cost via regression equations, which relate the cost of projects to technical performance metrics (e.g. weight, thrust, power, pointing accuracy, etc.). This paper examines the introduction of engineering management parameters to the set of explanatory variables. A number of specific engineering management variables are considered and exploratory regression analysis is performed to determine if there is statistical evidence for cost effects apart from technical aspects of the projects. It is concluded that there are other non-technical effects at work and that further research is warranted to determine if it can be shown that these cost effects are definitely related to engineering management.

  11. Improved variable reduction in partial least squares modelling by Global-Minimum Error Uninformative-Variable Elimination.

    Science.gov (United States)

    Andries, Jan P M; Vander Heyden, Yvan; Buydens, Lutgarde M C

    2017-08-22

    The calibration performance of Partial Least Squares regression (PLS) can be improved by eliminating uninformative variables. For PLS, many variable elimination methods have been developed. One is the Uninformative-Variable Elimination for PLS (UVE-PLS). However, the number of variables retained by UVE-PLS is usually still large. In UVE-PLS, variable elimination is repeated as long as the root mean squared error of cross validation (RMSECV) is decreasing. The set of variables in this first local minimum is retained. In this paper, a modification of UVE-PLS is proposed and investigated, in which UVE is repeated until no further reduction in variables is possible, followed by a search for the global RMSECV minimum. The method is called Global-Minimum Error Uninformative-Variable Elimination for PLS, denoted as GME-UVE-PLS or simply GME-UVE. After each iteration, the predictive ability of the PLS model, built with the remaining variable set, is assessed by RMSECV. The variable set with the global RMSECV minimum is then finally selected. The goal is to obtain smaller sets of variables with similar or improved predictability than those from the classical UVE-PLS method. The performance of the GME-UVE-PLS method is investigated using four data sets, i.e. a simulated set, NIR and NMR spectra, and a theoretical molecular descriptors set, resulting in twelve profile-response (X-y) calibrations. The selective and predictive performances of the models resulting from GME-UVE-PLS are statistically compared to those from UVE-PLS and 1-step UVE, one-sided paired t-tests. The results demonstrate that variable reduction with the proposed GME-UVE-PLS method, usually eliminates significantly more variables than the classical UVE-PLS, while the predictive abilities of the resulting models are better. With GME-UVE-PLS, a lower number of uninformative variables, without a chemical meaning for the response, may be retained than with UVE-PLS. The selectivity of the classical UVE method

  12. Sensitivity and fidelity of DNA microarray improved with integration of Amplified Differential Gene Expression (ADGE

    Directory of Open Access Journals (Sweden)

    Ile Kristina E

    2003-07-01

    Full Text Available Abstract Background The ADGE technique is a method designed to magnify the ratios of gene expression before detection. It improves the detection sensitivity to small change of gene expression and requires small amount of starting material. However, the throughput of ADGE is low. We integrated ADGE with DNA microarray (ADGE microarray and compared it with regular microarray. Results When ADGE was integrated with DNA microarray, a quantitative relationship of a power function between detected and input ratios was found. Because of ratio magnification, ADGE microarray was better able to detect small changes in gene expression in a drug resistant model cell line system. The PCR amplification of templates and efficient labeling reduced the requirement of starting material to as little as 125 ng of total RNA for one slide hybridization and enhanced the signal intensity. Integration of ratio magnification, template amplification and efficient labeling in ADGE microarray reduced artifacts in microarray data and improved detection fidelity. The results of ADGE microarray were less variable and more reproducible than those of regular microarray. A gene expression profile generated with ADGE microarray characterized the drug resistant phenotype, particularly with reference to glutathione, proliferation and kinase pathways. Conclusion ADGE microarray magnified the ratios of differential gene expression in a power function, improved the detection sensitivity and fidelity and reduced the requirement for starting material while maintaining high throughput. ADGE microarray generated a more informative expression pattern than regular microarray.

  13. Effect of Interaction between Chromatin Loops on Cell-to-Cell Variability in Gene Expression.

    Directory of Open Access Journals (Sweden)

    Tuoqi Liu

    2016-05-01

    Full Text Available According to recent experimental evidence, the interaction between chromatin loops, which can be characterized by three factors-connection pattern, distance between regulatory elements, and communication form, play an important role in determining the level of cell-to-cell variability in gene expression. These quantitative experiments call for a corresponding modeling effect that addresses the question of how changes in these factors affect variability at the expression level in a systematic rather than case-by-case fashion. Here we make such an effort, based on a mechanic model that maps three fundamental patterns for two interacting DNA loops into a 4-state model of stochastic transcription. We first show that in contrast to side-by-side loops, nested loops enhance mRNA expression and reduce expression noise whereas alternating loops have just opposite effects. Then, we compare effects of facilitated tracking and direct looping on gene expression. We find that the former performs better than the latter in controlling mean expression and in tuning expression noise, but this control or tuning is distance-dependent, remarkable for moderate loop lengths, and there is a limit loop length such that the difference in effect between two communication forms almost disappears. Our analysis and results justify the facilitated chromatin-looping hypothesis.

  14. Utilizing the Vertical Variability of Precipitation to Improve Radar QPE

    Science.gov (United States)

    Gatlin, Patrick N.; Petersen, Walter A.

    2016-01-01

    Characteristics of the melting layer and raindrop size distribution can be exploited to further improve radar quantitative precipitation estimation (QPE). Using dual-polarimetric radar and disdrometers, we found that the characteristic size of raindrops reaching the ground in stratiform precipitation often varies linearly with the depth of the melting layer. As a result, a radar rainfall estimator was formulated using D(sub m) that can be employed by polarimetric as well as dual-frequency radars (e.g., space-based radars such as the GPM DPR), to lower the bias and uncertainty of conventional single radar parameter rainfall estimates by as much as 20%. Polarimetric radar also suffers from issues associated with sampling the vertical distribution of precipitation. Hence, we characterized the vertical profile of polarimetric parameters (VP3)-a radar manifestation of the evolving size and shape of hydrometeors as they fall to the ground-on dual-polarimetric rainfall estimation. The VP3 revealed that the profile of ZDR in stratiform rainfall can bias dual-polarimetric rainfall estimators by as much as 50%, even after correction for the vertical profile of reflectivity (VPR). The VP3 correction technique that we developed can improve operational dual-polarimetric rainfall estimates by 13% beyond that offered by a VPR correction alone.

  15. Improving E. coli growth performance by manipulating small RNA expression.

    Science.gov (United States)

    Negrete, Alejandro; Shiloach, Joseph

    2017-11-14

    Efficient growth of E. coli, especially for production of recombinant proteins, has been a challenge for the biotechnological industry since the early 1970s. By employing multiple approaches, such as different media composition, various growth strategies and specific genetic manipulations, it is now possible to grow bacteria to concentrations exceeding 100 g/L and to achieve high concentrations of recombinant proteins. Although the growth conditions are carefully monitored and maintained, it is likely that during the growth process cells are exposed to periodic stress conditions, created by fluctuations in pH, dissolved oxygen, temperature, glucose, and salt concentration. These stress circumstances which can occur especially in large volume bioreactors, may affect the growth and production process. In the last several years, it has been recognized that small non-coding RNAs can act as regulators of bacterial gene expression. These molecules are found to be specifically involved in E. coli response to different environmental stress conditions; but so far, have not been used for improving production strains. The review provides summary of small RNAs identified on petri dish or in shake flask culture that can potentially affect growth characteristics of E. coli grown in bioreactor. Among them MicC and MicF that are involved in response to temperature changes, RyhB that responds to iron concentration, Gady which is associated with lower pH, Sgrs that is coupled with glucose transport and OxyS that responds to oxygen concentration. The manipulation of some of these small RNAs for improving growth of E. coli in Bioreactor is described in the last part of the review. Overexpression of SgrS was associated with improved growth and reduced acetate expression, over expression of GadY improved cell growth at acidic conditions and over expression of OxyS reduced the effect of oxidative stress. One of the possible advantages of manipulating sRNAs for improving cell growth is

  16. Improving the high variable bioavailability of griseofulvin by SEDDS.

    Science.gov (United States)

    Arida, Adi Issam; Al-Tabakha, Moawia Mohammed; Hamoury, Hantash Abdel Jalil

    2007-12-01

    To enhance the dissolution and oral absorption of poorly water-soluble griseofulvin (GF), self-emulsifying drug delivery system (SEDDS) composed of oil, surfactant and cosurfactant for oral administration of griseofulvin was formulated, and its physicochemical properties and pharmacokinetic parameters were evaluated. The solubility of griseofulvin was further improved by the addition of hydrochloric acid. Droplet size of griseofulvin emulsion was kept constant both in simulated gastric fluid without pepsin and simulated intestinal fluid throughout 12 weeks incubation period. Griseofulvin in the SEDDS rapidly dissolved in different dissolution media. This was not the case for the commercial GRIS-PEG tablets. In different fed diet groups, AUC 0-->24 h, Cp max, and T max of griseofulvin after oral administration of SEDDS in rats were comparable to those after oral dose of GRIS-PEG tablet. Although, in fed lipidic diet group, the mean AUC and Cp max after oral administration of GRIS-PEG in rats were 1.28 and 1.15 fold higher, respectively, compared with those of SEDDS, these have not shown to be significantly different. These results demonstrate that the SEDDS of griseofulvin composed of Capmul GMO-50, Poloxamer and Myvacet 9-45 greatly enhanced the dissolution of griseofulvin (without ultramicronisation). However, food intake effect on the bioavailability of griseofulvin has remained. Thus, this system may provide a useful dosage form for oral water-insoluble drugs which have problems in their dissolution.

  17. Transient expression assays in grapevine: a step towards genetic improvement.

    Science.gov (United States)

    Jelly, Noémie S; Valat, Laure; Walter, Bernard; Maillot, Pascale

    2014-12-01

    In the past few years, the usefulness of transient expression assays has continuously increased for the characterization of unknown gene function and metabolic pathways. In grapevine (Vitis vinifera L.), one of the most economically important fruit crops in the world, recent systematic sequencing projects produced many gene data sets that require detailed analysis. Due to their rapid nature, transient expression assays are well suited for large-scale genetic studies. Although genes and metabolic pathways of any species can be analysed by transient expression in model plants, a need for homologous systems has emerged to avoid the misinterpretation of results due to a foreign genetic background. Over the last 10 years, various protocols have thus been developed to apply this powerful technology to grapevine. Using cell suspension cultures, somatic embryos, leaves or whole plantlets, transient expression assays enabled the study of the function, regulation and subcellular localization of genes involved in specific metabolic pathways such as the biosynthesis of phenylpropanoids. Disease resistance genes that could be used for marker-assisted selection in conventional breeding or for stable transformation of elite cultivars have also been characterized. Additionally, transient expression assays have proved useful for shaping new tools for grapevine genetic improvement: synthetic promoters, silencing constructs, minimal linear cassettes or viral vectors. This review provides an update on the different tools (DNA constructs, reporter genes, vectors) and methods (Agrobacterium-mediated and direct gene transfer methods) available for transient gene expression in grapevine. The most representative results published thus far are then described. © 2014 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

  18. Improved expression of single-chain antibodies in Ustilago maydis.

    Science.gov (United States)

    Sarkari, Parveen; Reindl, Michèle; Stock, Janpeter; Müller, Olaf; Kahmann, Regine; Feldbrügge, Michael; Schipper, Kerstin

    2014-12-10

    To produce the full repertoire of biopharmaceutical proteins, alternative expression platforms are required. Systems that enable secretion of the target protein are favored because this facilitates downstream processing. Ustilago maydis is a promising fungal model organism for future applications in protein expression. Recently, we described the exploitation of a novel unconventional secretion mechanism for the export of heterologous proteins. In this mode of secretion, the endochitinase Cts1 functions as a carrier for export with the main advantage of avoiding potentially harmful N-glycosylation. The major limitation until now was a low yield of secreted full-length protein. For optimization, we identified two bottlenecks: mRNA amount and extracellular proteolytic activity. By generating novel expression vectors harboring a strong constitutive promoter as well as eliminating harmful proteases, yields were increased significantly. A scFv antibody fragment against the cMyc epitope served as proof-of-principle and could be purified in its active, full-length form from the culture supernatant. Thus, we improved the novel expression system in U. maydis such that it can now be investigated with respect to other targets with potential applications for instance in diagnostics and medicine. Copyright © 2014 Elsevier B.V. All rights reserved.

  19. Stable expression of two variable surface glycoproteins by cloned Trypanosoma equiperdum.

    Science.gov (United States)

    Baltz, T; Giroud, C; Baltz, D; Roth, C; Raibaud, A; Eisen, H

    African trypanosomes are thought to evade the host immune system by periodically changing their variable surface glycoprotein (VSG). VSG genes are activated by a complex process involving the duplicative transposition of silent basic copy genes to one of several expression sites. These expression-linked copies (ELCs) of the VSG genes are also subject to regulation within expression sites by as yet unknown mechanisms. It is generally assumed that trypanosomes can express only one VSG gene at a time. Nevertheless, the finding that they contain multiple VSG gene expression sites suggests that multiple expression is possible. We show here that Trypanosoma equiperdum can stably express two VSG genes in a simple axenic culture system and that both antigens are present on the cell surface. The two antigens do not co-cap or form heterodimers. Their corresponding genes show no cross-hybridization and are situated in different telomere-linked expression sites. Northern blot analysis reveals that both genes are active in the double expressors.

  20. How changes in extracellular matrix mechanics and gene expression variability might combine to drive cancer progression.

    Directory of Open Access Journals (Sweden)

    Justin Werfel

    Full Text Available Changes in extracellular matrix (ECM structure or mechanics can actively drive cancer progression; however, the underlying mechanism remains unknown. Here we explore whether this process could be mediated by changes in cell shape that lead to increases in genetic noise, given that both factors have been independently shown to alter gene expression and induce cell fate switching. We do this using a computer simulation model that explores the impact of physical changes in the tissue microenvironment under conditions in which physical deformation of cells increases gene expression variability among genetically identical cells. The model reveals that cancerous tissue growth can be driven by physical changes in the microenvironment: when increases in cell shape variability due to growth-dependent increases in cell packing density enhance gene expression variation, heterogeneous autonomous growth and further structural disorganization can result, thereby driving cancer progression via positive feedback. The model parameters that led to this prediction are consistent with experimental measurements of mammary tissues that spontaneously undergo cancer progression in transgenic C3(1-SV40Tag female mice, which exhibit enhanced stiffness of mammary ducts, as well as progressive increases in variability of cell-cell relations and associated cell shape changes. These results demonstrate the potential for physical changes in the tissue microenvironment (e.g., altered ECM mechanics to induce a cancerous phenotype or accelerate cancer progression in a clonal population through local changes in cell geometry and increased phenotypic variability, even in the absence of gene mutation.

  1. Surrogate variable analysis using partial least squares (SVA-PLS) in gene expression studies.

    Science.gov (United States)

    Chakraborty, Sutirtha; Datta, Somnath; Datta, Susmita

    2012-03-15

    In a typical gene expression profiling study, our prime objective is to identify the genes that are differentially expressed between the samples from two different tissue types. Commonly, standard analysis of variance (ANOVA)/regression is implemented to identify the relative effects of these genes over the two types of samples from their respective arrays of expression levels. But, this technique becomes fundamentally flawed when there are unaccounted sources of variability in these arrays (latent variables attributable to different biological, environmental or other factors relevant in the context). These factors distort the true picture of differential gene expression between the two tissue types and introduce spurious signals of expression heterogeneity. As a result, many genes which are actually differentially expressed are not detected, whereas many others are falsely identified as positives. Moreover, these distortions can be different for different genes. Thus, it is also not possible to get rid of these variations by simple array normalizations. This both-way error can lead to a serious loss in sensitivity and specificity, thereby causing a severe inefficiency in the underlying multiple testing problem. In this work, we attempt to identify the hidden effects of the underlying latent factors in a gene expression profiling study by partial least squares (PLS) and apply ANCOVA technique with the PLS-identified signatures of these hidden effects as covariates, in order to identify the genes that are truly differentially expressed between the two concerned tissue types. We compare the performance of our method SVA-PLS with standard ANOVA and a relatively recent technique of surrogate variable analysis (SVA), on a wide variety of simulation settings (incorporating different effects of the hidden variable, under situations with varying signal intensities and gene groupings). In all settings, our method yields the highest sensitivity while maintaining relatively

  2. Masked expression of life-history traits in a highly variable environment

    Science.gov (United States)

    DeBoer, Jason A.; Fontaine, Joseph J.; Chizinski, Christopher J.; Pope, Kevin L.

    2015-01-01

    Differing life-history strategies may act as a constraint on reproductive expression that ultimately limits the ability of individual species to respond to changes in the magnitude or frequency of environmental variation, and potentially underlies the variation often inherent in phenotypic and evolved responses to anthropogenic change. Alternatively, if there are environmental cues that predict reproductive potential, differential expression of life-history strategies may represent differences in the adaptive capacity to optimize current reproductive value given variation in environmental conditions. We compared several aspects of walleye Sander vitreus spawning ecology at two reservoirs that differ in environmental variability (i.e., annual water-level fluctuation) to identify the capacity of phenotypic expression and the corresponding association with age. Despite significant differences in female body and liver masses between reservoirs that differ in environmental variability, we found no difference in reproductive investment measured by egg size and fecundity. Walleye in a highly variable environment appear to exhibit reproductive traits more typical of a short-lived life-history strategy, which may be resultant from the interaction of environmental and anthropogenic pressures. This finding emphasizes the need to identify the degree to which life-history expression represents physiological constraints versus ecological optimization, particularly as anthropogenic change continues to alter environmental conditions. 

  3. Improved expression systems for regulated expression in Salmonella infecting eukaryotic cells.

    Directory of Open Access Journals (Sweden)

    Carlos Medina

    Full Text Available In this work we describe a series of improvements to the Salmonella-based salicylate-inducible cascade expression system comprised of a plasmid-borne expression module, where target gene expression is driven by the P(m promoter governed by the XylS2 regulator, and a genome-integrated regulatory module controlled by the nahR/P(sal system. We have constructed a set of high and low-copy number plasmids bearing modified versions of the expression module with a more versatile multiple cloning site and different combinations of the following elements: (i the nasF transcriptional attenuator, which reduces basal expression levels, (ii a strong ribosome binding site, and (iii the Type III Secretion System (TTSS signal peptide from the effector protein SspH2 to deliver proteins directly to the eukaryotic cytosol following bacterial infection of animal cells. We show that different expression module versions can be used to direct a broad range of protein production levels. Furthermore, we demonstrate that the efficient reduction of basal expression by the nasF attenuator allows the cloning of genes encoding highly cytotoxic proteins such as colicin E3 even in the absence of its immunity protein. Additionally, we show that the Salmonella TTSS is able to translocate most of the protein produced by this regulatory cascade to the cytoplasm of infected HeLa cells. Our results indicate that these vectors represent useful tools for the regulated overproduction of heterologous proteins in bacterial culture or in animal cells, for the cloning and expression of genes encoding toxic proteins and for pathogenesis studies.

  4. Physiological, Diurnal and Stress-Related Variability of Cadmium-Metallothionein Gene Expression in Land Snails.

    Directory of Open Access Journals (Sweden)

    Veronika Pedrini-Martha

    Full Text Available The terrestrial Roman snail Helix pomatia has successfully adapted to strongly fluctuating conditions in its natural soil habitat. Part of the snail's stress defense strategy is its ability to express Metallothioneins (MTs. These are multifunctional, cysteine-rich proteins that bind and inactivate transition metal ions (Cd(2+, Zn(2+, Cu(+ with high affinity. In Helix pomatia a Cadmium (Cd-selective, inducible Metallothionein Isoform (CdMT is mainly involved in detoxification of this harmful metal. In addition, the snail CdMT has been shown to also respond to certain physiological stressors. The aim of the present study was to investigate the physiological and diurnal variability of CdMT gene expression in snails exposed to Cd and non-metallic stressors such as desiccation and oxygen depletion. CdMT gene expression was upregulated by Cd exposure and desiccation, whereas no significant impact on the expression of CdMT was measured due to oxygen depletion. Overall, Cd was clearly more effective as an inducer of the CdMT gene expression compared to the applied non-metallic stressors. In unexposed snails, diurnal rhythmicity of CdMT gene expression was observed with higher mRNA concentrations at night compared to daytime. This rhythmicity was severely disrupted in Cd-exposed snails which exhibited highest CdMT gene transcription rates in the morning. Apart from diurnal rhythmicity, feeding activity also had a strong impact on CdMT gene expression. Although underlying mechanisms are not completely understood, it is clear that factors increasing MT expression variability have to be considered when using MT mRNA quantification as a biomarker for environmental stressors.

  5. Physiological, Diurnal and Stress-Related Variability of Cadmium-Metallothionein Gene Expression in Land Snails.

    Science.gov (United States)

    Pedrini-Martha, Veronika; Niederwanger, Michael; Kopp, Renate; Schnegg, Raimund; Dallinger, Reinhard

    2016-01-01

    The terrestrial Roman snail Helix pomatia has successfully adapted to strongly fluctuating conditions in its natural soil habitat. Part of the snail's stress defense strategy is its ability to express Metallothioneins (MTs). These are multifunctional, cysteine-rich proteins that bind and inactivate transition metal ions (Cd(2+), Zn(2+), Cu(+)) with high affinity. In Helix pomatia a Cadmium (Cd)-selective, inducible Metallothionein Isoform (CdMT) is mainly involved in detoxification of this harmful metal. In addition, the snail CdMT has been shown to also respond to certain physiological stressors. The aim of the present study was to investigate the physiological and diurnal variability of CdMT gene expression in snails exposed to Cd and non-metallic stressors such as desiccation and oxygen depletion. CdMT gene expression was upregulated by Cd exposure and desiccation, whereas no significant impact on the expression of CdMT was measured due to oxygen depletion. Overall, Cd was clearly more effective as an inducer of the CdMT gene expression compared to the applied non-metallic stressors. In unexposed snails, diurnal rhythmicity of CdMT gene expression was observed with higher mRNA concentrations at night compared to daytime. This rhythmicity was severely disrupted in Cd-exposed snails which exhibited highest CdMT gene transcription rates in the morning. Apart from diurnal rhythmicity, feeding activity also had a strong impact on CdMT gene expression. Although underlying mechanisms are not completely understood, it is clear that factors increasing MT expression variability have to be considered when using MT mRNA quantification as a biomarker for environmental stressors.

  6. Improved Genetic Algorithm with Two-Level Approximation for Truss Optimization by Using Discrete Shape Variables

    Directory of Open Access Journals (Sweden)

    Shen-yan Chen

    2015-01-01

    Full Text Available This paper presents an Improved Genetic Algorithm with Two-Level Approximation (IGATA to minimize truss weight by simultaneously optimizing size, shape, and topology variables. On the basis of a previously presented truss sizing/topology optimization method based on two-level approximation and genetic algorithm (GA, a new method for adding shape variables is presented, in which the nodal positions are corresponding to a set of coordinate lists. A uniform optimization model including size/shape/topology variables is established. First, a first-level approximate problem is constructed to transform the original implicit problem to an explicit problem. To solve this explicit problem which involves size/shape/topology variables, GA is used to optimize individuals which include discrete topology variables and shape variables. When calculating the fitness value of each member in the current generation, a second-level approximation method is used to optimize the continuous size variables. With the introduction of shape variables, the original optimization algorithm was improved in individual coding strategy as well as GA execution techniques. Meanwhile, the update strategy of the first-level approximation problem was also improved. The results of numerical examples show that the proposed method is effective in dealing with the three kinds of design variables simultaneously, and the required computational cost for structural analysis is quite small.

  7. An improved and explicit surrogate variable analysis procedure by coefficient adjustment.

    Science.gov (United States)

    Lee, Seunggeun; Sun, Wei; Wright, Fred A; Zou, Fei

    2017-06-01

    Unobserved environmental, demographic, and technical factors can negatively affect the estimation and testing of the effects of primary variables. Surrogate variable analysis, proposed to tackle this problem, has been widely used in genomic studies. To estimate hidden factors that are correlated with the primary variables, surrogate variable analysis performs principal component analysis either on a subset of features or on all features, but weighting each differently. However, existing approaches may fail to identify hidden factors that are strongly correlated with the primary variables, and the extra step of feature selection and weight calculation makes the theoretical investigation of surrogate variable analysis challenging. In this paper, we propose an improved surrogate variable analysis using all measured features that has a natural connection with restricted least squares, which allows us to study its theoretical properties. Simulation studies and real data analysis show that the method is competitive to state-of-the-art methods.

  8. Variable expressivity familial cherubism: woman transmitting cherubism without suffering the disease.

    Science.gov (United States)

    Pérez-Sayáns, Mario; Barros-Angueira, Francisco; Suárez-Peñaranda, Jos Ém; García-García, Abel

    2013-11-05

    Cherubism is classified within the group of benign osteo-fibrous lesions. Aside from facial deformities, it may account for major complications. It has been observed that the disease is caused by a mutation in the gene SH3BP2 (SH3-domain binding protein 2), which is located at chromosome 4pl6.3. Here we present two cases of familial cherubism, uncle and nephew, with variable clinical involvement ("Expressivity"), and one case of a woman (sister and mother, respectively), who transmitted cherubism without suffering the disease. In this article we have shown that, in familial cherubism cases, the mutation is inherited through an autosomal dominant transmission. Mutations affecting gene SH3BP2 cause variable clinical involvement (variable expressivity), involvement can be moderate, severe or may result merely in asymptomatic carriers. Since the possibility of transmission reaches 50% of chances, we believe that it is important to develop genetic counseling for both patients and carriers, in order to prevent or minimize new affected offspring. Cherubism; SH3BP2; Expressivity.

  9. Higher resting heart rate variability predicts skill in expressing some emotions.

    Science.gov (United States)

    Tuck, Natalie L; Grant, Rosemary C I; Sollers, John J; Booth, Roger J; Consedine, Nathan S

    2016-12-01

    Vagally mediated heart rate variability (vmHRV) is a measure of cardiac vagal tone, and is widely viewed as a physiological index of the capacity to regulate emotions. However, studies have not directly tested whether vmHRV is associated with the ability to facially express emotions. In extending prior work, the current report tested links between resting vmHRV and the objectively assessed ability to facially express emotions, hypothesizing that higher vmHRV would predict greater expressive skill. Eighty healthy women completed self-reported measures, before attending a laboratory session in which vmHRV and the ability to express six emotions in the face were assessed. A repeated measures analysis of variance revealed a marginal main effect for vmHRV on skill overall; individuals with higher resting vmHRV were only better able to deliberately facially express anger and interest. Findings suggest that differences in resting vmHRV are associated with the objectively assessed ability to facially express some, but not all, emotions, with potential implications for health and well-being. © 2016 Society for Psychophysiological Research.

  10. Laminin alpha2 chain-deficient congenital muscular dystrophy: variable epitope expression in severe and mild cases

    DEFF Research Database (Denmark)

    Cohn, R D; Herrmann, R; Sorokin, L

    1998-01-01

    To characterize the expression of distinct fragments of laminin alpha2 chain in patients with partial laminin alpha2 chain deficiency and variable clinical severity.......To characterize the expression of distinct fragments of laminin alpha2 chain in patients with partial laminin alpha2 chain deficiency and variable clinical severity....

  11. A Decline in Response Variability Improves Neural Signal Detection during Auditory Task Performance.

    Science.gov (United States)

    von Trapp, Gardiner; Buran, Bradley N; Sen, Kamal; Semple, Malcolm N; Sanes, Dan H

    2016-10-26

    The detection of a sensory stimulus arises from a significant change in neural activity, but a sensory neuron's response is rarely identical to successive presentations of the same stimulus. Large trial-to-trial variability would limit the central nervous system's ability to reliably detect a stimulus, presumably affecting perceptual performance. However, if response variability were to decrease while firing rate remained constant, then neural sensitivity could improve. Here, we asked whether engagement in an auditory detection task can modulate response variability, thereby increasing neural sensitivity. We recorded telemetrically from the core auditory cortex of gerbils, both while they engaged in an amplitude-modulation detection task and while they sat quietly listening to the identical stimuli. Using a signal detection theory framework, we found that neural sensitivity was improved during task performance, and this improvement was closely associated with a decrease in response variability. Moreover, units with the greatest change in response variability had absolute neural thresholds most closely aligned with simultaneously measured perceptual thresholds. Our findings suggest that the limitations imposed by response variability diminish during task performance, thereby improving the sensitivity of neural encoding and potentially leading to better perceptual sensitivity. The detection of a sensory stimulus arises from a significant change in neural activity. However, trial-to-trial variability of the neural response may limit perceptual performance. If the neural response to a stimulus is quite variable, then the response on a given trial could be confused with the pattern of neural activity generated when the stimulus is absent. Therefore, a neural mechanism that served to reduce response variability would allow for better stimulus detection. By recording from the cortex of freely moving animals engaged in an auditory detection task, we found that variability

  12. Intercellular Variability in Protein Levels from Stochastic Expression and Noisy Cell Cycle Processes.

    Science.gov (United States)

    Soltani, Mohammad; Vargas-Garcia, Cesar A; Antunes, Duarte; Singh, Abhyudai

    2016-08-01

    Inside individual cells, expression of genes is inherently stochastic and manifests as cell-to-cell variability or noise in protein copy numbers. Since proteins half-lives can be comparable to the cell-cycle length, randomness in cell-division times generates additional intercellular variability in protein levels. Moreover, as many mRNA/protein species are expressed at low-copy numbers, errors incurred in partitioning of molecules between two daughter cells are significant. We derive analytical formulas for the total noise in protein levels when the cell-cycle duration follows a general class of probability distributions. Using a novel hybrid approach the total noise is decomposed into components arising from i) stochastic expression; ii) partitioning errors at the time of cell division and iii) random cell-division events. These formulas reveal that random cell-division times not only generate additional extrinsic noise, but also critically affect the mean protein copy numbers and intrinsic noise components. Counter intuitively, in some parameter regimes, noise in protein levels can decrease as cell-division times become more stochastic. Computations are extended to consider genome duplication, where transcription rate is increased at a random point in the cell cycle. We systematically investigate how the timing of genome duplication influences different protein noise components. Intriguingly, results show that noise contribution from stochastic expression is minimized at an optimal genome-duplication time. Our theoretical results motivate new experimental methods for decomposing protein noise levels from synchronized and asynchronized single-cell expression data. Characterizing the contributions of individual noise mechanisms will lead to precise estimates of gene expression parameters and techniques for altering stochasticity to change phenotype of individual cells.

  13. Intercellular Variability in Protein Levels from Stochastic Expression and Noisy Cell Cycle Processes.

    Directory of Open Access Journals (Sweden)

    Mohammad Soltani

    2016-08-01

    Full Text Available Inside individual cells, expression of genes is inherently stochastic and manifests as cell-to-cell variability or noise in protein copy numbers. Since proteins half-lives can be comparable to the cell-cycle length, randomness in cell-division times generates additional intercellular variability in protein levels. Moreover, as many mRNA/protein species are expressed at low-copy numbers, errors incurred in partitioning of molecules between two daughter cells are significant. We derive analytical formulas for the total noise in protein levels when the cell-cycle duration follows a general class of probability distributions. Using a novel hybrid approach the total noise is decomposed into components arising from i stochastic expression; ii partitioning errors at the time of cell division and iii random cell-division events. These formulas reveal that random cell-division times not only generate additional extrinsic noise, but also critically affect the mean protein copy numbers and intrinsic noise components. Counter intuitively, in some parameter regimes, noise in protein levels can decrease as cell-division times become more stochastic. Computations are extended to consider genome duplication, where transcription rate is increased at a random point in the cell cycle. We systematically investigate how the timing of genome duplication influences different protein noise components. Intriguingly, results show that noise contribution from stochastic expression is minimized at an optimal genome-duplication time. Our theoretical results motivate new experimental methods for decomposing protein noise levels from synchronized and asynchronized single-cell expression data. Characterizing the contributions of individual noise mechanisms will lead to precise estimates of gene expression parameters and techniques for altering stochasticity to change phenotype of individual cells.

  14. Tools to minimize interlaboratory variability in vitellogenin gene expression monitoring programs

    Science.gov (United States)

    Jastrow, Aaron; Gordon, Denise A.; Auger, Kasie M.; Punska, Elizabeth C.; Arcaro, Kathleen F.; Keteles, Kristen; Winkelman, Dana L.; Lattier, David; Biales, Adam; Lazorchak, James M.

    2017-01-01

    The egg yolk precursor protein vitellogenin is widely used as a biomarker of estrogen exposure in male fish. However, standardized methodology is lacking and little is known regarding the reproducibility of results among laboratories using different equipment, reagents, protocols, and data analysis programs. To address this data gap we tested the reproducibility across laboratories to evaluate vitellogenin gene (vtg) expression and assessed the value of using a freely available software data analysis program. Samples collected from studies of male fathead minnows (Pimephales promelas) exposed to 17α-ethinylestradiol (EE2) and minnows exposed to processed wastewater effluent were evaluated for vtg expression in 4 laboratories. Our results indicate reasonable consistency among laboratories if the free software for expression analysis LinRegPCR is used, with 3 of 4 laboratories detecting vtg in fish exposed to 5 ng/L EE2 (n = 5). All 4 laboratories detected significantly increased vtg levels in 15 male fish exposed to wastewater effluent compared with 15 male fish held in a control stream. Finally, we were able to determine that the source of high interlaboratory variability from complementary deoxyribonucleic acid (cDNA) to quantitative polymerase chain reaction (qPCR) analyses was the expression analysis software unique to each real-time qPCR machine. We successfully eliminated the interlaboratory variability by reanalyzing raw fluorescence data with independent freeware, which yielded cycle thresholds and polymerase chain reaction (PCR) efficiencies that calculated results independently of proprietary software. Our results suggest that laboratories engaged in monitoring programs should validate their PCR protocols and analyze their gene expression data following the guidelines established in the present study for all gene expression biomarkers. 

  15. Intercellular Variability in Protein Levels from Stochastic Expression and Noisy Cell Cycle Processes

    Science.gov (United States)

    Soltani, Mohammad; Vargas-Garcia, Cesar A.; Antunes, Duarte; Singh, Abhyudai

    2016-01-01

    Inside individual cells, expression of genes is inherently stochastic and manifests as cell-to-cell variability or noise in protein copy numbers. Since proteins half-lives can be comparable to the cell-cycle length, randomness in cell-division times generates additional intercellular variability in protein levels. Moreover, as many mRNA/protein species are expressed at low-copy numbers, errors incurred in partitioning of molecules between two daughter cells are significant. We derive analytical formulas for the total noise in protein levels when the cell-cycle duration follows a general class of probability distributions. Using a novel hybrid approach the total noise is decomposed into components arising from i) stochastic expression; ii) partitioning errors at the time of cell division and iii) random cell-division events. These formulas reveal that random cell-division times not only generate additional extrinsic noise, but also critically affect the mean protein copy numbers and intrinsic noise components. Counter intuitively, in some parameter regimes, noise in protein levels can decrease as cell-division times become more stochastic. Computations are extended to consider genome duplication, where transcription rate is increased at a random point in the cell cycle. We systematically investigate how the timing of genome duplication influences different protein noise components. Intriguingly, results show that noise contribution from stochastic expression is minimized at an optimal genome-duplication time. Our theoretical results motivate new experimental methods for decomposing protein noise levels from synchronized and asynchronized single-cell expression data. Characterizing the contributions of individual noise mechanisms will lead to precise estimates of gene expression parameters and techniques for altering stochasticity to change phenotype of individual cells. PMID:27536771

  16. Expression analysis of the Theileria parva subtelomere-encoded variable secreted protein gene family.

    Directory of Open Access Journals (Sweden)

    Jacqueline Schmuckli-Maurer

    Full Text Available The intracellular protozoan parasite Theileria parva transforms bovine lymphocytes inducing uncontrolled proliferation. Proteins released from the parasite are assumed to contribute to phenotypic changes of the host cell and parasite persistence. With 85 members, genes encoding subtelomeric variable secreted proteins (SVSPs form the largest gene family in T. parva. The majority of SVSPs contain predicted signal peptides, suggesting secretion into the host cell cytoplasm.We analysed SVSP expression in T. parva-transformed cell lines established in vitro by infection of T or B lymphocytes with cloned T. parva parasites. Microarray and quantitative real-time PCR analysis revealed mRNA expression for a wide range of SVSP genes. The pattern of mRNA expression was largely defined by the parasite genotype and not by host background or cell type, and found to be relatively stable in vitro over a period of two months. Interestingly, immunofluorescence analysis carried out on cell lines established from a cloned parasite showed that expression of a single SVSP encoded by TP03_0882 is limited to only a small percentage of parasites. Epitope-tagged TP03_0882 expressed in mammalian cells was found to translocate into the nucleus, a process that could be attributed to two different nuclear localisation signals.Our analysis reveals a complex pattern of Theileria SVSP mRNA expression, which depends on the parasite genotype. Whereas in cell lines established from a cloned parasite transcripts can be found corresponding to a wide range of SVSP genes, only a minority of parasites appear to express a particular SVSP protein. The fact that a number of SVSPs contain functional nuclear localisation signals suggests that proteins released from the parasite could contribute to phenotypic changes of the host cell. This initial characterisation will facilitate future studies on the regulation of SVSP gene expression and the potential biological role of these enigmatic

  17. Experience and expression of anger among Australian prisoners and the relationship between anger and reintegration variables.

    Science.gov (United States)

    Shinkfield, Alison J; Graffam, Joseph

    2014-04-01

    We examined the experience and expression of anger among a group of Australian prisoners prior to and following prison release, as well as the relationship between anger and several reintegration variables. Participants were 79 adult prisoners (54 male, 25 female) who completed the State-Trait Anger Expression Inventory (STAXI-2) 1 month prior to release and again at 1 to 4 weeks and 3 to 4 months post-release. A postrelease questionnaire was also administered at the two postrelease points focusing on the quality of life conditions experienced following release. Mean state and trait anger scores were significantly higher at pre-release than post-release. As well, higher levels of anger expression and anger control were reported at pre-release compared with post-release. Higher age was related to lower state anger at post-release, whereas several variables were related to trait anger at post-release. Theoretical implications for reintegration theory are discussed, together with practical applications.

  18. Expressing Environment Assumptions and Real-time Requirements for a Distributed Embedded System with Shared Variables

    DEFF Research Database (Denmark)

    Tjell, Simon; Fernandes, João Miguel

    2008-01-01

    In a distributed embedded system, it is often necessary to share variables among its computing nodes to allow the distribution of control algorithms. It is therefore necessary to include a component in each node that provides the service of variable sharing. For that type of component, this paper...... discusses how to create a Colored Petri Nets (CPN) model that formally expresses the following elements in a clearly separated structure: (1) assumptions about the behavior of the environment of the component, (2) real-time requirements for the component, and (3) a possible solution in terms of an algorithm...... for the component. The CPN model can be used to validate the environment assumptions and the requirements. The validation is performed by execution of the model during which traces of events and states are automatically generated and evaluated against the requirements....

  19. What to use to express the variability of data: Standard deviation or standard error of mean?

    Science.gov (United States)

    Barde, Mohini P; Barde, Prajakt J

    2012-07-01

    Statistics plays a vital role in biomedical research. It helps present data precisely and draws the meaningful conclusions. While presenting data, one should be aware of using adequate statistical measures. In biomedical journals, Standard Error of Mean (SEM) and Standard Deviation (SD) are used interchangeably to express the variability; though they measure different parameters. SEM quantifies uncertainty in estimate of the mean whereas SD indicates dispersion of the data from mean. As readers are generally interested in knowing the variability within sample, descriptive data should be precisely summarized with SD. Use of SEM should be limited to compute CI which measures the precision of population estimate. Journals can avoid such errors by requiring authors to adhere to their guidelines.

  20. What to use to express the variability of data: Standard deviation or standard error of mean?

    Directory of Open Access Journals (Sweden)

    Mohini P Barde

    2012-01-01

    Full Text Available Statistics plays a vital role in biomedical research. It helps present data precisely and draws the meaningful conclusions. While presenting data, one should be aware of using adequate statistical measures. In biomedical journals, Standard Error of Mean (SEM and Standard Deviation (SD are used interchangeably to express the variability; though they measure different parameters. SEM quantifies uncertainty in estimate of the mean whereas SD indicates dispersion of the data from mean. As readers are generally interested in knowing the variability within sample, descriptive data should be precisely summarized with SD. Use of SEM should be limited to compute CI which measures the precision of population estimate. Journals can avoid such errors by requiring authors to adhere to their guidelines.

  1. VARIABILITY IN PHENOTYPIC EXPRESSION OF SEED QUALITY TRAITS IN SOYBEAN GERMPLASM

    Directory of Open Access Journals (Sweden)

    Aleksandra Sudarić

    2017-01-01

    Full Text Available The aim of this research was to determine the genetic variability of chosen soybean lines in seed quality by determining diversity in phenotypic expression of 1000 seed weight, as well as protein and oil concentrations in the seed. Field trials were set up in a randomized, complete block design with two replications, at the Agricultural Institute Osijek during three growing seasons (2010-2012. Each year, after harvest, 1000 seed weight, and protein and oil concentrations in the seed were determined. Statistical analyses of the results included: calculating basic measures of variation and analysis of variance. The analyzed data showed the existence of plant material's diversity in phenotypic expression of investigated seed quality traits, as well as the existence of statistically significant genotype and year effects.

  2. Improvement of SET variability in TaO x based resistive RAM devices

    Science.gov (United States)

    Schönhals, Alexander; Waser, Rainer; Wouters, Dirk J.

    2017-11-01

    Improvement or at least control of variability is one of the key challenges for Redox based resistive switching memory technology. In this paper, we investigate the impact of a serial resistor as a voltage divider on the SET variability in Pt/Ta2O5/Ta/Pt nano crossbar devices. A partial RESET in a competing complementary switching (CS) mode is identified as a possible failure mechanism of bipolar switching SET in our devices. Due to a voltage divider effect, serial resistance value shows unequal impact on switching voltages of both modes which allows for a selective suppression of the CS mode. The impact of voltage divider on SET variability is demonstrated. A combination of appropriate write voltage and serial resistance allows for a significant improvement of the SET variability.

  3. Network-based group variable selection for detecting expression quantitative trait loci (eQTL

    Directory of Open Access Journals (Sweden)

    Zhang Xuegong

    2011-06-01

    Full Text Available Abstract Background Analysis of expression quantitative trait loci (eQTL aims to identify the genetic loci associated with the expression level of genes. Penalized regression with a proper penalty is suitable for the high-dimensional biological data. Its performance should be enhanced when we incorporate biological knowledge of gene expression network and linkage disequilibrium (LD structure between loci in high-noise background. Results We propose a network-based group variable selection (NGVS method for QTL detection. Our method simultaneously maps highly correlated expression traits sharing the same biological function to marker sets formed by LD. By grouping markers, complex joint activity of multiple SNPs can be considered and the dimensionality of eQTL problem is reduced dramatically. In order to demonstrate the power and flexibility of our method, we used it to analyze two simulations and a mouse obesity and diabetes dataset. We considered the gene co-expression network, grouped markers into marker sets and treated the additive and dominant effect of each locus as a group: as a consequence, we were able to replicate results previously obtained on the mouse linkage dataset. Furthermore, we observed several possible sex-dependent loci and interactions of multiple SNPs. Conclusions The proposed NGVS method is appropriate for problems with high-dimensional data and high-noise background. On eQTL problem it outperforms the classical Lasso method, which does not consider biological knowledge. Introduction of proper gene expression and loci correlation information makes detecting causal markers more accurate. With reasonable model settings, NGVS can lead to novel biological findings.

  4. Situational Variability of Means of Expression of Positive Emotions in Modern English

    Directory of Open Access Journals (Sweden)

    Alina K. Kisil

    2017-06-01

    Full Text Available The article investigates situational variability of means of expression of positive emotions in Modern English. This problem is topical for linguistics of emotions, pragma- and sociolinguistics. The author analyzes verbal, paraverbal and nonverbal means of expressing positive emotions of joy and surprise in three communicative registers: official, neutral and unofficial. These registers are singled out on the basis of situational context and participants of the situation. The investigation gave the author the opportunity to come to the conclusion that in the official register emotions are controlled and very often are subject to strategic purposes. They implement the upgrading strategy the aim of which is to give a high evaluation of the addressee and of everything what is happening. It stipulates the use of corresponding expressive words and word combinations, exclamatory sentences, repetitions and rhetorical questions. Paraverbal means include only light laughter and nonverbal – a smile, the expression of the eyes, nods and tangled breath. The range of the means in question is wider in the neutral register where the speaker can use such verbal means as interjections with long sounds, expletives, pauses, descriptions of own emotions. Such paraverbal means as the emotional color of the voice and its volume, intonation, different kinds of laughter and such nonverbal means as different kinds of smile, the expression of the face, gestures and movements are also used. Unofficial register is especially rich in means of expressing positive emotions. Besides means typical of other registers such verbal means as obscene lexicon, phrasal words and graphical means are used here. Paraverbal means include numerous verbs reflecting the volume of voice and nonverbal – rich mimic, friendly hugs and kisses.

  5. Facial expression recognition based on improved local ternary pattern and stacked auto-encoder

    Science.gov (United States)

    Wu, Yao; Qiu, Weigen

    2017-08-01

    In order to enhance the robustness of facial expression recognition, we propose a method of facial expression recognition based on improved Local Ternary Pattern (LTP) combined with Stacked Auto-Encoder (SAE). This method uses the improved LTP extraction feature, and then uses the improved depth belief network as the detector and classifier to extract the LTP feature. The combination of LTP and improved deep belief network is realized in facial expression recognition. The recognition rate on CK+ databases has improved significantly.

  6. Latent variable modeling improves AKI risk factor identification and AKI prediction compared to traditional methods

    OpenAIRE

    Smith, Loren E.; Smith, Derek K.; Blume, Jeffrey D.; Siew, Edward D.; Billings, Frederic T.

    2017-01-01

    Background Acute kidney injury (AKI) is diagnosed based on postoperative serum creatinine change, but AKI models have not consistently performed well, in part due to the omission of clinically important but practically unmeasurable variables that affect creatinine. We hypothesized that a latent variable mixture model of postoperative serum creatinine change would partially account for these unmeasured factors and therefore increase power to identify risk factors of AKI and improve predictive ...

  7. Probabilistic Requirements (Partial) Verification Methods Best Practices Improvement. Variables Acceptance Sampling Calculators: Empirical Testing. Volume 2

    Science.gov (United States)

    Johnson, Kenneth L.; White, K. Preston, Jr.

    2012-01-01

    The NASA Engineering and Safety Center was requested to improve on the Best Practices document produced for the NESC assessment, Verification of Probabilistic Requirements for the Constellation Program, by giving a recommended procedure for using acceptance sampling by variables techniques as an alternative to the potentially resource-intensive acceptance sampling by attributes method given in the document. In this paper, the results of empirical tests intended to assess the accuracy of acceptance sampling plan calculators implemented for six variable distributions are presented.

  8. Size and Topology Optimization for Trusses with Discrete Design Variables by Improved Firefly Algorithm

    Directory of Open Access Journals (Sweden)

    Yue Wu

    2017-01-01

    Full Text Available Firefly Algorithm (FA, for short is inspired by the social behavior of fireflies and their phenomenon of bioluminescent communication. Based on the fundamentals of FA, two improved strategies are proposed to conduct size and topology optimization for trusses with discrete design variables. Firstly, development of structural topology optimization method and the basic principle of standard FA are introduced in detail. Then, in order to apply the algorithm to optimization problems with discrete variables, the initial positions of fireflies and the position updating formula are discretized. By embedding the random-weight and enhancing the attractiveness, the performance of this algorithm is improved, and thus an Improved Firefly Algorithm (IFA, for short is proposed. Furthermore, using size variables which are capable of including topology variables and size and topology optimization for trusses with discrete variables is formulated based on the Ground Structure Approach. The essential techniques of variable elastic modulus technology and geometric construction analysis are applied in the structural analysis process. Subsequently, an optimization method for the size and topological design of trusses based on the IFA is introduced. Finally, two numerical examples are shown to verify the feasibility and efficiency of the proposed method by comparing with different deterministic methods.

  9. Familial hypomagnesemia with hypercalciuria and nephrocalcinosis: variable phenotypic expression in three affected sisters from Mexican ancestry.

    Science.gov (United States)

    Arteaga, María E; Hunziker, Walter; Teo, Audrey S M; Hillmer, Axel M; Mutchinick, Osvaldo M

    2015-02-01

    Familial hypomagnesemia with hypercalciuria and nephrocalcinosis is a rare autosomal recessive renal disease caused by mutations in genes for the tight junction transmembrane proteins Claudin-16 (CLDN16) and Claudin-19 (CLDN19). We present the first case report of a Mexican family with three affected sisters carrying a p.Gly20Asp mutation in CLDN19 whose heterozygous mother showed evident hypercalciuria and normal low magnesemia without any other clinical, laboratory, and radiological symptoms of renal disease making of her an unsuitable donor. The affected sisters showed variable phenotypic expression including age of first symptoms, renal urinary tract infections, nephrolithiasis, nephrocalcinosis, and eye symptoms consisting in retinochoroiditis, strabismus, macular scars, bilateral anisocoria, and severe myopia and astigmatism. End stage renal disease due to renal failure needed kidney transplantation in the three of them. Interesting findings were a heterozygous mother with asymptomatic hypercalciuria warning on the need of carefully explore clinical, laboratory, kidney ultrasonograpy, and mutation status in first degree asymptomatic relatives to avoid inappropriate kidney donors; an evident variable phenotypic expression among patients; the identification of a mutation almost confined to Spanish cases and a 3.5 Mb block of genomic homozygosis strongly suggesting a common remote parental ancestor for the gene mutation reported.

  10. Re-expression of an inactivated variable surface glycoprotein gene in Trypanosoma equiperdum.

    Science.gov (United States)

    Buck, G A; Jacquemot, C; Baltz, T; Eisen, H

    1984-12-01

    Variable surface glycoprotein (VSG) genes in African trypanosomes are often activated by the duplicative transposition of a silent basic copy (BC) gene into an unlinked telomerically located expression site, producing an active expression-linked copy (ELC) of that gene. However, some BC genes that are already linked to a telomere are activated without apparent duplication or transposition. We have recently shown that an active VSG ELC can be inactivated in situ, apparently without rearrangement. To explain these observations it has been suggested that VSG genes that are associated with chromosome telomeres are activated by chromosome end exchanges that occur at a considerable distance upstream from the genes themselves and place them cis to a unique VSG expression element. In an attempt to test this model we derived five VSG-1 expressing variants from BoTat-2, a VSG-2 expressing variant of Trypanosoma equiperdum which carries an inactive residual VSG-1 ELC (R-ELC) as well as the active VSG-2 ELC near unlinked chromosome telomeres. We examined the fates of the VSG-2 ELC and the VSG-1 R-ELC in these variants. All five had maintained the VSG-1 R-ELC; three in a reactivated form and two in an inactive state. The latter two variants carried new, active VSG-1 ELCs: one in the site that had previously contained the VSG-2 ELC and one in a previously unidentified site. The VSG-2 ELC was lost in all five of the variants. The results are not consistent with the simple chromosome end exchange model, which predicts that the VSG-2 ELC would be inactivated but not deleted when the VSG-1 R-ELC was reactivated.

  11. Strain engineering for improved expression of recombinant proteins in bacteria

    Science.gov (United States)

    2011-01-01

    Protein expression in Escherichia coli represents the most facile approach for the preparation of non-glycosylated proteins for analytical and preparative purposes. So far, the optimization of recombinant expression has largely remained a matter of trial and error and has relied upon varying parameters, such as expression vector, media composition, growth temperature and chaperone co-expression. Recently several new approaches for the genome-scale engineering of E. coli to enhance recombinant protein expression have been developed. These methodologies now enable the generation of optimized E. coli expression strains in a manner analogous to metabolic engineering for the synthesis of low-molecular-weight compounds. In this review, we provide an overview of strain engineering approaches useful for enhancing the expression of hard-to-produce proteins, including heterologous membrane proteins. PMID:21569582

  12. Latent variable modeling improves AKI risk factor identification and AKI prediction compared to traditional methods.

    Science.gov (United States)

    Smith, Loren E; Smith, Derek K; Blume, Jeffrey D; Siew, Edward D; Billings, Frederic T

    2017-02-08

    Acute kidney injury (AKI) is diagnosed based on postoperative serum creatinine change, but AKI models have not consistently performed well, in part due to the omission of clinically important but practically unmeasurable variables that affect creatinine. We hypothesized that a latent variable mixture model of postoperative serum creatinine change would partially account for these unmeasured factors and therefore increase power to identify risk factors of AKI and improve predictive accuracy. We constructed a two-component latent variable mixture model and a linear model using data from a prospective, 653-subject randomized clinical trial of AKI following cardiac surgery (NCT00791648) and included established AKI risk factors and covariates known to affect serum creatinine. We compared model fit, discrimination, power to detect AKI risk factors, and ability to predict AKI between the latent variable mixture model and the linear model. The latent variable mixture model demonstrated superior fit (likelihood ratio of 6.68 × 1071) and enhanced discrimination (permutation test of Spearman's correlation coefficients, p variable mixture model was 94% (-13 to 1132%) more powerful (median [range]) at identifying risk factors than the linear model, and demonstrated increased ability to predict change in serum creatinine (relative mean square error reduction of 6.8%). A latent variable mixture model better fit a clinical cohort of cardiac surgery patients than a linear model, thus providing better assessment of the associations between risk factors of AKI and serum creatinine change and more accurate prediction of AKI. Incorporation of latent variable mixture modeling into AKI research will allow clinicians and investigators to account for clinically meaningful patient heterogeneity resulting from unmeasured variables, and therefore provide improved ability to examine risk factors, measure mechanisms and mediators of kidney injury, and more accurately predict AKI in

  13. Lactobacilli expressing variable domain of llama heavy-chain antibody fragments (lactobodies) confer protection against rotavirus-induced diarrhea

    NARCIS (Netherlands)

    Pant, N.; Hultberg, A.; Zhao, Y.; Svensson, L.; Pan-Hammarström, Q.; Johansen, K.; Pouwels, P.H.; Ruggeri, F.M.; Hermans, P.; Frenken, L.; Borén, T.; Marcotte, H.; Hammarström, L.

    2006-01-01

    Background. Rotavirus-induced diarrhea poses a worldwide medical problem in causing substantial morbidity and mortality among children in developing countries. We therefore developed a system for passive immunotherapy in which recombinant lactobacilli constitutively express neutralizing variable

  14. The Use of Variable Q1 Isolation Windows Improves Selectivity in LC-SWATH-MS Acquisition.

    Science.gov (United States)

    Zhang, Ying; Bilbao, Aivett; Bruderer, Tobias; Luban, Jeremy; Strambio-De-Castillia, Caterina; Lisacek, Frédérique; Hopfgartner, Gérard; Varesio, Emmanuel

    2015-10-02

    As tryptic peptides and metabolites are not equally distributed along the mass range, the probability of cross fragment ion interference is higher in certain windows when fixed Q1 SWATH windows are applied. We evaluated the benefits of utilizing variable Q1 SWATH windows with regards to selectivity improvement. Variable windows based on equalizing the distribution of either the precursor ion population (PIP) or the total ion current (TIC) within each window were generated by an in-house software, swathTUNER. These two variable Q1 SWATH window strategies outperformed, with respect to quantification and identification, the basic approach using a fixed window width (FIX) for proteomic profiling of human monocyte-derived dendritic cells (MDDCs). Thus, 13.8 and 8.4% additional peptide precursors, which resulted in 13.1 and 10.0% more proteins, were confidently identified by SWATH using the strategy PIP and TIC, respectively, in the MDDC proteomic sample. On the basis of the spectral library purity score, some improvement warranted by variable Q1 windows was also observed, albeit to a lesser extent, in the metabolomic profiling of human urine. We show that the novel concept of "scheduled SWATH" proposed here, which incorporates (i) variable isolation windows and (ii) precursor retention time segmentation further improves both peptide and metabolite identifications.

  15. Size and Topology Optimization for Trusses with Discrete Design Variables by Improved Firefly Algorithm

    NARCIS (Netherlands)

    Wu, Yue; Li, Q.; Hu, Qingjie; Borgart, A.

    2017-01-01

    Firefly Algorithm (FA, for short) is inspired by the social behavior of fireflies and their phenomenon of bioluminescent communication. Based on the fundamentals of FA, two improved strategies are proposed to conduct size and topology optimization for trusses with discrete design variables. Firstly,

  16. Improved hyperbolic function method and exact solutions for variable coefficient Benjamin-Bona-Mahony-Burgers equation

    Directory of Open Access Journals (Sweden)

    Ma Hong-Cai

    2015-01-01

    Full Text Available By using the improved hyperbolic function method, we investigate the variable coefficient Benjamin-Bona-Mahony-Burgers equation which is very important in fluid mechanics. Some exact solutions are obtained. Under some conditions, the periodic wave leads to the kink-like wave.

  17. An improved car-following model considering variable safety headway distance

    Science.gov (United States)

    Jia, Yu-han; Du, Yi-man; Wu, Jian-ping

    2014-12-01

    Considering high speed following on expressway or highway, an improved car-following model is developed in this paper by introducing variable safety headway distance. Stability analysis of the new model is carried out using the control theory method. Finally, numerical simulations are implemented and the results show good consistency with theoretical study.

  18. [Clonal variability in expression of geo- and photoorientation in cercariae of Himasthla elongata (Trematoda: Echinostomatidae)].

    Science.gov (United States)

    Prokof'ev, V V; Levakin, I A; Losev, E A; Zavirinskiĭ, Ia V; Galaktionov, K V

    2011-01-01

    The study was carried out on Himasthla elongata, a digenean common in the coastal ecosystems of the northern European seas. This species utilises intertidal prosobranchs Littorina spp. as the first intermediate host, bivalves (in the White Sea, Mytilus edulis) as the second intermediate host and gulls as the final host. The periwinkles Littorina littorea infected with H. elongata rediae (parthenogenetic generations) were sampled in the intertidal of the White Sea (66 degrees 20' N, 33 degrees 38' E) and used as the source of cercariae. Periwinkles were collected from the settlement with the low prevalence of H. elongata. As shown earlier with the use of AFLP (Amplified Fragment Length Polymorphisms) method, rediae groups in all the infected periwinkles of this settlement arise from the infection of a mollusc with a single miracidium. Therefore, the cercariae shed by an infected mollusc have the same genotype or, in other words, represent a clone. Photo- and geoorientation of cercariae originating from different clones and aged 1 h and 6 h were analysed separately. It was shown that in general the larvae of each clone followed the behavioural pattern characteristics of the species (positive geoorientation and negative photoorientation). However, the degree of expression of this typical behaviour was different in different clones. An especially high variability was observed in the manifestation of geoorientation (in several clones, most larvae demonstrated negative geoorientation). Differences in the distribution of cercariae in the illumination gradient were almost equally associated with the interclonal variability and the age of the larvae. On the whole, as the age of cercariae increased, the positive geoorientation became more prominent, whereas the ratio of cercariae with the typical (negative) photoorientation decreased. Statistical analysis revealed significant differences between the cercarial clones both in the initial manifestation of geo- and

  19. Novel Sonic Hedgehog Mutation in a Couple with Variable Expression of Holoprosencephaly

    Directory of Open Access Journals (Sweden)

    M. Aguinaga

    2011-01-01

    Full Text Available Holoprosencephaly (HPE is the most common developmental defect of the forebrain and midface in humans. sporadic and inherited mutations in the human sonic hedgehog (SHH gene cause 37% of familial HPE. A couple was referred to our unit with a family history of two spontaneous first trimester miscarriages and a daughter with HPE who presented early neonatal death. The father had a repaired median cleft lip, absence of central incisors, facial medial hypoplasia, and cleft palate. Intelligence and a brain CT scan were normal. Direct paternal sequencing analysis showed a novel nonsense mutation (W127X. Facial characteristics are considered as HPE microforms, and the pedigree suggested autosomal dominant inheritance with a variable expression of the phenotype. This study reinforces the importance of an exhaustive evaluation of couples with a history of miscarriages and neonatal deaths with structural defects.

  20. Variability in Cadence During Forced Cycling Predicts Motor Improvement in Individuals With Parkinson’s Disease

    Science.gov (United States)

    Ridgel, Angela L.; Abdar, Hassan Mohammadi; Alberts, Jay L.; Discenzo, Fred M.; Loparo, Kenneth A.

    2014-01-01

    Variability in severity and progression of Parkinson’s disease symptoms makes it challenging to design therapy interventions that provide maximal benefit. Previous studies showed that forced cycling, at greater pedaling rates, results in greater improvements in motor function than voluntary cycling. The precise mechanism for differences in function following exercise is unknown. We examined the complexity of biomechanical and physiological features of forced and voluntary cycling and correlated these features to improvements in motor function as measured by the Unified Parkinson’s Disease Rating Scale (UPDRS). Heart rate, cadence, and power were analyzed using entropy signal processing techniques. Pattern variability in heart rate and power were greater in the voluntary group when compared to forced group. In contrast, variability in cadence was higher during forced cycling. UPDRS Motor III scores predicted from the pattern variability data were highly correlated to measured scores in the forced group. This study shows how time series analysis methods of biomechanical and physiological parameters of exercise can be used to predict improvements in motor function. This knowledge will be important in the development of optimal exercise-based rehabilitation programs for Parkinson’s disease. PMID:23144045

  1. Variability in cadence during forced cycling predicts motor improvement in individuals with Parkinson's disease.

    Science.gov (United States)

    Ridgel, Angela L; Abdar, Hassan Mohammadi; Alberts, Jay L; Discenzo, Fred M; Loparo, Kenneth A

    2013-05-01

    Variability in severity and progression of Parkinson's disease symptoms makes it challenging to design therapy interventions that provide maximal benefit. Previous studies showed that forced cycling, at greater pedaling rates, results in greater improvements in motor function than voluntary cycling. The precise mechanism for differences in function following exercise is unknown. We examined the complexity of biomechanical and physiological features of forced and voluntary cycling and correlated these features to improvements in motor function as measured by the Unified Parkinson's Disease Rating Scale (UPDRS). Heart rate, cadence, and power were analyzed using entropy signal processing techniques. Pattern variability in heart rate and power were greater in the voluntary group when compared to forced group. In contrast, variability in cadence was higher during forced cycling. UPDRS Motor III scores predicted from the pattern variability data were highly correlated to measured scores in the forced group. This study shows how time series analysis methods of biomechanical and physiological parameters of exercise can be used to predict improvements in motor function. This knowledge will be important in the development of optimal exercise-based rehabilitation programs for Parkinson's disease.

  2. Transcranial direct current stimulation improves the QT variability index and autonomic cardiac control in healthy subjects older than 60 years

    Directory of Open Access Journals (Sweden)

    Piccirillo G

    2016-11-01

    Full Text Available Gianfranco Piccirillo,1 Cristina Ottaviani,2 Claudia Fiorucci,1 Nicola Petrocchi,2 Federica Moscucci,1 Claudia Di Iorio,1 Fabiola Mastropietri,1 Ilaria Parrotta,1 Matteo Pascucci,1 Damiano Magrì3 1Department of Cardiovascular, Respiratory, Nephrological, Anestesiological and Geriatric Sciences, “Sapienza” University, 2Neuroimaging Laboratory, IRCCS Santa Lucia Foundation, 3Department of Clinical and Molecular Medicine, University of Rome “Sapienza”, Rome, Italy Background: Noninvasive brain stimulation technique is an interesting tool to investigate the causal relation between cortical functioning and autonomic nervous system (ANS responses. Objective: The objective of this report is to evaluate whether anodal transcranial direct current stimulation (tDCS over the temporal cortex influences short-period temporal ventricular repolarization dispersion and cardiovascular ANS control in elderly subjects. Subjects and methods: In 50 healthy subjects (29 subjects younger than 60 years and 21 subjects older than 60 years matched for gender, short-period RR and systolic blood pressure spectral variability, QT variability index (QTVI, and noninvasive hemodynamic data were obtained during anodal tDCS or sham stimulation. Results: In the older group, the QTVI, low-frequency (LF power expressed in normalized units, the ratio between LF and high-frequency (HF power, and systemic peripheral resistances decreased, whereas HF power expressed in normalized units and α HF power increased during the active compared to the sham condition (P<0.05. Conclusion: In healthy subjects older than 60 years, tDCS elicits cardiovascular and autonomic changes. Particularly, it improves temporal ventricular repolarization dispersion, reduces sinus sympathetic activity and systemic peripheral resistance, and increases vagal sinus activity and baroreflex sensitivity. Keywords: transcranial direct current stimulation, QT variability, heart rate variability

  3. Improving stability and curving passing performance for railway vehicles with a variable stiffness MRF rubber joint

    Science.gov (United States)

    Harris, B. J.; Sun, S. S.; Li, W. H.

    2017-03-01

    With the growing need for effective intercity transport, the need for more advanced rail vehicle technology has never been greater. The conflicting primary longitudinal suspension requirements of high speed stability and curving performance limit the development of rail vehicle technology. This paper presents a novel magnetorheological fluid based joint with variable stiffness characteristics for the purpose of overcoming this parameter conflict. Firstly, the joint design and working principle is developed. Following this, a prototype is tested by MTS to characterize its variable stiffness properties under a range of conditions. Lastly, the performance of the proposed MRF rubber joint with regard to improving train stability and curving performance is numerically evaluated.

  4. Cross-Validated Variable Selection in Tree-Based Methods Improves Predictive Performance.

    Science.gov (United States)

    Painsky, Amichai; Rosset, Saharon

    2016-12-07

    Recursive partitioning methods producing tree-like models are a long standing staple of predictive modeling. However, a fundamental flaw in the partitioning (or splitting) rule of commonly used tree building methods precludes them from treating different types of variables equally. This most clearly manifests in these methods' inability to properly utilize categorical variables with a large number of categories, which are ubiquitous in the new age of big data. We propose a framework to splitting using leave-one-out (LOO) cross validation (CV) for selecting the splitting variable, then performing a regular split (in our case, following CART's approach) for the selected variable. The most important consequence of our approach is that categorical variables with many categories can be safely used in tree building and are only chosen if they contribute to predictive power. We demonstrate in extensive simulation and real data analysis that our splitting approach significantly improves the performance of both single tree models and ensemble methods that utilize trees. Importantly, we design an algorithm for LOO splitting variable selection which under reasonable assumptions does not substantially increase the overall computational complexity compared to CART for two-class classification.

  5. Analysis of biological and technical variability in gene expression assays from formalin-fixed paraffin-embedded classical Hodgkin lymphomas.

    Science.gov (United States)

    Vera-Lozada, Gabriela; Scholl, Vanesa; Barros, Mário Henrique M; Sisti, Davide; Guescini, Michele; Stocchi, Vilberto; Stefanoff, Claudio Gustavo; Hassan, Rocio

    2014-12-01

    Formalin-fixed paraffin-embedded (FFPE) tissues are invaluable sources of biological material for research and diagnostic purposes. In this study, we aimed to identify biological and technical variability in RT-qPCR TaqMan® assays performed with FFPE-RNA from lymph nodes of classical Hodgkin lymphoma samples. An ANOVA-nested 6-level design was employed to evaluate BCL2, CASP3, IRF4, LYZ and STAT1 gene expression. The most variable genes were CASP3 (low expression) and LYZ (high expression). Total variability decreased after normalization for all genes, except by LYZ. Genes with moderate and low expression were identified and suffered more the effects of the technical manipulation than high-expression genes. Pre-amplification was shown to introduce significant technical variability, which was partially alleviated by lowering to a half the amount of input RNA. Ct and Cy0 quantification methods, based on cycle-threshold and the kinetic of amplification curves, respectively, were compared. Cy0 method resulted in higher quantification values, leading to the decrease of total variability in CASP3 and LYZ genes. The mean individual noise was 0.45 (0.31 to 0.61 SD), indicating a variation of gene expression over ~1.5 folds from one case to another. We showed that total variability in RT-qPCR from FFPE-RNA is not higher than that reported for fresh complex tissues, and identified gene-, and expression level-sources of biological and technical variability, which can allow better strategies for designing RT-qPCR assays from highly degraded and inhibited samples. Copyright © 2014 Elsevier Inc. All rights reserved.

  6. Novel redox nanomedicine improves gene expression of polyion complex vector

    Directory of Open Access Journals (Sweden)

    Kazuko Toh, Toru Yoshitomi, Yutaka Ikeda and Yukio Nagasaki

    2011-01-01

    Full Text Available Gene therapy has generated worldwide attention as a new medical technology. While non-viral gene vectors are promising candidates as gene carriers, they have several issues such as toxicity and low transfection efficiency. We have hypothesized that the generation of reactive oxygen species (ROS affects gene expression in polyplex supported gene delivery systems. The effect of ROS on the gene expression of polyplex was evaluated using a nitroxide radical-containing nanoparticle (RNP as an ROS scavenger. When polyethyleneimine (PEI/pGL3 or PEI alone was added to the HeLa cells, ROS levels increased significantly. In contrast, when (PEI/pGL3 or PEI was added with RNP, the ROS levels were suppressed. The luciferase expression was increased by the treatment with RNP in a dose-dependent manner and the cellular uptake of pDNA was also increased. Inflammatory cytokines play an important role in ROS generation in vivo. In particular, tumor necrosis factor (TNF-α caused intracellular ROS generation in HeLa cells and decreased gene expression. RNP treatment suppressed ROS production even in the presence of TNF-α and increased gene expression. This anti-inflammatory property of RNP suggests that it may be used as an effective adjuvant for non-viral gene delivery systems.

  7. Improving Fault Ride-Through Capability of Variable Speed Wind Turbines in Distribution Networks

    DEFF Research Database (Denmark)

    Mokryani, Geev; Siano, P.; Piccolo, Antonio

    2013-01-01

    In this paper, a fuzzy controller for improving the fault ride-through (FRT) capability of variable speed wind turbines (WTs) equipped with a doubly fed induction generator (DFIG) is presented. DFIGs can be used as reactive power sources to control the voltage at the point of common coupling (PCC...... on a real 37-bus weak distribution system confirmed that the proposed controller can enhance the FRT capability....

  8. Improved Sleep in Military Personnel is Associated with Changes in the Expression of Inflammatory Genes and Improvement in Depression Symptoms

    Directory of Open Access Journals (Sweden)

    Whitney S. Livingston

    2015-04-01

    Full Text Available Study Objectives: Sleep disturbances are common in military personnel and are associated with increased risk for psychiatric morbidity, including posttraumatic stress disorder and depression, as well as inflammation. Improved sleep quality is linked to reductions in inflammatory bio-markers; however, the underlying mechanisms remain elusive. Methods: In this study we examine whole genome expression changes related to improved sleep in 68 military personnel diagnosed with insomnia. Subjects were classified into the following groups and then compared: improved sleep (n=46, or non-improved sleep (n=22 following three months of standard of care treatment for insomnia. Within subject differential expression was determined from microarray data using the Partek Genomics Suite analysis program and the interactive pathway analysis was used to determine key regulators of observed expression changes. Changes in symptoms of depression and posttraumatic stress disorder were also compared. Results: At baseline both groups were similar in demographics, clinical characteristics, and gene-expression profiles. The microarray data revealed that 217 coding genes were differentially expressed at the follow-up-period compared to baseline in the participants with improved sleep. Expression of inflammatory cytokines were reduced including IL-1β, IL-6, IL-8 and IL-13, with fold changes ranging from -3.19 to -2.1, and there were increases in the expression of inflammatory regulatory genes including toll-like receptors 1, 4, 7, and 8 in the improved sleep group. Interactive pathway analysis revealed 6 gene networks, including ubiquitin which was a major regulator in these gene-expression changes. The improved sleep group also had a significant reduction in the severity of depressive symptoms.Conclusions: Interventions that restore sleep likely reduce the expression of inflammatory genes, which relate to ubiquitin genes and relate to reductions in depressive symptoms.

  9. A hypothesis on improving foreign accents by optimizing variability in vocal learning brain circuits

    Directory of Open Access Journals (Sweden)

    Anna J Simmonds

    2015-11-01

    Full Text Available Rapid vocal motor learning is observed when acquiring a language in early childhood, or learning to speak another language later in life. Accurate pronunciation is one of the hardest things for late learners to master and they are almost always left with a non-native accent. Here I propose a novel hypothesis that this accent could be improved by optimizing variability in vocal learning brain circuits during learning. Much of the neurobiology of human vocal motor learning has been inferred from studies on songbirds. Jarvis (2004 proposed the hypothesis that as in songbirds there are two pathways in humans: one for learning speech (the striatal vocal learning pathway, and one for production of previously learnt speech (the motor pathway. Learning new motor sequences necessary for accurate non-native pronunciation is challenging and I argue that in late learners of a foreign language the vocal learning pathway becomes inactive prematurely. The motor pathway is engaged once again and learners maintain their original native motor patterns for producing speech, resulting in speaking with a foreign accent. Further, I argue that variability in neural activity within vocal motor circuitry generates vocal variability that supports accurate non-native pronunciation. Recent theoretical and experimental work on motor learning suggests that variability in the motor movement is necessary for the development of expertise. I propose that there is little trial-by-trial variability when using the motor pathway. When using the vocal learning pathway variability gradually increases, reflecting an exploratory phase in which learners try out different ways of pronouncing words, before decreasing and stabilizing once the ‘best’ performance has been identified. The hypothesis proposed here could be tested using behavioral interventions that optimize variability and engage the vocal learning pathway for longer, with the prediction that this would allow learners to

  10. Role of Metastasis in Hypertabastic Survival Analysis of Breast Cancer: Interaction with Clinical and Gene Expression Variables

    Directory of Open Access Journals (Sweden)

    Mohammad A. Tabatabai Ph.D.

    2012-01-01

    Full Text Available This paper analyzes the survival of breast cancer patients, exploring the role of a metastasis variable in combination with clinical and gene expression variables. We use the hypertabastic model in a detailed analysis of 295 breast cancer patients from the Netherlands Cancer Institute given in. 1 In comparison to Cox regression the increase in accuracy is complemented by the ability to analyze the time course of the disease progression using the explicitly described hazard and survival curves. We also demonstrate the ability to compute deciles for survival and probability of survival to a given time. Our primary concern in this article is the introduction of a variable representing the existence of metastasis and the effects on the other clinical and gene expression variables. In addition to making a quantitative assessment of the impact of metastasis on the prospects for survival, we are able to look at its interactions with the other prognostic variables. The estrogen receptor status increase in importance, while the significance of the gene expression variables used in the combined model diminishes. When considering only the subgroup of patients who experienced metastasis, the covariates in the model are only the clinical variables for estrogen receptor status and tumor grade.

  11. Genetic variability in the methylenetetrahydrofolate reductase gene (MTHFR) affects clinical expression of Wilson's disease.

    Science.gov (United States)

    Gromadzka, Grażyna; Rudnicka, Magdalena; Chabik, Grzegorz; Przybyłkowski, Adam; Członkowska, Anna

    2011-10-01

    Wilson's disease (WND) is an autosomal recessive disorder of copper (Cu) transport, resulting from pathogenic mutations in the ATP7B gene. The reason for the high variability in phenotypic expressions of WND is unknown. Hepatotoxic and neurotoxic effects of homocysteine (Hcy), as well as interrelationships between Hcy and Cu toxicity, were documented. We genotyped the two 5,10-methylenetetrahydrofolate reductase (one of the key folate/Hcy pathway enzymes) gene (MTHFR) polymorphisms: C677T and A1298C in 245 WND patients. Next, we tested the modulation of WND phenotypes by genotypes of MTHFR. MTHFR C677T genotype distribution deviated from that expected from a population in Hardy-Weinberg equilibrium (C677T, χ(2) = 12.14, p = 0.0005). Patients with the MTHFR 1298C allele were younger at symptoms' onset than those without this allele (median (IQR) age, 24.9 (14.0) years vs. 28.5 (12.0) years, p = 0.006). Carriers of MTHFR "high activity" diplotype (double wild-type homozygotes 677CC/1298AA) manifested WND at older age, than non-carriers (median (IQR) age, 33.5 (9.0) years vs. 25.0 (13.0) years, p = 0.0009). Patients with the MTHFR 677T allele less frequently exhibited the neurological WND phenotype (31 (29.5%) vs. 36 (48.0%)), and more frequently presented with hepatic WND (44 (41.9%) vs. 22 (29.3%)), compared with subjects MTHFR 677T(-). We postulate that MTHFR polymorphism contributes to the phenotypic variability of WND. Copyright © 2011 European Association for the Study of the Liver. Published by Elsevier B.V. All rights reserved.

  12. Physical Exercise Improves Heart Rate Variability in Patients with Type 2 Diabetes: A Systematic Review.

    Science.gov (United States)

    Villafaina, Santos; Collado-Mateo, Daniel; Fuentes, Juan Pedro; Merellano-Navarro, Eugenio; Gusi, Narcis

    2017-09-23

    The aim of the present systematic review is to provide an up-to-date analysis of the research on the effects of exercise programs on heart rate variability (HRV) in individuals with type 2 diabetes mellitus (T2DM). An electronic search of the literature (PubMed, PEDro and Web of Science) was performed. "HRV", "heart rate variability", "exercise", "physical" and "diabetes" were the terms used for article retrieval. Lastly, 15 articles were selected. PRISMA methodology was employed and data were extracted according to the PICOS approach. Although HRV is not routinely measured in the management of T2DM, it is an important measure due to its relation with mortality and diabetic neuropathy. Physical exercise has become a therapy for T2DM, because it improves physical fitness and functional capacity, enhances metabolic control and insulin sensitivity, reduces inflammatory markers and neuropathy symptoms and can increase the regenerative capacity of cutaneous axons, slowing or preventing neuropathy progression. However, it is not clear to what extent physical exercise can improve HRV in this population. Participation in the 15 selected studies was similar in men and women (48.01% men and 51.99% women). All the intervention programs included aerobic training, and it was complemented by strength training in four studies. Duration of physical exercise sessions ranged between 30 and 75 min, the frequency being between 2 and 7 days/week. Statistically significant improvements in groups with diabetes, relative to baseline, were observed in nine studies. More than 3 days per week of aerobic training, complemented by strength training, during at least 3 months seems to improve HRV in T2DM. Weekly frequency might be the most important factor to improve HRV. These aspects could help to design better programs based in scientific evidence, incorporating HRV as an important variable associated with diabetic neuropathy and mortality.

  13. Understanding Variability in Beach Slope to Improve Forecasts of Storm-induced Water Levels

    Science.gov (United States)

    Doran, K. S.; Stockdon, H. F.; Long, J.

    2014-12-01

    The National Assessment of Hurricane-Induced Coastal Erosion Hazards combines measurements of beach morphology with storm hydrodynamics to produce forecasts of coastal change during storms for the Gulf of Mexico and Atlantic coastlines of the United States. Wave-induced water levels are estimated using modeled offshore wave height and period and measured beach slope (from dune toe to shoreline) through the empirical parameterization of Stockdon et al. (2006). Spatial and temporal variability in beach slope leads to corresponding variability in predicted wave setup and swash. Seasonal and storm-induced changes in beach slope can lead to differences on the order of a meter in wave runup elevation, making accurate specification of this parameter essential to skillful forecasts of coastal change. Spatial variation in beach slope is accounted for through alongshore averaging, but temporal variability in beach slope is not included in the final computation of the likelihood of coastal change. Additionally, input morphology may be years old and potentially very different than the conditions present during forecast storm. In order to improve our forecasts of hurricane-induced coastal erosion hazards, the temporal variability of beach slope must be included in the final uncertainty of modeled wave-induced water levels. Frequently collected field measurements of lidar-based beach morphology are examined for study sites in Duck, North Carolina, Treasure Island, Florida, Assateague Island, Virginia, and Dauphin Island, Alabama, with some records extending over a period of 15 years. Understanding the variability of slopes at these sites will help provide estimates of associated water level uncertainty which can then be applied to other areas where lidar observations are infrequent, and improve the overall skill of future forecasts of storm-induced coastal change. Stockdon, H. F., Holman, R. A., Howd, P. A., and Sallenger Jr, A. H. (2006). Empirical parameterization of setup

  14. Biologically variable ventilation improves gas exchange and respiratory mechanics in a model of severe bronchospasm.

    Science.gov (United States)

    Mutch, W Alan C; Buchman, Timothy G; Girling, Linda G; Walker, Elizabeth K-Y; McManus, Bruce M; Graham, M Ruth

    2007-07-01

    Mechanical ventilation can be lifesaving for status asthmaticus, but how best to accomplish mechanical ventilation is unclear. Biologically variable ventilation (mechanical ventilation that emulates healthy variation) and conventional control mode ventilation (monotonously regular) were compared in an animal model of bronchospasm to determine which approach yields better gas exchange and respiratory mechanics. A randomized prospective trial of biologically variable ventilation vs. control mode ventilation in swine. University research laboratory. Eighteen farm-raised pigs. Methacholine was administered as a nebulized aerosol to initiate bronchospasm, defined as doubling of peak inspiratory pressure and respiratory system resistance, and then randomized (n = 9 each group) to either continue control mode ventilation or switch to biologically variable ventilation at the same minute ventilation. Over the next 4 hrs, hemodynamics, blood gases, respiratory mechanics, and carbon dioxide expirograms were recorded hourly. At end-experiment, tracheobronchial lavage was undertaken to determine interleukin-6 and -10 concentrations. Measurements of physiologic variables and inflammatory cytokines showed that biologically variable ventilation significantly improved gas exchange, with greater arterial oxygen tensions (p = .006; group x time interaction), lower arterial carbon dioxide tensions (p = .0003; group effect), lower peak inspiratory pressures (p = .0001; group x time), greater static compliance (p = .0001; group x time), greater dynamic compliance (p = .0001; group x time), and lower total respiratory system resistance (p = .028; group x time), compared with conventional ventilation. The appearance of inflammatory cytokines in bronchoalveolar lavage fluid (interleukin-6 and -10) was not affected by mode of ventilation. In this experimental model, biologically variable ventilation was superior to control mode ventilation in terms of gas exchange and respiratory mechanics

  15. Familial clustering of medullary sponge kidney is autosomal dominant with reduced penetrance and variable expressivity.

    Science.gov (United States)

    Fabris, Antonia; Lupo, Antonio; Ferraro, Pietro M; Anglani, Franca; Pei, York; Danza, Francesco M; Gambaro, Giovanni

    2013-02-01

    Medullary sponge kidney (MSK) is a renal malformation typically associated with nephrocalcinosis and recurrent calcium nephrolithiasis. Approximately 12% of recurrent stone formers have MSK, which is generally considered a sporadic disorder. Since its discovery, three pedigrees have been described in which an apparently autosomal dominant inheritance was suggested. Here, family members of 50 patients with MSK were systematically investigated by means of interviews, renal imaging, and biochemical studies in an effort to establish whether MSK is an inheritable disorder. Twenty-seven MSK probands had 59 first- and second-degree relatives of both genders with MSK in all generations. There were progressively lower mean levels of serum calcium, urinary sodium, pH, and volume, combined with higher serum phosphate and potassium from probands to relatives with bilateral, to those with unilateral, and to those unaffected by MSK. This suggests that most affected relatives have a milder form of MSK than the probands, which would explain why they had not been so diagnosed. Thus, our study provides strong evidence that familial clustering of MSK is common, and has an autosomal dominant inheritance, a reduced penetrance, and variable expressivity.

  16. A Latent Variable Approach for Meta-Analysis of Gene Expression Data from Multiple Microarray Experiments

    Directory of Open Access Journals (Sweden)

    Chinnaiyan Arul M

    2007-09-01

    Full Text Available Abstract Background With the explosion in data generated using microarray technology by different investigators working on similar experiments, it is of interest to combine results across multiple studies. Results In this article, we describe a general probabilistic framework for combining high-throughput genomic data from several related microarray experiments using mixture models. A key feature of the model is the use of latent variables that represent quantities that can be combined across diverse platforms. We consider two methods for estimation of an index termed the probability of expression (POE. The first, reported in previous work by the authors, involves Markov Chain Monte Carlo (MCMC techniques. The second method is a faster algorithm based on the expectation-maximization (EM algorithm. The methods are illustrated with application to a meta-analysis of datasets for metastatic cancer. Conclusion The statistical methods described in the paper are available as an R package, metaArray 1.8.1, which is at Bioconductor, whose URL is http://www.bioconductor.org/.

  17. Calculating Contrast Stretching Variables in Order to Improve Dental Radiology Image Quality

    Science.gov (United States)

    Widodo, Haris B.; Soelaiman, Arief; Ramadhani, Yogi; Supriyanti, Retno

    2016-01-01

    Teeth are one of the body's digestive tract that serves as a softener food that can be digested easily. One branch of science that was instrumental in the treatment and diagnosis of teeth is Dental Radiology. However, in reality many dental radiology images has low resolution, thus inhibiting in making diagnosis of dental disease perfectly. This research aims to improve low resolution dental radiology image using image processing techniques. This paper discussed the use of contrast stretching method to improve the dental radiology image quality, especially relating to the calculation of the variable contrast stretching method. The results showed that contrast stretching method is promising for use in improving the image quality in a simple but efficient.

  18. Variable ventilation improves pulmonary function and reduces lung damage without increasing bacterial translocation in a rat model of experimental pneumonia.

    Science.gov (United States)

    de Magalhães, Raquel F; Samary, Cynthia S; Santos, Raquel S; de Oliveira, Milena V; Rocha, Nazareth N; Santos, Cintia L; Kitoko, Jamil; Silva, Carlos A M; Hildebrandt, Caroline L; Goncalves-de-Albuquerque, Cassiano F; Silva, Adriana R; Faria-Neto, Hugo C; Martins, Vanessa; Capelozzi, Vera L; Huhle, Robert; Morales, Marcelo M; Olsen, Priscilla; Pelosi, Paolo; de Abreu, Marcelo Gama; Rocco, Patricia R M; Silva, Pedro L

    2016-11-25

    Variable ventilation has been shown to improve pulmonary function and reduce lung damage in different models of acute respiratory distress syndrome. Nevertheless, variable ventilation has not been tested during pneumonia. Theoretically, periodic increases in tidal volume (VT) and airway pressures might worsen the impairment of alveolar barrier function usually seen in pneumonia and could increase bacterial translocation into the bloodstream. We investigated the impact of variable ventilation on lung function and histologic damage, as well as markers of lung inflammation, epithelial and endothelial cell damage, and alveolar stress, and bacterial translocation in experimental pneumonia. Thirty-two Wistar rats were randomly assigned to receive intratracheal of Pseudomonas aeruginosa (PA) or saline (SAL) (n = 16/group). After 24-h, animals were anesthetized and ventilated for 2 h with either conventional volume-controlled (VCV) or variable volume-controlled ventilation (VV), with mean VT = 6 mL/kg, PEEP = 5cmH2O, and FiO2 = 0.4. During VV, tidal volume varied randomly with a coefficient of variation of 30% and a Gaussian distribution. Additional animals assigned to receive either PA or SAL (n = 8/group) were not ventilated (NV) to serve as controls. In both SAL and PA, VV improved oxygenation and lung elastance compared to VCV. In SAL, VV decreased interleukin (IL)-6 expression compared to VCV (median [interquartile range]: 1.3 [0.3-2.3] vs. 5.3 [3.6-7.0]; p = 0.02) and increased surfactant protein-D expression compared to NV (2.5 [1.9-3.5] vs. 1.2 [0.8-1.2]; p = 0.0005). In PA, compared to VCV, VV reduced perivascular edema (2.5 [2.0-3.75] vs. 6.0 [4.5-6.0]; p < 0.0001), septum neutrophils (2.0 [1.0-4.0] vs. 5.0 [3.3-6.0]; p = 0.0008), necrotizing vasculitis (3.0 [2.0-5.5] vs. 6.0 [6.0-6.0]; p = 0.0003), and ultrastructural lung damage scores (16 [14-17] vs. 24 [14-27], p < 0.0001). Blood colony-forming-unit (CFU) counts

  19. Quality Improvement Initiative to Decrease Variability of Emergency Physician Opioid Analgesic Prescribing

    Directory of Open Access Journals (Sweden)

    John H. Burton

    2016-05-01

    Full Text Available Introduction: Addressing pain is a crucial aspect of emergency medicine. Prescription opioids are commonly prescribed for moderate to severe pain in the emergency department (ED; unfortunately, prescribing practices are variable. High variability of opioid prescribing decisions suggests a lack of consensus and an opportunity to improve care. This quality improvement (QI initiative aimed to reduce variability in ED opioid analgesic prescribing. Methods: We evaluated the impact of a three-part QI initiative on ED opioid prescribing by physicians at seven sites. Stage 1: Retrospective baseline period (nine months. Stage 2: Physicians were informed that opioid prescribing information would be prospectively collected and feedback on their prescribing and that of the group would be shared at the end of the stage (three months. Stage 3: After physicians received their individual opioid prescribing data with blinded comparison to the group means (from Stage 2 they were informed that individual prescribing data would be unblinded and shared with the group after three months. The primary outcome was variability of the standard error of the mean and standard deviation of the opioid prescribing rate (defined as number of patients discharged with an opioid divided by total number of discharges for each provider. Secondary observations included mean quantity of pills per opioid prescription, and overall frequency of opioid prescribing. Results: The study group included 47 physicians with 149,884 ED patient encounters. The variability in prescribing decreased through each stage of the initiative as represented by the distributions for the opioid prescribing rate: Stage 1 mean 20%; Stage 2 mean 13% (46% reduction, p<0.01, and Stage 3 mean 8% (60% reduction, p<0.01. The mean quantity of pills prescribed per prescription was 16 pills in Stage 1, 14 pills in Stage 2 (18% reduction, p<0.01, and 13 pills in Stage 3 (18% reduction, p<0.01. The group mean

  20. RBCS1 expression in coffee: Coffea orthologs, Coffea arabica homeologs, and expression variability between genotypes and under drought stress.

    Science.gov (United States)

    Marraccini, Pierre; Freire, Luciana P; Alves, Gabriel S C; Vieira, Natalia G; Vinecky, Felipe; Elbelt, Sonia; Ramos, Humberto J O; Montagnon, Christophe; Vieira, Luiz G E; Leroy, Thierry; Pot, David; Silva, Vânia A; Rodrigues, Gustavo C; Andrade, Alan C

    2011-05-16

    In higher plants, the inhibition of photosynthetic capacity under drought is attributable to stomatal and non-stomatal (i.e., photochemical and biochemical) effects. In particular, a disruption of photosynthetic metabolism and Rubisco regulation can be observed. Several studies reported reduced expression of the RBCS genes, which encode the Rubisco small subunit, under water stress. Expression of the RBCS1 gene was analysed in the allopolyploid context of C. arabica, which originates from a natural cross between the C. canephora and C. eugenioides species. Our study revealed the existence of two homeologous RBCS1 genes in C. arabica: one carried by the C. canephora sub-genome (called CaCc) and the other carried by the C. eugenioides sub-genome (called CaCe). Using specific primer pairs for each homeolog, expression studies revealed that CaCe was expressed in C. eugenioides and C. arabica but was undetectable in C. canephora. On the other hand, CaCc was expressed in C. canephora but almost completely silenced in non-introgressed ("pure") genotypes of C. arabica. However, enhanced CaCc expression was observed in most C. arabica cultivars with introgressed C. canephora genome. In addition, total RBCS1 expression was higher for C. arabica cultivars that had recently introgressed C. canephora genome than for "pure" cultivars. For both species, water stress led to an important decrease in the abundance of RBCS1 transcripts. This was observed for plants grown in either greenhouse or field conditions under severe or moderate drought. However, this reduction of RBCS1 gene expression was not accompanied by a decrease in the corresponding protein in the leaves of C. canephora subjected to water withdrawal. In that case, the amount of RBCS1 was even higher under drought than under unstressed (irrigated) conditions, which suggests great stability of RBCS1 under adverse water conditions. On the other hand, for C. arabica, high nocturnal expression of RBCS1 could also explain the

  1. Reducing variability of workforce as a tool to improve plan reliability

    DEFF Research Database (Denmark)

    Wandahl, Søren; Yicheng, S.; Zygmunt, K. J.

    Variability of flow is recognized as the greatest obstacle to production management. Since the work flow and labour flow are two dominators of work performance, it is important to manage them simultaneously. The objective of this paper is to examine whether by reducing the variance of a labour flow......, a plan reliability can be improved, therefore, three different construction labour data sets have been examined by utilizing Monte Carlo Simulation, to analyze the probability to finish simulated projects within a certain time. The research findings revealed that reducing variance in the workforce flow...

  2. Reducing Variability of Workforce as a Tool to Improve Plan Reliability

    DEFF Research Database (Denmark)

    Yicheng, Shen; Zygmunt, Katarzyna Julia; Wandahl, Søren

    2017-01-01

    Variability of flow is recognized as one of the greatest obstacles to production management. Since the work flow and labour flow are two dominators of work performance, it is important to manage them simultaneously. The objective of this paper is to examine if an increased plan reliability could...... of the workforce flow does not necessarily shorten the project length, nevertheless it increases probability to finish the tasks within a critical path duration. Additionally, it was concluded, that reducing the variance of crew allocation can improve the productivity....

  3. H-ABC syndrome and DYT4: Variable expressivity or pleiotropy of TUBB4 mutations?

    Science.gov (United States)

    Erro, Roberto; Hersheson, Joshua; Ganos, Christos; Mencacci, Niccoló E; Stamelou, Maria; Batla, Amit; Thust, Stefanie Catherine; Bras, Jose M; Guerreiro, Rita J; Hardy, John; Quinn, Niall P; Houlden, Henry; Bhatia, Kailash P

    2015-05-01

    Recently, mutations in the TUBB4A gene have been found to underlie hypomyelination with atrophy of the basal ganglia and cerebellum (H-ABC) syndrome, a rare neurodegenerative disorder of infancy and childhood. TUBB4A mutations also have been described as causative of DYT4 ("hereditary whispering dysphonia"). However, in DYT4, brain imaging has been reported to be normal and, therefore, H-ABC syndrome and DYT4 have been construed to be different disorders, despite some phenotypic overlap. Hence, the question of whether these disorders reflect variable expressivity or pleiotropy of TUBB4A mutations has been raised. We report four unrelated patients with imaging findings either partially or totally consistent with H-ABC syndrome, who were found to have TUBB4A mutations. All four subjects had a relatively homogenous phenotype characterized by severe generalized dystonia with superimposed pyramidal and cerebellar signs, and also bulbar involvement leading to complete aphonia and swallowing difficulties, even though one of the cases had an intermediate phenotype between H-ABC syndrome and DYT4. Genetic analysis of the TUBB4A gene showed one previously described and two novel mutations (c.941C>T; p.Ala314Val and c.900G>T; p.Met300Ile) in the exon 4 of the gene. While expanding the genetic spectrum of H-ABC syndrome, we confirm its radiological heterogeneity and demonstrate that phenotypic overlap with DYT4. Moreover, reappraisal of previously reported cases would also argue against pleiotropy of TUBB4A mutations. We therefore suggest that H-ABC and DYT4 belong to a continuous phenotypic spectrum associated with TUBB4A mutations. © 2014 International Parkinson and Movement Disorder Society.

  4. Determination of the Footballers' Anger Expression Styles in Terms of Some Variable at Different Universities and High Schools in Turkey

    Science.gov (United States)

    Nas, Kazim

    2016-01-01

    This research aims at revealing whether or not footballers' anger expression styles show an alteration in terms of different variables. The descriptive method which is one of the quantitative research methods was adopted as the research model. Research group consists of 154 footballers who play in 8 teams from 12 teams in fifth-group in the…

  5. Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments

    Directory of Open Access Journals (Sweden)

    Wesselkamper Scott C

    2006-12-01

    Full Text Available Abstract Background The small sample sizes often used for microarray experiments result in poor estimates of variance if each gene is considered independently. Yet accurately estimating variability of gene expression measurements in microarray experiments is essential for correctly identifying differentially expressed genes. Several recently developed methods for testing differential expression of genes utilize hierarchical Bayesian models to "pool" information from multiple genes. We have developed a statistical testing procedure that further improves upon current methods by incorporating the well-documented relationship between the absolute gene expression level and the variance of gene expression measurements into the general empirical Bayes framework. Results We present a novel Bayesian moderated-T, which we show to perform favorably in simulations, with two real, dual-channel microarray experiments and in two controlled single-channel experiments. In simulations, the new method achieved greater power while correctly estimating the true proportion of false positives, and in the analysis of two publicly-available "spike-in" experiments, the new method performed favorably compared to all tested alternatives. We also applied our method to two experimental datasets and discuss the additional biological insights as revealed by our method in contrast to the others. The R-source code for implementing our algorithm is freely available at http://eh3.uc.edu/ibmt. Conclusion We use a Bayesian hierarchical normal model to define a novel Intensity-Based Moderated T-statistic (IBMT. The method is completely data-dependent using empirical Bayes philosophy to estimate hyperparameters, and thus does not require specification of any free parameters. IBMT has the strength of balancing two important factors in the analysis of microarray data: the degree of independence of variances relative to the degree of identity (i.e. t-tests vs. equal variance assumption

  6. Vector Control Algorithm for Electric Vehicle AC Induction Motor Based on Improved Variable Gain PID Controller

    Directory of Open Access Journals (Sweden)

    Gang Qin

    2015-01-01

    Full Text Available The acceleration performance of EV, which affects a lot of performances of EV such as start-up, overtaking, driving safety, and ride comfort, has become increasingly popular in recent researches. An improved variable gain PID control algorithm to improve the acceleration performance is proposed in this paper. The results of simulation with Matlab/Simulink demonstrate the effectiveness of the proposed algorithm through the control performance of motor velocity, motor torque, and three-phase current of motor. Moreover, it is investigated that the proposed controller is valid by comparison with the other PID controllers. Furthermore, the AC induction motor experiment set is constructed to verify the effect of proposed controller.

  7. Shared Gaussian Process Latent Variable Model for Multi-view Facial Expression Recognition

    NARCIS (Netherlands)

    Eleftheriadis, Stefanos; Rudovic, Ognjen; Pantic, Maja

    Facial-expression data often appear in multiple views either due to head-movements or the camera position. Existing methods for multi-view facial expression recognition perform classification of the target expressions either by using classifiers learned separately for each view or by using a single

  8. Improving single-variable and multivariable techniques for estimating missing hydrological data

    Science.gov (United States)

    Bennis, S.; Berrada, F.; Kang, N.

    1997-04-01

    A highly efficient technique is developed to obtain the best least-squares approximation of the missing hydrological data in the single-variable case, and this is presented here. The technique is based on an appropriate weighing of the estimated values generated by two autoregressive processes operating, respectively, in the forward and backward directions of time. For the multivariable case, the originally of the work presented here consists in the use of the linear regression model with variable coefficients to estimate missing data. As for the single-variable case, two multivariable regression models are calibrated recursively on available data preceding and following the period of missing data. The use of Kalman filter (KF) has improved the accuracy in the estimation of the first missing data including the peak flow. For subsequent missing data the confidence of the estimates is greater when using a static model identified by the ordinary least squares (OLS) technique. It has been found that there is a critical rank for which there is an inversion of performance between the KF and OLS technique. When the period of missing data is smaller than the critical rank we use only KF technique. When the period of missing data extends past the critical rank, it is recommended that KF be used to estimate the first missing data and then use OLS technique to estimate data coming after the critical rank.

  9. Improving breast cancer classification with mammography, supported on an appropriate variable selection analysis

    Science.gov (United States)

    Pérez, Noel; Guevara, Miguel A.; Silva, Augusto

    2013-02-01

    This work addresses the issue of variable selection within the context of breast cancer classification with mammography. A comprehensive repository of feature vectors was used including a hybrid subset gathering image-based and clinical features. It aimed to gather experimental evidence of variable selection in terms of cardinality, type and find a classification scheme that provides the best performance over the Area Under Receiver Operating Characteristics Curve (AUC) scores using the ranked features subset. We evaluated and classified a total of 300 subsets of features formed by the application of Chi-Square Discretization, Information-Gain, One-Rule and RELIEF methods in association with Feed-Forward Backpropagation Neural Network (FFBP), Support Vector Machine (SVM) and Decision Tree J48 (DTJ48) Machine Learning Algorithms (MLA) for a comparative performance evaluation based on AUC scores. A variable selection analysis was performed for Single-View Ranking and Multi-View Ranking groups of features. Features subsets representing Microcalcifications (MCs), Masses and both MCs and Masses lesions achieved AUC scores of 0.91, 0.954 and 0.934 respectively. Experimental evidence demonstrated that classification performance was improved by combining image-based and clinical features. The most important clinical and image-based features were StromaDistortion and Circularity respectively. Other less important but worth to use due to its consistency were Contrast, Perimeter, Microcalcification, Correlation and Elongation.

  10. Variable expressivity and genetic heterogeneity involving DPT and SEMA3D genes in autosomal dominant familial Meniere's disease.

    Science.gov (United States)

    Martín-Sierra, Carmen; Gallego-Martinez, Alvaro; Requena, Teresa; Frejo, Lidia; Batuecas-Caletrío, Angel; Lopez-Escamez, Jose A

    2017-02-01

    Autosomal dominant (AD) familial Meniere's disease (FMD) is a rare disorder involving the inner ear defined by sensorineural hearing loss, tinnitus and episodic vertigo. Here, we have identified two novel and rare heterozygous variants in the SEMA3D and DPT genes segregating with the complete phenotype that have variable expressivity in two pedigrees with AD-FMD. A detailed characterization of the phenotype within each family illustrates the clinical heterogeneity in the onset and progression of the disease. We also showed the expression of both genes in the human cochlea and performed in silico analyses of these variants. Three-dimensional protein modelling showed changes in the structure of the protein indicating potential physical interactions. These results confirm a genetic heterogeneity in FMD with incomplete penetrance and variable expressivity.

  11. Haptic feedback enhances rhythmic motor control by reducing variability, not improving convergence rate.

    Science.gov (United States)

    Ankarali, M Mert; Tutkun Sen, H; De, Avik; Okamura, Allison M; Cowan, Noah J

    2014-03-01

    Stability and performance during rhythmic motor behaviors such as locomotion are critical for survival across taxa: falling down would bode well for neither cheetah nor gazelle. Little is known about how haptic feedback, particularly during discrete events such as the heel-strike event during walking, enhances rhythmic behavior. To determine the effect of haptic cues on rhythmic motor performance, we investigated a virtual paddle juggling behavior, analogous to bouncing a table tennis ball on a paddle. Here, we show that a force impulse to the hand at the moment of ball-paddle collision categorically improves performance over visual feedback alone, not by regulating the rate of convergence to steady state (e.g., via higher gain feedback or modifying the steady-state hand motion), but rather by reducing cycle-to-cycle variability. This suggests that the timing and state cues afforded by haptic feedback decrease the nervous system's uncertainty of the state of the ball to enable more accurate control but that the feedback gain itself is unaltered. This decrease in variability leads to a substantial increase in the mean first passage time, a measure of the long-term metastability of a stochastic dynamical system. Rhythmic tasks such as locomotion and juggling involve intermittent contact with the environment (i.e., hybrid transitions), and the timing of such transitions is generally easy to sense via haptic feedback. This timing information may improve metastability, equating to less frequent falls or other failures depending on the task.

  12. Improving evapotranspiration in a land surface model using biophysical variables derived from MSG/SEVIRI satellite

    Directory of Open Access Journals (Sweden)

    N. Ghilain

    2012-08-01

    Full Text Available Monitoring evapotranspiration over land is highly dependent on the surface state and vegetation dynamics. Data from spaceborn platforms are desirable to complement estimations from land surface models. The success of daily evapotranspiration monitoring at continental scale relies on the availability, quality and continuity of such data. The biophysical variables derived from SEVIRI on board the geostationary satellite Meteosat Second Generation (MSG and distributed by the Satellite Application Facility on Land surface Analysis (LSA-SAF are particularly interesting for such applications, as they aimed at providing continuous and consistent daily time series in near-real time over Africa, Europe and South America. In this paper, we compare them to monthly vegetation parameters from a database commonly used in numerical weather predictions (ECOCLIMAP-I, showing the benefits of the new daily products in detecting the spatial and temporal (seasonal and inter-annual variability of the vegetation, especially relevant over Africa. We propose a method to handle Leaf Area Index (LAI and Fractional Vegetation Cover (FVC products for evapotranspiration monitoring with a land surface model at 3–5 km spatial resolution. The method is conceived to be applicable for near-real time processes at continental scale and relies on the use of a land cover map. We assess the impact of using LSA-SAF biophysical variables compared to ECOCLIMAP-I on evapotranspiration estimated by the land surface model H-TESSEL. Comparison with in-situ observations in Europe and Africa shows an improved estimation of the evapotranspiration, especially in semi-arid climates. Finally, the impact on the land surface modelled evapotranspiration is compared over a north–south transect with a large gradient of vegetation and climate in Western Africa using LSA-SAF radiation forcing derived from remote sensing. Differences are highlighted. An evaluation against remote sensing derived land

  13. Perspective: Is Random Monoallelic Expression a Contributor to Phenotypic Variability of Autosomal Dominant Disorders?

    National Research Council Canada - National Science Library

    Baoheng Gui; Jesse Slone; Taosheng Huang

    2017-01-01

    Several factors have been proposed as contributors to interfamilial and intrafamilial phenotypic variability in autosomal dominant disorders, including allelic variation, modifier genes, environmental...

  14. Eight weeks of intermittent hypoxic training improves submaximal physiological variables in highly trained runners.

    Science.gov (United States)

    Holliss, Ben A; Burden, Richard J; Jones, Andrew M; Pedlar, Charles R

    2014-08-01

    It is unclear whether intermittent hypoxic training (IHT) results in improvements in physiological variables associated with endurance running. Twelve highly trained runners (VO2peak 70.0 ± 3.5 ml·kg-1·min-1) performed incremental treadmill tests to exhaustion in normobaric normoxia and hypoxia (16.0% FIO2) to assess submaximal and maximal physiological variables and the limit of tolerance (T-Lim). Participants then completed 8 weeks of moderate to heavy intensity normoxic training (control [CONT]) or IHT (twice weekly 40 minutes runs, in combination with habitual training), in a single blinded manner, before repeating the treadmill tests. Submaximal heart rate decreased significantly more after IHT (-5 ± 5 b·min-1; p = 0.001) than after CONT ( -1 ± 5 b·min-1; p = 0.021). Changes in submaximal V[Combining Dot Above]O2 were significantly different between groups (p ≤ 0.05); decreasing in the IHT group in hypoxia (-2.6 ± 1.7 ml·kg-1·min-1; p = 0.001) and increasing in the CONT group in normoxia (+1.1 ± 2.1 ml·kg-1·min-1; p = 0.012). There were no VO2peak changes within either group, and while T-Lim improved post-IHT in hypoxia (p = 0.031), there were no significant differences between groups. Intermittent hypoxic training resulted in a degree of enhanced cardiovascular fitness that was evident during submaximal, but not maximal intensity exercise. These results suggest that moderate to heavy intensity IHT provides a mean of improving the capacity for submaximal exercise and may be useful for pre-acclimatization for subsequent exercise in hypoxia, but additional research is required to establish its efficacy for athletic performance at sea level.

  15. Improving plot- and regional-scale crop models for simulating impacts of climate variability and extremes

    Science.gov (United States)

    Tao, F.; Rötter, R.

    2013-12-01

    Many studies on global climate report that climate variability is increasing with more frequent and intense extreme events1. There are quite large uncertainties from both the plot- and regional-scale models in simulating impacts of climate variability and extremes on crop development, growth and productivity2,3. One key to reducing the uncertainties is better exploitation of experimental data to eliminate crop model deficiencies and develop better algorithms that more adequately capture the impacts of extreme events, such as high temperature and drought, on crop performance4,5. In the present study, in a first step, the inter-annual variability in wheat yield and climate from 1971 to 2012 in Finland was investigated. Using statistical approaches the impacts of climate variability and extremes on wheat growth and productivity were quantified. In a second step, a plot-scale model, WOFOST6, and a regional-scale crop model, MCWLA7, were calibrated and validated, and applied to simulate wheat growth and yield variability from 1971-2012. Next, the estimated impacts of high temperature stress, cold damage, and drought stress on crop growth and productivity based on the statistical approaches, and on crop simulation models WOFOST and MCWLA were compared. Then, the impact mechanisms of climate extremes on crop growth and productivity in the WOFOST model and MCWLA model were identified, and subsequently, the various algorithm and impact functions were fitted against the long-term crop trial data. Finally, the impact mechanisms, algorithms and functions in WOFOST model and MCWLA model were improved to better simulate the impacts of climate variability and extremes, particularly high temperature stress, cold damage and drought stress for location-specific and large area climate impact assessments. Our studies provide a good example of how to improve, in parallel, the plot- and regional-scale models for simulating impacts of climate variability and extremes, as needed for

  16. Improving scFv antibody expression levels in the plant cytosol.

    NARCIS (Netherlands)

    Schouten, A.; Roosien, J.; Boer, de J.M.; Wilmink, A.; rosso, M.N.; Bosch, D.; Stiekema, W.J.; gommers, F.J.; Bakker, J.; Schots, A.

    1997-01-01

    Expression of single-chain antibody fragments (scFvs) in the plant cytosol is often cumbersome. It was unexpectedly shown that addition at the C-terminus of the ER retention signal KDEL resulted in significantly improved expression levels. In this report the cytosolic location of the scFv-CK was

  17. Improved classification of Alzheimer's disease data via removal of nuisance variability.

    Directory of Open Access Journals (Sweden)

    Juha Koikkalainen

    Full Text Available Diagnosis of Alzheimer's disease is based on the results of neuropsychological tests and available supporting biomarkers such as the results of imaging studies. The results of the tests and the values of biomarkers are dependent on the nuisance features, such as age and gender. In order to improve diagnostic power, the effects of the nuisance features have to be removed from the data. In this paper, four types of interactions between classification features and nuisance features were identified. Three methods were tested to remove these interactions from the classification data. In stratified analysis, a homogeneous subgroup was generated from a training set. Data correction method utilized linear regression model to remove the effects of nuisance features from data. The third method was a combination of these two methods. The methods were tested using all the baseline data from the Alzheimer's Disease Neuroimaging Initiative database in two classification studies: classifying control subjects from Alzheimer's disease patients and discriminating stable and progressive mild cognitive impairment subjects. The results show that both stratified analysis and data correction are able to statistically significantly improve the classification accuracy of several neuropsychological tests and imaging biomarkers. The improvements were especially large for the classification of stable and progressive mild cognitive impairment subjects, where the best improvements observed were 6% units. The data correction method gave better results for imaging biomarkers, whereas stratified analysis worked well with the neuropsychological tests. In conclusion, the study shows that the excess variability caused by nuisance features should be removed from the data to improve the classification accuracy, and therefore, the reliability of diagnosis making.

  18. A Variable Interval Rescheduling Strategy for Dynamic Flexible Job Shop Scheduling Problem by Improved Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Lei Wang

    2017-01-01

    Full Text Available In real-world manufacturing systems, production scheduling systems are often implemented under random or dynamic events like machine failure, unexpected processing times, stochastic arrival of the urgent orders, cancellation of the orders, and so on. These dynamic events will lead the initial scheduling scheme to be nonoptimal and/or infeasible. Hence, appropriate dynamic rescheduling approaches are needed to overcome the dynamic events. In this paper, we propose a dynamic rescheduling method based on variable interval rescheduling strategy (VIRS to deal with the dynamic flexible job shop scheduling problem considering machine failure, urgent job arrival, and job damage as disruptions. On the other hand, an improved genetic algorithm (GA is proposed for minimizing makespan. In our improved GA, a mix of random initialization population by combining initialization machine and initialization operation with random initialization is designed for generating high-quality initial population. In addition, the elitist strategy (ES and improved population diversity strategy (IPDS are used to avoid falling into the local optimal solution. Experimental results for static and several dynamic events in the FJSP show that our method is feasible and effective.

  19. Improvement of Circadian Rhythm of Heart Rate Variability by Eurythmy Therapy Training

    Directory of Open Access Journals (Sweden)

    Georg Seifert

    2013-01-01

    Full Text Available Background. Impairment of circadian rhythm is associated with various clinical problems. It not only has a negative impact on quality of life but can also be associated with a significantly poorer prognosis. Eurythmy therapy (EYT is an anthroposophic movement therapy aimed at reducing fatigue symptoms and stress levels. Objective. This analysis of healthy subjects was conducted to examine whether the improvement in fatigue symptoms was accompanied by improvements in the circadian rhythm of heart rate variability (HRV. Design. Twenty-three women performed 10 hours of EYT over six weeks. Electrocardiograms (ECGs were recorded before and after the EYT trial. HRV was quantified by parameters of the frequency and time domains and the nonlinear parameters of symbolic dynamics. Results. The day-night contrast with predominance of vagal activity at night becomes more pronounced after the EYT training, and with decreased Ultralow and very low frequencies, the HRV shows evidence of calmer sleep. During the night, the complexity of the HRV is significantly increased indicated by nonlinear parameters. Conclusion. The analysis of the circadian patterns of cardiophysiological parameters before and after EYT shows significant improvements in HRV in terms of greater day-night contrast caused by an increase of vagal activity and calmer and more complex HRV patterns during sleep.

  20. Improved subtilisin YaB production in Bacillus subtilis using engineered synthetic expression control sequences.

    Science.gov (United States)

    Wang, Jyh-Perng; Yeh, Chuan-Mei; Tsai, Ying-Chieh

    2006-12-13

    Alkaline elastase YaB, a favorable meat tenderizer, is an extracellular subtilisin-type protease produced by wild strain alkalophilic Bacillus YaB. The gene ale coding for subtilisin YaB with its own expression control sequence has been cloned and expressed in Bacillus subtilis, but at levels much lower than in the parental strain Bacillus YaB. This study investigates the influence of various expression control sequences including expression control sequences of cdd and veg from B. subtilis, a synthetic expression control sequence (SECS), and engineered synthetic expression control sequences (engineered SECSs) on the expression of subtilisin YaB in B. subtilis. The engineered SECSs were generated by using the Polymerase Chain Reaction; their UP element, Shine-Dargarno (SD) sequence, or both were different from those of the native SECS. The expression efficiencies of SECS and engineered SECSs were higher than those of expression control sequences of ale, cdd, and veg. Substitution of the SD sequence of SECS resulted in higher expression of subtilisin YaB than substitution of the UP element, whereas combined substitution of both gave the highest expression. These results demonstrate that engineering of SECSs is an approach for improving subtilisin YaB production in B. subtilis. Moreover, it is suggested that these enginnered SECSs could potentially be used to express homologous and heterologous proteins in B. subtilis at high level.

  1. Exploring total cardiac variability in healthy and pathophysiological subjects using improved refined multiscale entropy.

    Science.gov (United States)

    Marwaha, Puneeta; Sunkaria, Ramesh Kumar

    2017-02-01

    Multiscale entropy (MSE) and refined multiscale entropy (RMSE) techniques are being widely used to evaluate the complexity of a time series across multiple time scales 't'. Both these techniques, at certain time scales (sometimes for the entire time scales, in the case of RMSE), assign higher entropy to the HRV time series of certain pathologies than that of healthy subjects, and to their corresponding randomized surrogate time series. This incorrect assessment of signal complexity may be due to the fact that these techniques suffer from the following limitations: (1) threshold value 'r' is updated as a function of long-term standard deviation and hence unable to explore the short-term variability as well as substantial variability inherited in beat-to-beat fluctuations of long-term HRV time series. (2) In RMSE, entropy values assigned to different filtered scaled time series are the result of changes in variance, but do not completely reflect the real structural organization inherited in original time series. In the present work, we propose an improved RMSE (I-RMSE) technique by introducing a new procedure to set the threshold value by taking into account the period-to-period variability inherited in a signal and evaluated it on simulated and real HRV database. The proposed I-RMSE assigns higher entropy to the age-matched healthy subjects than that of patients suffering from atrial fibrillation, congestive heart failure, sudden cardiac death and diabetes mellitus, for the entire time scales. The results strongly support the reduction in complexity of HRV time series in female group, old-aged, patients suffering from severe cardiovascular and non-cardiovascular diseases, and in their corresponding surrogate time series.

  2. Study on an improved variable stiffness tuned mass damper based on conical magnetorheological elastomer isolators

    Science.gov (United States)

    Wang, Qi; Dong, Xufeng; Li, Luyu; Ou, Jinping

    2017-10-01

    Use of a variable stiffness tuned mass damper (VSTMD) is an effective approach to reduce the dynamic responses of a structure with shifting natural frequencies. Magnetorheological elastomer (MRE) isolators can be used to build VSTMD due to their tunable stiffness by applying a magnetic field. However, conventional MRE isolators show deformation limits, huge energy consumption and uneconomic production. Focused on developing a MRE VSTMD system to improve this situation, a conical MRE isolator has been proposed and tested. Compared to conventional MRE isolators, the conical isolator shows much higher efficiency, better overall stability, greater deformability and a larger tunable range. The experimental results indicate that the prototype can provide a 46.29% increase in frequency and a 75 N control force range with a 25 W power source. The quick responding MRE VSTMD system has the potential to accurately provide the desired stiffness in two directions to achieve a better structure control.

  3. Agricultural biotechnology for crop improvement in a variable climate: hope or hype?

    Science.gov (United States)

    Varshney, Rajeev K; Bansal, Kailash C; Aggarwal, Pramod K; Datta, Swapan K; Craufurd, Peter Q

    2011-07-01

    Developing crops that are better adapted to abiotic stresses is important for food production in many parts of the world today. Anticipated changes in climate and its variability, particularly extreme temperatures and changes in rainfall, are expected to make crop improvement even more crucial for food production. Here, we review two key biotechnology approaches, molecular breeding and genetic engineering, and their integration with conventional breeding to develop crops that are more tolerant of abiotic stresses. In addition to a multidisciplinary approach, we also examine some constraints that need to be overcome to realize the full potential of agricultural biotechnology for sustainable crop production to meet the demands of a projected world population of nine billion in 2050. Copyright © 2011 Elsevier Ltd. All rights reserved.

  4. Computational Package for Copolymerization Reactivity Ratio Estimation: Improved Access to the Error-in-Variables-Model

    Directory of Open Access Journals (Sweden)

    Alison J. Scott

    2018-01-01

    Full Text Available The error-in-variables-model (EVM is the most statistically correct non-linear parameter estimation technique for reactivity ratio estimation. However, many polymer researchers are unaware of the advantages of EVM and therefore still choose to use rather erroneous or approximate methods. The procedure is straightforward but it is often avoided because it is seen as mathematically and computationally intensive. Therefore, the goal of this work is to make EVM more accessible to all researchers through a series of focused case studies. All analyses employ a MATLAB-based computational package for copolymerization reactivity ratio estimation. The basis of the package is previous work in our group over many years. This version is an improvement, as it ensures wider compatibility and enhanced flexibility with respect to copolymerization parameter estimation scenarios that can be considered.

  5. Improving the Prediction of Maturity From Anthropometric Variables Using a Maturity Ratio.

    Science.gov (United States)

    Fransen, Job; Bush, Stephen; Woodcock, Stephen; Novak, Andrew; Deprez, Dieter; Baxter-Jones, Adam D G; Vaeyens, Roel; Lenoir, Matthieu

    2017-10-12

    This study aimed to improve the prediction accuracy of age at peak height velocity (APHV) from anthropometric assessment using nonlinear models and a maturity ratio rather than a maturity offset. The dataset used to develop the original prediction equations was used to test a new prediction model, utilizing the maturity ratio and a polynomial prediction equation. This model was then applied to a sample of male youth academy soccer players (n = 1330) to validate the new model in youth athletes. A new equation was developed to estimate APHV more accurately than the original model (new model: Akaike information criterion: -6062.1, R(2) = 90.82%; original model: Akaike information criterion = 3048.7, R(2) = 88.88%) within a general population of boys, particularly with relatively high/low APHVs. This study has also highlighted the successful application of the new model to estimate APHV using anthropometric variables in youth athletes, thereby supporting the use of this model in sports talent identification and development. This study argues that this newly developed equation should become standard practice for the estimation of maturity from anthropometric variables in boys from both a general and an athletic population.

  6. Improving voltage stability by utilizing reactive power injection capability of variable speed wind turbines

    Energy Technology Data Exchange (ETDEWEB)

    Ullah, N.R.; Thiringer, T. [Chalmer Univ. of Technology, Goteborg (Sweden). Dept. of Energy and Environment

    2008-07-01

    The effect of wind power generation on voltage stability was investigated by studying various reactive power control algorithms in combination with different wind power systems. The impact of reactive power injection by the systems on steady-state power transfer limits was analyzed. Critical load and wind generation situations were also determined. A power system model based on the Swedish transmission system was used. The wind farm installation was connected to ta 400 kV transmission grid. Four different wind turbine systems were considered: (1) traditional fixed speed; (2) variable speed wind turbine producing active power at unity power factor; (3) a variable speed turbine with a full power grid side converter; and (4) a wind turbine system with a large grid side converter. Simulations were conducted to consider the tap changing action of the transformer for all 4 types of wind turbine. Results of the study showed that use of the reactive power injection capability of wind turbine systems can increase the grid voltage stability limit. The wind farm also assisted in delaying voltage collapse events and prevented the transformer's tap from operating. It was concluded that the use of grid side converters substantially improved maximum deliverable loads. 14 refs., 2 tabs., 15 figs.

  7. Mesenchymal Stem Cells Improve Heart Rate Variability and Baroreflex Sensitivity in Rats with Chronic Heart Failure

    Science.gov (United States)

    de Morais, Sharon Del Bem Velloso; da Silva, Luiz Eduardo Virgilio; Lataro, Renata Maria; Silva, Carlos Alberto Aguiar; de Oliveira, Luciano Fonseca Lemos; de Carvalho, Eduardo Elias Vieira; Simões, Marcus Vinicius; da Silva Meirelles, Lindolfo; Fazan, Rubens

    2015-01-01

    Heart failure induced by myocardial infarct (MI) attenuates the heart rate variability (HRV) and baroreflex sensitivity, which are important risk factors for life-threatening cardiovascular events. Therapies with mesenchymal stem cells (MSCs) have shown promising results after MI. However, the effects of MSCs on hemodynamic (heart rate and arterial pressure) variability and baroreflex sensitivity in chronic heart failure (CHF) following MI have not been evaluated thus far. Male Wistar rats received MSCs or saline solution intravenously 1 week after ligation of the left coronary artery. Control (noninfarcted) rats were also evaluated. MI size was assessed using single-photon emission computed tomography (SPECT). The left ventricular ejection fraction (LVEF) was evaluated using radionuclide ventriculography. Four weeks after MSC injection, the animals were anesthetized and instrumented for chronic ECG recording and catheters were implanted in the femoral artery to record arterial pressure. Arterial pressure and HRVs were determined in time and frequency domain (spectral analysis) while HRV was also examined using nonlinear methods: DFA (detrended fluctuation analysis) and sample entropy. The initial MI size was the same among all infarcted rats but was reduced by MSCs. CHF rats exhibited increased myocardial interstitial collagen and sample entropy combined with the attenuation of the following cardiocirculatory parameters: DFA indices, LVEF, baroreflex sensitivity, and HRV. Nevertheless, MSCs hampered all these alterations, except the LVEF reduction. Therefore, 4 weeks after MSC therapy was applied to CHF rats, MI size and myocardial interstitial fibrosis decreased, while baroreflex sensitivity and HRV improved. PMID:26059001

  8. Plan for improving the organizational climate variables that affect work performance in a state enterprise

    Directory of Open Access Journals (Sweden)

    Bibiana Cubillos Rivera

    2014-07-01

    Full Text Available This investigation presents an analysis on the assessments of organizational climate and work performance of a state enterprise. From this analytical process and based on the results obtained in interviews applied to the managers of the organization, as well as in the theoretical review of these two variables and their relationship to each other, those aspects of organizational climate that most affect the results of the staff are determined. An improvement plan is proposed for the organization, focused on two strategies that directly affect work performance through the intervention of the organizational climate variables that affect it negatively, thus ensuring that this, in turn, is reflected in the scope of both individual and corporate goals. This will also check that, from the area of human management, it can directly influence the strategy of the organizations, ceasing to be seen as an area of support and showing that it can be fully aligned with the mission, vision and in the overall organizational planning.

  9. Biologically variable ventilation improves oxygenation and respiratory mechanics during one-lung ventilation.

    Science.gov (United States)

    McMullen, Michael C; Girling, Linda G; Graham, M Ruth; Mutch, W Alan C

    2006-07-01

    Hypoxemia is common during one-lung ventilation (OLV). Atelectasis contributes to the problem. Biologically variable ventilation (BVV), using microprocessors to reinstitute physiologic variability to respiratory rate and tidal volume, has been shown to be advantageous over conventional monotonous control mode ventilation (CMV) in improving oxygenation during the period of lung reinflation after OLV in an experimental model. Here, using a porcine model, the authors compared BVV with CMV during OLV to assess gas exchange and respiratory mechanics. Eight pigs (25-30 kg) were studied in each of two groups. After induction of anesthesia-tidal volume 12 ml/kg with CMV and surgical intervention-tidal volume was reduced to 9 ml/kg. OLV was initiated with an endobronchial blocker, and the animals were randomly allocated to either continue CMV or switch to BVV for 90 min. After OLV, a recruitment maneuver was undertaken, and both lungs were ventilated for a further 60 min. At predetermined intervals, hemodynamics, respiratory gases (arterial, venous, and end-tidal samples) and mechanics (airway pressures, static and dynamic compliances) were measured. Derived indices (pulmonary vascular resistance, shunt fraction, and dead space ventilation) were calculated. By 15 min of OLV, arterial oxygen tension was greater in the BVV group (group x time interaction, P = 0.003), and shunt fraction was lower with BVV from 30 to 90 min (group effect, P = 0.0004). From 60 to 90 min, arterial carbon dioxide tension was lower with BVV (group x time interaction, P = 0.0001) and dead space ventilation was less from 60 to 90 min (group x time interaction, P = 0.0001). Static compliance was greater by 60 min of BVV and remained greater during return to ventilation of both lungs (group effect, P = 0.0001). In this model of OLV, BVV resulted in superior gas exchange and respiratory mechanics when compared with CMV. Improved static compliance persisted with restoration of two-lung ventilation.

  10. Exploring Expressive Vocabulary Variability in Two-Year-Olds: The Role of Working Memory.

    Science.gov (United States)

    Newbury, Jayne; Klee, Thomas; Stokes, Stephanie F; Moran, Catherine

    2015-12-01

    This study explored whether measures of working memory ability contribute to the wide variation in 2-year-olds' expressive vocabulary skills. Seventy-nine children (aged 24-30 months) were assessed by using standardized tests of vocabulary and visual cognition, a processing speed measure, and behavioral measures of verbal working memory and phonological short-term memory. Strong correlations were observed between phonological short-term memory, verbal working memory, and expressive vocabulary. Speed of spoken word recognition showed a moderate significant correlation with expressive vocabulary. In a multivariate regression model for expressive vocabulary, the most powerful predictor was a measure of phonological short-term memory (accounting for 66% unique variance), followed by verbal working memory (6%), sex (2%), and age (1%). Processing speed did not add significant unique variance. These findings confirm previous research positing a strong role for phonological short-term memory in early expressive vocabulary acquisition. They also extend previous research in two ways. First, a unique association between verbal working memory and expressive vocabulary in 2-year-olds was observed. Second, processing speed was not a unique predictor of variance in expressive vocabulary when included alongside measures of working memory.

  11. Baseline Chromatin Modification Levels May Predict Interindividual Variability in Ozone-Induced Gene Expression

    Science.gov (United States)

    Traditional toxicological paradigms have relied on factors such as age, genotype, and disease status to explain variability in responsiveness to toxicant exposure; however, these are neither sufficient to faithfully identify differentially responsive individuals nor are they modi...

  12. Collaborative Research: Improving Decadal Prediction of Arctic Climate Variability and Change Using a Regional Arctic

    Energy Technology Data Exchange (ETDEWEB)

    Gutowski, William J. [Iowa State Univ., Ames, IA (United States)

    2017-12-28

    This project developed and applied a regional Arctic System model for enhanced decadal predictions. It built on successful research by four of the current PIs with support from the DOE Climate Change Prediction Program, which has resulted in the development of a fully coupled Regional Arctic Climate Model (RACM) consisting of atmosphere, land-hydrology, ocean and sea ice components. An expanded RACM, a Regional Arctic System Model (RASM), has been set up to include ice sheets, ice caps, mountain glaciers, and dynamic vegetation to allow investigation of coupled physical processes responsible for decadal-scale climate change and variability in the Arctic. RASM can have high spatial resolution (~4-20 times higher than currently practical in global models) to advance modeling of critical processes and determine the need for their explicit representation in Global Earth System Models (GESMs). The pan-Arctic region is a key indicator of the state of global climate through polar amplification. However, a system-level understanding of critical arctic processes and feedbacks needs further development. Rapid climate change has occurred in a number of Arctic System components during the past few decades, including retreat of the perennial sea ice cover, increased surface melting of the Greenland ice sheet, acceleration and thinning of outlet glaciers, reduced snow cover, thawing permafrost, and shifts in vegetation. Such changes could have significant ramifications for global sea level, the ocean thermohaline circulation and heat budget, ecosystems, native communities, natural resource exploration, and commercial transportation. The overarching goal of the RASM project has been to advance understanding of past and present states of arctic climate and to improve seasonal to decadal predictions. To do this the project has focused on variability and long-term change of energy and freshwater flows through the arctic climate system. The three foci of this research are: - Changes

  13. Improvement of lentiviral transfer vectors using cis-acting regulatory elements for increased gene expression.

    Science.gov (United States)

    Real, Gonçalo; Monteiro, Francisca; Burger, Christa; Alves, Paula M

    2011-09-01

    Lentiviral vectors are an important tool for gene delivery in vivo and in vitro. The success of gene transfer approaches relies on high and stable levels of gene expression. To this end, several molecular strategies have been employed to manipulate these vectors towards improving gene expression in the targeted animal cells. Low gene expression can be accepted due to the weak transcription from the majority of available mammalian promoters; however, this obstacle can be in part overcome by the insertion of cis-acting elements that enhance gene expression in various expression contexts. In this work, we created different lentiviral vectors in which several posttranscriptional regulatory elements, namely the Woodchuck hepatitis posttranscriptional regulatory element (WPRE) and different specialized poly(A) termination sequences (BGH and SV40) were used to develop vectors leading to improved transgene expression. These vectors combine the advantages of restriction enzyme/ligation-independent cloning eliminating the instability and recombinogenic problems occurring from traditional cloning methods in lentiviral expression vectors and were tested by expressing GFP and the firefly Luciferase reporter gene from different cellular promoters in different cell lines. We show that the promoter activity varies between cell lines and is affected by the lentiviral genomic context. Moreover, we show that the combination of the WPRE element with the BGH poly(A) signal significantly enhances transgene expression. The vectors herein created can be easily modified and adapted without the need for extensive recloning making them a valuable tool for viral vector development.

  14. Variable Speed Limits: Strategies to Improve Safety and Traffic Parameters for a Bottleneck

    Directory of Open Access Journals (Sweden)

    M. Z. Hasanpour

    2017-04-01

    Full Text Available The primary purpose of the speed limit system is to enforce reasonable and safe speed. To reduce secondary problems such as accidents and queuing, Variable Speed Limits (VSL has been suggested. In this paper VSL is used to better safety and traffic parameters. Traffic parameters including speed, queue length and stopping time have been pondering. For VLS, an optimization decision tree algorithm with the function of microscopic simulation was used. The results in case of sub saturated, saturated and supersaturated at a bottleneck are examined and compared with the Allaby logic tree. The results show that the proposed decision tree shows an improved performance in terms of safety and comfort along the highway. The VSL pilot project is part of the Road Safety Improvement Program included in Iran’s road safety action plan that is in the research process in the BHRC Research Institute, Road and Housing & Urban Development Research that is planned for next 10-year Transportation safety view Plan.

  15. Phage exposure causes dynamic shifts in the expression states of specific phase-variable genes of Campylobacter jejuni

    DEFF Research Database (Denmark)

    Aidley, Jack; Holst Sørensen, Martine C.; Bayliss, Christopher D.

    2017-01-01

    Phase variation (PV) creates phenotypic heterogeneity at high frequencies and in a reversible manner. This phenomenon allows bacteria to adapt to a variety of different environments and selective pressures. In Campylobacter jejuni this reversible adaptive process is mediated by mutations...... in homopolymeric G/C tracts. Many C. jejuni-specific phages are dependent on phase-variable surface structures for successful infection. We previously identified the capsular polysaccharide (CPS) moiety, MeOPN-GalfNAc, as a receptor for phage F336 and showed that phase-variable expression of the transferase...... for this CPS modification, cj1421, and two other phase-variable CPS genes generated phage resistance in C. jejuni. Here we investigate the population dynamics of C. jejuni NCTC11168 when exposed to phage F336 in vitro using a newly described method - the 28-locus-CJ11168 PV analysis. Dynamic switching...

  16. The pathogen recognition sensor, NOD2, is variably expressed in patients with pulmonary tuberculosis

    Directory of Open Access Journals (Sweden)

    Johnson Margaret A

    2007-08-01

    Full Text Available Abstract Background NOD2, an intracellular pathogen recognition sensor, modulates innate defences to muropeptides derived from various bacterial species, including Mycobacterium tuberculosis (MTB. Experimentally, NOD2 attenuates two key putative mycobactericidal mechanisms. TNF-α synthesis is markedly reduced in MTB-antigen stimulated-mononuclear cells expressing mutant NOD2 proteins. NOD2 agonists also induce resistance to apoptosis, and may thus facilitate the survival of MTB in infected macrophages. To further define a role for NOD2 in disease pathogenesis, we analysed NOD2 transcriptional responses in pulmonary leucocytes and mononuclear cells harvested from patients with pulmonary tuberculosis (PTB. Methods We analysed NOD2 mRNA expression by real-time polymerase chain-reaction in alveolar lavage cells obtained from 15 patients with pulmonary tuberculosis and their matched controls. We compared NOD2 transcriptional responses, in peripheral leucocytes, before and after anti-tuberculous treatment in 10 patients. In vitro, we measured NOD2 mRNA levels in MTB-antigen stimulated-mononuclear cells. Results No significant differences in NOD2 transcriptional responses were detected in patients and controls. In some patients, however, NOD2 expression was markedly increased and correlated with toll-like-receptor 2 and 4 expression. In whole blood, NOD2 mRNA levels increased significantly after completion of anti-tuberculosis treatment. NOD2 expression levels did not change significantly in mononuclear cells stimulated with mycobacterial antigens in vitro. Conclusion There are no characteristic NOD2 transcriptional responses in PTB. Nonetheless, the increased levels of NOD2 expression in some patients with severe tuberculosis, and the increases in expression levels within peripheral leucocytes following treatment merit further studies in selected patient and control populations.

  17. Improving the knowledge about dissolved oxygen and chlorophyll variability at ESTOC by using autonomous vehicles.

    Science.gov (United States)

    Cianca, A.; Caudet, E.; Vega, D.; Barrera, C.; Hernandez Brito, J.

    2016-02-01

    The European Station for Time Series in the Ocean, Canary Islands "ESTOC" is located in the Eastern Subtropical North Atlantic Gyre (29'10ºN, 15'30ºW). ESTOC started operations in 1994 based on a monthly ship-based sampling, in addition to hydrographic and sediment trap moorings. Since 2002, ESTOC is part of the European network for deep sea ocean observatories through several projects, among others ANIMATE (Atlantic Network of Interdisciplinary Moorings and Time-series for Europe), EuroSITES (European Ocean Observatory Network) and Fixed point Open Ocean Observatory network (FixO3). The main purpose of these projects was to improve the time-resolution of the biogeochemical measurements through moored biogeochemical sensors. Additionally, ESTOC is included in the Marine-Maritime observational network of the Macaronesian region, which is supported by the European overseas territories programs since 2009. This network aims to increase the quantity and quality of marine environmental observations. The goal is to understand phenomena which impact in the environment, and consequently at the socio-economy of the region to attempt their prediction. With this purpose, ESTOC has included the use of autonomous vehicles "glider" in order to increase the observational resolution and, by comparison with the parallel observational programs, to study the biogeochemical processes at different time scale resolutions. This study investigates the time variability of the dissolved oxygen and chlorophyll distributions in the water column focusing on the diel cycle, looking at the relevance of this variability in the already known seasonal distributions. Our interest is assessing net community production and remineralization rates through the use of oxygen variations, establishing the relationship between the DO anomalies values and those from the chlorophyll distribution in the water column.

  18. Expressing product diversification - Categorizing and classifying variability in software product family engineering

    NARCIS (Netherlands)

    Jaring, M; Bosch, J

    2004-01-01

    In a software product family context, software architects design architectures that support product diversification in both space (multiple contexts) and time (changing contexts). Product diversification is based on the concept of variability: a single architecture and a set of components support a

  19. Variable salinity responses of 12 alfalfa genotypes and comparative expression analyses of salt-response genes

    Science.gov (United States)

    Twelve alfalfa genotypes that were selected for biomass under salinity, differences in Na and Cl concentrations in shoots and K/Na ratio were evaluated in this long-term salinity experiment. The selected plants were cloned to reduce genetic variability within each genotype. Salt tolerance (ST) index...

  20. Age Dependent Variability in Gene Expression in Fischer 344 Rat Retina.

    Science.gov (United States)

    Recent evidence suggests older adults may be a sensitive population with regard to environmental exposure to toxic compounds. One source of this sensitivity could be an enhanced variability in response. Studies on phenotypic differences have suggested that variation in response d...

  1. VARIABLE EXPRESSION OF THE POPLITEAL PTERYGIUM SYNDROME IN 2 3-GENERATION FAMILIES

    NARCIS (Netherlands)

    SOEKARMAN, D; COBBEN, JM; VOGELS, A; SPAUWEN, PH; FRYNS, JP

    Three successive generations in two families affected with the popliteal pterygium syndrome are reported. While expression of the syndrome was relatively mild in the first and second generation, the patients in the third generation showed the full-blown syndrome. Differential diagnosis between

  2. Exploring Expressive Vocabulary Variability in Two-Year-Olds: The Role of Working Memory

    Science.gov (United States)

    Newbury, Jayne; Klee, Thomas; Stokes, Stephanie F.; Moran, Catherine

    2015-01-01

    Purpose: This study explored whether measures of working memory ability contribute to the wide variation in 2-year-olds' expressive vocabulary skills. Method: Seventy-nine children (aged 24-30 months) were assessed by using standardized tests of vocabulary and visual cognition, a processing speed measure, and behavioral measures of verbal working…

  3. Rhythm in vocal emotional expressions : the normalized pairwise variability index differentiates emotions across languages

    NARCIS (Netherlands)

    Goudbeek, Martijn; Broersma, M.

    2015-01-01

    The voice is an important channel for emotional expression. Emotions are of- ten characterized by differences in pitch, loudness, the duration of segments, and spectral characteristics (Scherer, 2003). The rhythmic aspect of emotional speech has been largely neglected, most studies limit themselves

  4. VARIABLE BOUND-SITE CHARGING CONTRIBUTIONS TO SURFACE COMPLEXATION MASS ACTION EXPRESSIONS

    Science.gov (United States)

    One and two pK models of surface complexation reactions between reactive surface sites (>SOH) and the proton (H+) use mass action expressions of the form: Ka={[>SOHn-1z-1]g>SOH(0-1)aH+EXP(-xeY/kT)}/{[>SOHnz]g>SOH(n)} where Ka=the acidity constant, [ ]=reactive species concentrati...

  5. A combined strategy improving the expression and solubility of deoxynivalenol single-chain variable fragment antibodies

    Science.gov (United States)

    Deoxynivalenol (DON) is a secondary metabolite produced by certain species of fungi, in particular Fusarium graminearum and F. culmorum. These fungi can infest small grains causing significant economic damage to cereal crops worldwide. Animal exposure to DON can lead to reduced food or feed consumpt...

  6. Variability in school closure decisions in response to 2009 H1N1: a qualitative systems improvement analysis

    Directory of Open Access Journals (Sweden)

    Kraemer John D

    2011-02-01

    Full Text Available Abstract Background School closure was employed as a non-pharmaceutical intervention against pandemic 2009 H1N1, particularly during the first wave. More than 700 schools in the United States were closed. However, closure decisions reflected significant variation in rationales, decision triggers, and authority for closure. This variability presents the opportunity for improved efficiency and decision-making. Methods We identified media reports relating to school closure as a response to 2009 H1N1 by monitoring high-profile sources and searching Lexis-Nexis and Google news alerts, and reviewed reports for key themes. News stories were supplemented by observing conference calls and meetings with health department and school officials, and by discussions with decision-makers and community members. Results There was significant variation in the stated goal of closure decision, including limiting community spread of the virus, protecting particularly vulnerable students, and responding to staff shortages or student absenteeism. Because the goal of closure is relevant to its timing, nature, and duration, unclear rationales for closure can challenge its effectiveness. There was also significant variation in the decision-making authority to close schools in different jurisdictions, which, in some instances, was reflected in open disagreement between school and public health officials. Finally, decision-makers did not appear to expect the level of scientific uncertainty encountered early in the pandemic, and they often expressed significant frustration over changing CDC guidance. Conclusions The use of school closure as a public health response to epidemic disease can be improved by ensuring that officials clarify the goals of closure and tailor closure decisions to those goals. Additionally, authority to close schools should be clarified in advance, and decision-makers should expect to encounter uncertainty disease emergencies unfold and plan

  7. Improvement of menopausal symptoms with acupuncture not reflected in changes to heart rate variability.

    Science.gov (United States)

    Wright, Cheryl L; Aickin, Mikel

    2011-03-01

    Hypothesis Studies indicate that menopausal symptoms are relieved by acupuncture. Additional studies have suggested that acupuncture may affect heart rate variability (HRV). This paper reports a pilot study that investigated whether menopausal symptoms responded to acupuncture, and if changes in the spectral analysis of HRV, either suppression of low frequency or augmentation of high frequency bands, corresponded with symptom report. Methods/interventions 12 healthy menopausal subjects were enrolled in this feasibility study. At baseline, subjects were experiencing moderately distressing menopausal symptoms, scoring at least 22 of a possible 44 points on the Menopausal Rating Scale. 10 traditional Chinese medicine-based, protocol acupuncture treatments were administered over a 4 week period, three times a week for 2 weeks, followed by twice a week for 2 weeks. Outcome measures Menopausal Rating Scale questionnaire, 11 menopausal symptoms were evaluated on a zero to four severity scale via self-administered daily checklist for 4 weeks. Dynamic measures of HRV (autoregressive model) were captured before, during and after acupuncture at each session. Spectral analysis of the heart rate was used to compute power in the low frequency and high frequency bands, and their ratio. All subjects complied fully with the protocol without any reported adverse events. While all 11 symptoms showed significant improvement, and one HRV measure changed, on average over the study period, there was essentially no support for a relationship between HRV, menopausal symptom report and acupuncture intervention.

  8. Improving the reliability of single-subject fMRI by weighting intra-run variability.

    Science.gov (United States)

    de Bertoldi, F; Finos, L; Maieron, M; Weis, L; Campanella, M; Ius, T; Fadiga, L

    2015-07-01

    At present, functional magnetic resonance imaging (fMRI) is one of the most useful methods of studying cognitive processes in the human brain in vivo, both for basic science and clinical goals. Although neuroscience studies often rely on group analysis, clinical applications must investigate single subjects (patients) only. Particularly for the latter, issues regarding the reliability of fMRI readings remain to be resolved. To determine the ability of intra-run variability (IRV) weighting to consistently detect active voxels, we first acquired fMRI data from a sample of healthy subjects, each of whom performed 4 runs (4 blocks each) of self-paced finger-tapping. Each subject's data was analyzed using single-run general linear model (GLM), and each block was then analyzed separately to calculate the IRV weighting. Results show that integrating IRV information into standard single-subject GLM activation maps significantly improved the reliability (p=0.007) of the single-subject fMRI data. This suggests that taking IRV into account can help identify the most constant and relevant neuronal activity at the single-subject level. Copyright © 2015. Published by Elsevier Inc.

  9. Variable-order sequence modeling improves bacterial strain discrimination for Ion Torrent DNA reads.

    Science.gov (United States)

    Poulsen, Thomas M; Frith, Martin

    2017-06-12

    Genome sequencing provides a powerful tool for pathogen detection and can help resolve outbreaks that pose public safety and health risks. Mapping of DNA reads to genomes plays a fundamental role in this approach, where accurate alignment and classification of sequencing data is crucial. Standard mapping methods crudely treat bases as independent from their neighbors. Accuracy might be improved by using higher order paired hidden Markov models (HMMs), which model neighbor effects, but introduce design and implementation issues that have typically made them impractical for read mapping applications. We present a variable-order paired HMM that we term VarHMM, which addresses central issues involved with higher order modeling for sequence alignment. Compared with existing alignment methods, VarHMM is able to model higher order distributions and quantify alignment probabilities with greater detail and accuracy. In a series of comparison tests, in which Ion Torrent sequenced DNA was mapped to similar bacterial strains, VarHMM consistently provided better strain discrimination than any of the other alignment methods that we compared with. Our results demonstrate the advantages of higher ordered probability distribution modeling and also suggest that further development of such models would benefit read mapping in a range of other applications as well.

  10. Cohort-specific imputation of gene expression improves prediction of warfarin dose for African Americans.

    Science.gov (United States)

    Gottlieb, Assaf; Daneshjou, Roxana; DeGorter, Marianne; Bourgeois, Stephane; Svensson, Peter J; Wadelius, Mia; Deloukas, Panos; Montgomery, Stephen B; Altman, Russ B

    2017-11-24

    Genome-wide association studies are useful for discovering genotype-phenotype associations but are limited because they require large cohorts to identify a signal, which can be population-specific. Mapping genetic variation to genes improves power and allows the effects of both protein-coding variation as well as variation in expression to be combined into "gene level" effects. Previous work has shown that warfarin dose can be predicted using information from genetic variation that affects protein-coding regions. Here, we introduce a method that improves dose prediction by integrating tissue-specific gene expression. In particular, we use drug pathways and expression quantitative trait loci knowledge to impute gene expression-on the assumption that differential expression of key pathway genes may impact dose requirement. We focus on 116 genes from the pharmacokinetic and pharmacodynamic pathways of warfarin within training and validation sets comprising both European and African-descent individuals. We build gene-tissue signatures associated with warfarin dose in a cohort-specific manner and identify a signature of 11 gene-tissue pairs that significantly augments the International Warfarin Pharmacogenetics Consortium dosage-prediction algorithm in both populations. Our results demonstrate that imputed expression can improve dose prediction and bridge population-specific compositions. MATLAB code is available at https://github.com/assafgo/warfarin-cohort.

  11. Logic Learning Machine and standard supervised methods for Hodgkin's lymphoma prognosis using gene expression data and clinical variables.

    Science.gov (United States)

    Parodi, Stefano; Manneschi, Chiara; Verda, Damiano; Ferrari, Enrico; Muselli, Marco

    2018-03-01

    This study evaluates the performance of a set of machine learning techniques in predicting the prognosis of Hodgkin's lymphoma using clinical factors and gene expression data. Analysed samples from 130 Hodgkin's lymphoma patients included a small set of clinical variables and more than 54,000 gene features. Machine learning classifiers included three black-box algorithms ( k-nearest neighbour, Artificial Neural Network, and Support Vector Machine) and two methods based on intelligible rules (Decision Tree and the innovative Logic Learning Machine method). Support Vector Machine clearly outperformed any of the other methods. Among the two rule-based algorithms, Logic Learning Machine performed better and identified a set of simple intelligible rules based on a combination of clinical variables and gene expressions. Decision Tree identified a non-coding gene ( XIST) involved in the early phases of X chromosome inactivation that was overexpressed in females and in non-relapsed patients. XIST expression might be responsible for the better prognosis of female Hodgkin's lymphoma patients.

  12. Ivabradine Improves Heart Rate Variability in Patients with Nonischemic Dilated Cardiomyopathy

    Directory of Open Access Journals (Sweden)

    Ertugrul Kurtoglu

    2014-10-01

    Full Text Available Background: Ivabradine is a novel specific heart rate (HR-lowering agent that improves event-free survival in patients with heart failure (HF. Objectives: We aimed to evaluate the effect of ivabradine on time domain indices of heart rate variability (HRV in patients with HF. Methods: Forty-eight patients with compensated HF of nonischemic origin were included. Ivabradine treatment was initiated according to the latest HF guidelines. For HRV analysis, 24-h Holter recording was obtained from each patient before and after 8 weeks of treatment with ivabradine. Results: The mean RR interval, standard deviation of all normal to normal RR intervals (SDNN, the standard deviation of 5-min mean RR intervals (SDANN, the mean of the standard deviation of all normal-to-normal RR intervals for all 5-min segments (SDNN index, the percentage of successive normal RR intervals exceeding 50 ms (pNN50, and the square root of the mean of the squares of the differences between successive normal to normal RR intervals (RMSSD were low at baseline before treatment with ivabradine. After 8 weeks of treatment with ivabradine, the mean HR (83.6 ± 8.0 and 64.6 ± 5.8, p < 0.0001, mean RR interval (713 ± 74 and 943 ± 101 ms, p < 0.0001, SDNN (56.2 ± 15.7 and 87.9 ± 19.4 ms, p < 0.0001, SDANN (49.5 ± 14.7 and 76.4 ± 19.5 ms, p < 0.0001, SDNN index (24.7 ± 8.8 and 38.3 ± 13.1 ms, p < 0.0001, pNN50 (2.4 ± 1.6 and 3.2 ± 2.2 %, p < 0.0001, and RMSSD (13.5 ± 4.6 and 17.8 ± 5.4 ms, p < 0.0001 substantially improved, which sustained during both when awake and while asleep. Conclusion: Our findings suggest that treatment with ivabradine improves HRV in nonischemic patients with HF.

  13. Intravenous immunoglobulin treatment of the post-polio syndrome: sustained effects on quality of life variables and cytokine expression after one year follow up

    Directory of Open Access Journals (Sweden)

    Gonzalez Henrik

    2012-07-01

    Full Text Available Abstract Background Expression of inflammatory cytokines in cerebrospinal fluid (CSF has led to the hypothesis of intrathecal chronic inflammation to explain the denervation observed in post-polio syndrome (PPS. It has been shown that therapy with intravenous immunoglobulin (IVIG improves physical performance and dampens down the inflammatory process at 6 months in PPS patients. We here examined the effects of IVIG on cytokine expression and clinical outcome one year after IVIG treatment. Methods From a previous study with 135 PPS patients included, 41 patients were further evaluated before un-blinding for one year (21 placebo and 20 treated with IVIG, Xepol® 50 mg/ml, and were assessed for clinical variables by performing the Short Form-36 survey (SF-36 questionnaire assessment, the 6 minute walk distance test (6MWT and registering pain level by Visual Analogue Scale (VAS after IVIG treatment. A separate cohort of 37 PPS patients went through lumbar puncture (LP at baseline and 20 patients, treated with IVIG, repeated the LP one year later. Thirty patients affected with other neurological diseases (OND were used as control group. Inflammatory cytokines TNF, TGFβ, IFNγ, IL-23, IL-13 and IL-10 were measured in blood cells and CSF cells with RT-PCR. Results Scores of the physical components of SF-36 were significantly higher at the one year follow up time-point in the IVIG-treated patients when compared to baseline as well as to the control subjects. Pain VAS score and 6MWT improved significantly in the IVIG-treated patients when compared with baseline Relative expression of TNF and IFN-γ in both PBMCs and CSF from PPS patients were increased compared to OND subjects at baseline (p  Conclusions IVIG has effects on relevant QoL variables and inflammatory cytokines up to one year in patients with PPS. This gives a basis for scheduling IVIG in upcoming trials with this therapy.

  14. Variable Ventilation Improved Respiratory System Mechanics and Ameliorated Pulmonary Damage in a Rat Model of Lung Ischemia-Reperfusion

    Directory of Open Access Journals (Sweden)

    Patricia R. M. Rocco

    2017-05-01

    Full Text Available Lung ischemia-reperfusion injury remains a major complication after lung transplantation. Variable ventilation (VV has been shown to improve respiratory function and reduce pulmonary histological damage compared to protective volume-controlled ventilation (VCV in different models of lung injury induced by endotoxin, surfactant depletion by saline lavage, and hydrochloric acid. However, no study has compared the biological impact of VV vs. VCV in lung ischemia-reperfusion injury, which has a complex pathophysiology different from that of other experimental models. Thirty-six animals were randomly assigned to one of two groups: (1 ischemia-reperfusion (IR, in which the left pulmonary hilum was completely occluded and released after 30 min; and (2 Sham, in which animals underwent the same surgical manipulation but without hilar clamping. Immediately after surgery, the left (IR-injured and right (contralateral lungs from 6 animals per group were removed, and served as non-ventilated group (NV for molecular biology analysis. IR and Sham groups were further randomized to one of two ventilation strategies: VCV (n = 6/group [tidal volume (VT = 6 mL/kg, positive end-expiratory pressure (PEEP = 2 cmH2O, fraction of inspired oxygen (FiO2 = 0.4]; or VV, which was applied on a breath-to-breath basis as a sequence of randomly generated VT values (n = 1200; mean VT = 6 mL/kg, with a 30% coefficient of variation. After 5 min of ventilation and at the end of a 2-h period (Final, respiratory system mechanics and arterial blood gases were measured. At Final, lungs were removed for histological and molecular biology analyses. Respiratory system elastance and alveolar collapse were lower in VCV than VV (mean ± SD, VCV 3.6 ± 1.3 cmH20/ml and 2.0 ± 0.8 cmH20/ml, p = 0.005; median [interquartile range], VCV 20.4% [7.9–33.1] and VV 5.4% [3.1–8.8], p = 0.04, respectively. In left lungs of IR animals, VCV increased the expression of interleukin-6 and intercellular

  15. Variable Ventilation Improved Respiratory System Mechanics and Ameliorated Pulmonary Damage in a Rat Model of Lung Ischemia-Reperfusion.

    Science.gov (United States)

    Soluri-Martins, André; Moraes, Lillian; Santos, Raquel S; Santos, Cintia L; Huhle, Robert; Capelozzi, Vera L; Pelosi, Paolo; Silva, Pedro L; de Abreu, Marcelo Gama; Rocco, Patricia R M

    2017-01-01

    Lung ischemia-reperfusion injury remains a major complication after lung transplantation. Variable ventilation (VV) has been shown to improve respiratory function and reduce pulmonary histological damage compared to protective volume-controlled ventilation (VCV) in different models of lung injury induced by endotoxin, surfactant depletion by saline lavage, and hydrochloric acid. However, no study has compared the biological impact of VV vs. VCV in lung ischemia-reperfusion injury, which has a complex pathophysiology different from that of other experimental models. Thirty-six animals were randomly assigned to one of two groups: (1) ischemia-reperfusion (IR), in which the left pulmonary hilum was completely occluded and released after 30 min; and (2) Sham, in which animals underwent the same surgical manipulation but without hilar clamping. Immediately after surgery, the left (IR-injured) and right (contralateral) lungs from 6 animals per group were removed, and served as non-ventilated group (NV) for molecular biology analysis. IR and Sham groups were further randomized to one of two ventilation strategies: VCV (n = 6/group) [tidal volume (VT) = 6 mL/kg, positive end-expiratory pressure (PEEP) = 2 cmH2O, fraction of inspired oxygen (FiO2) = 0.4]; or VV, which was applied on a breath-to-breath basis as a sequence of randomly generated VT values (n = 1200; mean VT = 6 mL/kg), with a 30% coefficient of variation. After 5 min of ventilation and at the end of a 2-h period (Final), respiratory system mechanics and arterial blood gases were measured. At Final, lungs were removed for histological and molecular biology analyses. Respiratory system elastance and alveolar collapse were lower in VCV than VV (mean ± SD, VCV 3.6 ± 1.3 cmH20/ml and 2.0 ± 0.8 cmH20/ml, p = 0.005; median [interquartile range], VCV 20.4% [7.9-33.1] and VV 5.4% [3.1-8.8], p = 0.04, respectively). In left lungs of IR animals, VCV increased the expression of interleukin-6 and intercellular adhesion

  16. VARIABILITY AND microRNA EXPRESSION LEVEL IN TISSUES OF HEAD AND NECK TUMORS

    Directory of Open Access Journals (Sweden)

    Е. G. Nikitina

    2014-01-01

    Full Text Available Small non-coding RNAs (miRNAs are not only an important regulator of gene expression by participating in almost all basic processes in the cell, but are specific molecules and can be used for many applications in clinical diagnostics. In our study, we assessed the level of miRNA expression in tumor tissue of patients with head and neck tumors of various sites. New data regarding the expression pattern of eight miRNAs in tumor tissue from patients with cancer of the larynx, tongue and papillary thyroid carcinoma, namely: miR-18a, -21, -155, -200a, -200c, -205, -221 and -494 were obtained. The spectrum of miRNA-specific localizations was analyzed, suggesting the existence of differences in the mechanisms of participation of the same miRNA in carcinogenesis of tumors of different epitopes of the head and neck. The panel of miR-200a, -200c, -21 and -205 was shown to be specific for determining the two locations (laryngeal and thyroid cancers and probably can be used to define the site of a secondary tumor and / or metastasis of unknown origin.

  17. Advances in catchment scale bank erosion modelling - quantifying the improved representation of temporal and spatial variability

    Science.gov (United States)

    Janes, Victoria; Holman, Ian; O'Donnell, Greg; Birkinshaw, Stephen; Kilsby, Chris

    2015-04-01

    Channel bank erosion processes are influenced by numerous factors resulting in high spatial and temporal variability of sediment production. The representation of channel bank erosion is overly simplistic within most catchment models, despite its significance to catchment sediment budgets. Within this study, the physically-based distributed SHETRAN model is modified to incorporate bank vegetation and channel sinuosity factors that influence spatial and temporal bank erosion rates. The modified model simulates the temporal variation of bank erosion in response to high magnitude events with the potential to remove bank vegetation and de-stabilise banks, thereby increasing erodibility. As vegetation re-establishes, simulated bank erodibility decreases. During the recovery period, banks have increased vulnerability to further high magnitude events that will result in increased bank erosion. This enables the model to represent the impact of flood clustering on sediment generation. The modified model also represents the spatial variation of bank erosion as a result of varying channel planform. Channel geometry has also been linked to bank erosion rates as a result of flow circulation within channels. Channel sinuosity shows a non-linear relationship with bank erosion, with bank erosion increasing up to a threshold value of sinuosity and decreasing as sinuosity increases above this point. The original and modified models have been applied to the Eden catchment in north east England. Bank erosion data derived from a GIS overlay methodology covering 150 years has been used to validate the models, indicating annual sediment generation from bank erosion processes within the catchment is 410-4500 t yr-1, equivalent to 2-11% of the catchment sediment budget. Comparison of the original and modified models highlights the improved ability of the modified model to simulate annual variation of bank eroded sediment production; annual sediment production from the original model ranged

  18. HER4 expression status correlates with improved outcome in both neoadjuvant and adjuvant Trastuzumab treated invasive breast carcinoma

    Science.gov (United States)

    Portier, Bryce P; Minca, Eugen C; Wang, Zhen; Lanigan, Christopher; Gruver, Aaron M; Downs-Kelly, Erinn; Budd, G Thomas; Tubbs, Raymond R

    2013-01-01

    Prognostic and predictive markers utilized in invasive breast carcinoma are limited and include ER, PR, Ki67, and ERBB2 (HER2). In the case of HER2, over-expression or amplification serves as eligibility for anti-HER2 based therapy, including trastuzumab (Herceptin®, Genentech). While clinical trials have shown trastuzumab improves overall survival and time to progression, an individual's response to anti-HER2 based therapy is highly variable. This suggests that, in a “uniform” HER2 positive population, additional markers could help in predicting patient outcome to therapy. Here we utilized a recently validated high-specificity HER4 antibody (E200) and generated a standard clinical HER4 scoring algorithm (HER4 H-Score) utilizing two breast carcinoma cohorts: 1) patients receiving neoadjuvant trastuzumab (n=47) and 2) patients receiving trastuzumab for metastatic disease (n=33). Our HER4 H-Score showed significant correlation with high sensitivity RT-qPCR performed on matched patients (p=<0.0001). In addition, patients with HER2/HER4 co-over-expression status showed a significant delay in development of metastasis after neo-adjuvant trastuzumab therapy (p= 0.04) and showed a significant improvement in progression free survival after adjuvant trastuzumab therapy (p=0.03). These findings suggest HER4 IHC, used in conjunction with a standard HER2 testing algorithm, could aid in predicting clinical outcome and help identify patients likely to show improved response to trastuzumab therapy. PMID:24091566

  19. Expressed prostatic secretion biomarkers improve stratification of NCCN active surveillance candidates: performance of secretion capacity and TMPRSS2:ERG models.

    Science.gov (United States)

    Whelan, Christopher; Kawachi, Mark; Smith, David D; Linehan, Jennifer; Babilonia, Gail; Mejia, Rosa; Wilson, Timothy; Smith, Steven S

    2014-01-01

    Active surveillance is a viable patient option for prostate cancer provided that a clinical determination of low risk and presumably organ confined disease can be made. To standardize risk stratification schemes the NCCN (National Comprehensive Cancer Network®) provides guidelines for the active surveillance option. We determined the effectiveness of expressed prostatic secretion biomarkers for detecting occult risk factors in NCCN active surveillance candidates. Expressed prostatic secretion specimens were obtained before robot-assisted radical prostatectomy. Secretion capacity biomarkers, including total RNA and expressed prostatic secretion specimen volume, were measured by standard techniques. RNA expression biomarkers, including TXNRD1 mRNA, prostate specific antigen mRNA, TMPRSS2:ERG fusion mRNA and PCA3 mRNA, were measured by quantitative reverse-transcription polymerase chain reaction. Of the 528 patients from whom expressed prostatic secretions were collected 216 were eligible for active surveillance under NCCN guidelines. Variable selection on logistic regression identified 2 models, including one featuring types III and VI TMPRSS2:ERG variants, and one featuring 2 secretion capacity biomarkers. Of the 2 high performing models the secretion capacity model was most effective for detecting cases in this group that were up-staged or up-staged plus upgraded. It decreased the risk of up-staging in patients with a negative test almost eightfold and decreased the risk of up-staging plus upgrading about fivefold while doubling the prevalence of up-staging in the positive test group. Noninvasive expressed prostatic secretion testing may improve patient acceptance of active surveillance by dramatically reducing the presence of occult risk factors among those eligible for active surveillance under NCCN guidelines. Copyright © 2014 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

  20. Phage exposure causes dynamic shifts in the expression states of specific phase-variable genes of Campylobacter jejuni

    DEFF Research Database (Denmark)

    Aidley, Jack; Holst Sørensen, Martine C.; Bayliss, Christopher D.

    2017-01-01

    Phase variation (PV) creates phenotypic heterogeneity at high frequencies and in a reversible manner. This phenomenon allows bacteria to adapt to a variety of different environments and selective pressures. In Campylobacter jejuni this reversible adaptive process is mediated by mutations in homop......Phase variation (PV) creates phenotypic heterogeneity at high frequencies and in a reversible manner. This phenomenon allows bacteria to adapt to a variety of different environments and selective pressures. In Campylobacter jejuni this reversible adaptive process is mediated by mutations...... in homopolymeric G/C tracts. Many C. jejuni-specific phages are dependent on phase-variable surface structures for successful infection. We previously identified the capsular polysaccharide (CPS) moiety, MeOPN-GalfNAc, as a receptor for phage F336 and showed that phase-variable expression of the transferase...

  1. Highly variable clinical phenotype of carbamylphosphate synthetase 1 deficiency in one family: an effect of allelic variation in gene expression?

    DEFF Research Database (Denmark)

    Klaus, V; Vermeulen, T; Minassian, B

    2009-01-01

    report two patients from one family with highly divergent clinical course, one presenting neonatally with a fatal form and the other at age 45 with benign diet-responsive disease. The patients are compound heterozygous for two mutations of the CPS1 gene, c.3558 + 1G > C and c.4101 + 2T > C...... of mRNA from the allele with the c.3558 + 1G > C mutation, whereas in the adult-onset case the two types of clones are equal, indicating skewed expression towards the c.4101 + 2T > C allele in the neonatal case. Although we are yet to understand the mechanism of this differential expression, our work...... suggests that allelic imbalance may explain clinical variability in CPS1 deficiency in some families....

  2. Variable phenotype and severity of sialidosis expressed in two siblings presenting with ataxia and macular cherry-red spots.

    Science.gov (United States)

    Vieira de Rezende Pinto, Wladimir Bocca; Sgobbi de Souza, Paulo Victor; Pedroso, José Luiz; Barsottini, Orlando G P

    2013-09-01

    Sialidosis is a rare lysosomal storage disease with a wide clinical spectrum ranging from nearly asymptomatic to severe presentations. We present two Brazilian siblings with sialidosis, the first patient with sialidosis type I, and the second with sialidosis type II. Our report reinforces the relevance of ophthalmologic evaluation in patients with early and late-onset ataxias, if an association with myoclonus or dysmorphic features is present or not. Also, we demonstrate that sialidosis might represent a single genetic entity with variable clinical expression through these two siblings. Copyright © 2013 Elsevier Ltd. All rights reserved.

  3. Improved Approximate String Matching and Regular Expression Matching on Ziv-Lempel Compressed Texts

    DEFF Research Database (Denmark)

    Bille, Philip; Fagerberg, Rolf; Gørtz, Inge Li

    2009-01-01

    We study the approximate string matching and regular expression matching problem for the case when the text to be searched is compressed with the Ziv-Lempel adaptive dictionary compression schemes. We present a time-space trade-off that leads to algorithms improving the previously known...... complexities for both problems. In particular, we significantly improve the space bounds, which in practical applications are likely to be a bottleneck....

  4. Improved Approximate String Matching and Regular Expression Matching on Ziv-Lempel Compressed Texts

    DEFF Research Database (Denmark)

    Bille, Philip; Fagerberg, Rolf; Gørtz, Inge Li

    2007-01-01

    We study the approximate string matching and regular expression matching problem for the case when the text to be searched is compressed with the Ziv-Lempel adaptive dictionary compression schemes. We present a time-space trade-off that leads to algorithms improving the previously known...... complexities for both problems. In particular, we significantly improve the space bounds. In practical applications the space is likely to be a bottleneck and therefore this is of crucial importance....

  5. Functional Characterization of AAV-Expressed Recombinant Anti-VEGF Single-Chain Variable Fragments In Vitro.

    Science.gov (United States)

    Wimmer, Tobias; Lorenz, Birgit; Stieger, Knut

    2015-06-01

    Most retinal neovascular disorders are caused by upregulation of vascular endothelial growth factor (VEGF) expression. These disorders are treated with repeated injections of anti-VEGF molecules, which may have severe side effects. The expression of anti-VEGF molecules by the retina itself in a controlled manner following adeno-associated viral (AAV) gene transfer could be a replacement of this therapy. The open reading frames (orf) of the light and the heavy chain of ranibizumab were cloned into an expression plasmid separated by an internal ribosomal entry site (IRES). The construct was mutated to generate ranibizumab single-chain variable fragments (scFv). Expression was verified by western blotting and the concentrations were measured with a custom-made ranibizumab ELISA. Biological activity, VEGF-binding properties, and the doxycycline-dependent induction of anti-VEGF expression were tested. An AAV2/5 vector was generated containing the optimal variant Ra02. Ra01-Ra05 molecules were detected in the cell culture medium. While the VEGF-binding affinity was significantly lower for Ra01 and Ra02 compared to Lucentis(®), the inhibition of cell migration was comparable and the maximum inhibition of Ra01 and Ra02 was reached at lower doses. The expression of Ra01 and Ra02 was shown to be regulable with the TetOn-system(®) as plasmid (Ra01, Ra02) and AAV vector construct (Ra02). Ra01 and Ra02 can be produced in eukaryotic cells after AAV-mediated gene transfer in a regulable manner in vitro and display comparable biological activity as Lucentis. These results are the basis for in vivo studies in human VEGF-overexpressing mice, a model for human neovascular disorders.

  6. Losartan improves heart rate variability and heart rate turbulence in heart failure due to ischemic cardiomyopathy.

    Science.gov (United States)

    Ozdemir, Murat; Arslan, Uğur; Türkoğlu, Sedat; Balcioğlu, Serhat; Cengel, Atiye

    2007-12-01

    Heart rate variability (HRV) and heart rate turbulence are known to be disturbed and associated with excess mortality in heart failure. The aim of this study was to investigate whether losartan, when added on top of beta-blocker and angiotensin-converting enzyme inhibitor (ACEI) therapy, could improve these indices in patients with systolic heart failure. Seventy-seven patients (mean age 60.4 +/- 8.0, 80.5% male) with ischemic cardiomyopathy (mean ejection fraction 34.5 +/- 4.4%) and New York Heart Association Class II-III heart failure symptoms, already receiving a beta-blocker and an ACEI, were randomly assigned to either open-label losartan (losartan group) or no additional drug (control group) in a 2:1 ratio and the patients were followed for 12 weeks. The HRV and heart rate turbulence indices were calculated from 24-hour Holter recordings both at the beginning and at the end of follow-up. The baseline clinical characteristics, HRV, and heart rate turbulence indices were similar in the 2 groups. At 12 weeks of follow-up, all HRV parameters except pNN50 increased (SDNN: 113.2 +/- 34.2 versus 127.8 +/- 24.1, P = .001; SDANN: 101.5 +/- 31.7 versus 115.2 +/- 22.0, P = .001; triangular index: 29.9 +/- 11.1 versus 34.2 +/- 7.9, P = .008; RMSSD: 29.1 +/- 20.2 versus 34.3 +/- 23.0, P = .009; NN50: 5015.3 +/- 5554.9 versus 6446.7 +/- 6101.1, P = .024; NN50: 5.65 +/- 6.41 versus 7.24 +/- 6.99, P = .089; SDNNi: 45.1 +/- 13.3 versus 50.3 +/- 14.5, P = .004), turbulence onset decreased (-0. 61 +/- 1.70 versus -1.24 +/- 1.31, P = .003) and turbulence slope increased (4.107 +/- 3.881 versus 5.940 +/- 4.281, P = .004) significantly in the losartan group as compared with controls. A 12-week-long losartan therapy significantly improved HRV and heart rate turbulence in patients with Class II-III heart failure and ischemic cardiomyopathy already on beta-blockers and ACEI.

  7. Cohort-specific imputation of gene expression improves prediction of warfarin dose for African Americans

    Directory of Open Access Journals (Sweden)

    Assaf Gottlieb

    2017-11-01

    Full Text Available Abstract Background Genome-wide association studies are useful for discovering genotype–phenotype associations but are limited because they require large cohorts to identify a signal, which can be population-specific. Mapping genetic variation to genes improves power and allows the effects of both protein-coding variation as well as variation in expression to be combined into “gene level” effects. Methods Previous work has shown that warfarin dose can be predicted using information from genetic variation that affects protein-coding regions. Here, we introduce a method that improves dose prediction by integrating tissue-specific gene expression. In particular, we use drug pathways and expression quantitative trait loci knowledge to impute gene expression—on the assumption that differential expression of key pathway genes may impact dose requirement. We focus on 116 genes from the pharmacokinetic and pharmacodynamic pathways of warfarin within training and validation sets comprising both European and African-descent individuals. Results We build gene-tissue signatures associated with warfarin dose in a cohort-specific manner and identify a signature of 11 gene-tissue pairs that significantly augments the International Warfarin Pharmacogenetics Consortium dosage-prediction algorithm in both populations. Conclusions Our results demonstrate that imputed expression can improve dose prediction and bridge population-specific compositions. MATLAB code is available at https://github.com/assafgo/warfarin-cohort

  8. Plasma boundary variability at Mars as observed by Mars Global Surveyor and Mars Express

    Directory of Open Access Journals (Sweden)

    N. J. T. Edberg

    2009-09-01

    Full Text Available We have used Mars Express (MEX and Mars Global Surveyor (MGS simultaneous and non-simultaneous measurements to study the Martian plasma environment. In particular, we have derived quantitative expressions for the altitude of the terminator bow shock (BS and magnetic pileup boundary (MPB as functions of solar wind dynamic pressure, crustal magnetic fields and solar EUV flux. We have also studied the influence of the interplanetary magnetic field (IMF direction. Through simultaneous two-spacecraft case studies we have shown that the dynamic pressure has a strong influence on the location and shape of these boundaries, which is also confirmed through a large statistical study. A higher dynamic pressure pushes the boundaries downward. The IMF direction has a weaker but still significant influence on both boundaries and causes them to move outward in the hemisphere of locally upward electric field. However, the MPB in the Southern Hemisphere is found to actually move inward when the electric field is directed locally upward. The crustal magnetic fields in the Southern Hemisphere have a strong influence on the MPB and cause it to move to higher altitudes over strong crustal magnetic fields. The influence of the crustal magnetic fields on the BS is more ambiguous since there are few crossings over the strongest crustal fields, but there appears to be at least a small trend of a higher BS for stronger crustal fields. An increased solar EUV flux has been found to cause the BS to move outward and the MPB to move inward.

  9. Employing Noncognitive Variables to Improve Admissions, and Increase Student Diversity and Retention

    Science.gov (United States)

    Kalsbeek, David; Sandlin, Michele; Sedlacek, William

    2013-01-01

    Today, a growing number of North American postsecondary institutions are incorporating the use of noncognitive variables into their requirements for a holistic admissions process. Why is there more and more interest in utilizing these nonacademic variables for students who are applying to these institutions? It is all about student success and…

  10. Phase variable expression of capsular polysaccharide modifications allows Campylobacter jejuni to avoid bacteriophage infection in chickens

    Directory of Open Access Journals (Sweden)

    Martine Camilla Holst Sørensen

    2012-02-01

    Full Text Available Bacteriophages are estimated to be the most abundant entities on earth and can be found in every niche where their bacterial hosts reside. The initial interaction between phages and Campylobacter jejuni, a common coloniser of poultry intestines and a major source of foodborne bacterial gastroenteritis in humans, is not well understood. Recently, we isolated and characterised a phage F336 resistant variant of C. jejuni NCTC11168 called 11168R. Comparisons of 11168R with the wildtype lead to the identification of a novel phage receptor, the phase variable O-methyl phosphoramidate (MeOPN moiety of the C. jejuni capsular polysaccharide (CPS. In this study we demonstrate that the 11168R strain has gained cross-resistance to four other phages in our collection (F198, F287, F303 and F326. The reduced plaquing efficiencies suggested that MeOPN is recognized as a receptor by several phages infecting C. jejuni. To further explore the role of CPS modifications in C. jejuni phage recognition and infectivity, we tested the ability of F198, F287, F303, F326 and F336 to infect different CPS variants of NCTC11168, including defined CPS mutants. These strains were characterised by high-resolution magic angle spinning NMR spectroscopy. We found that in addition to MeOPN, the phase variable 3-O-Me and 6-O-Me groups of the NCTC11168 CPS structure may influence the plaquing efficiencies of the phages. Furthermore, co-infection of chickens with both C. jejuni NCTC11168 and phage F336 resulted in selection of resistant C. jejuni bacteria, which either lack MeOPN or gain 6-O-Me groups on their surface, demonstrating that resistance can be acquired in vivo. In summary, we have shown that phase variable CPS structures modulate phage infectivity in C. jejuni and suggest that the constant phage predation in the avian gut selects for changes in these structures leading to a continuing phage-host co-evolution.

  11. Transient gene expression optimization and expression vector comparison to improve HIV-1 VLP production in HEK293 cell lines.

    Science.gov (United States)

    Fuenmayor, Javier; Cervera, Laura; Gutiérrez-Granados, Sonia; Gòdia, Francesc

    2017-11-04

    Transient gene expression (TGE) has been used at small and medium scale for the production of biologicals in sufficient quantities to perform pre-clinical and characterization studies. Polyethyleneimine (PEI)-mediated transfection offers a low toxicity and non-expensive method for cell transfection. DNA and PEI concentration for transient gene expression has been extensively optimized in order to increase product titers. However, the possibility to extrapolate the optimal concentrations found for a specific bioprocess when expression vectors or cell lines need to be changed has not been investigated.In this work, the combination of three different HEK293 cell lines with three different vectors was studied for the production of HIV-1 virus-like particles (VLPs). The concentration of DNA and PEI was optimized for the nine combinations. The obtained results were very similar in all cases (DNA = 2.34 ± 0.18 μg/mL and PEI = 5.81 ± 0.18 μg/mL), revealing that transfection efficiency is not dependent on the cell line or vector type, but on DNA and PEI quantities. Furthermore, two of the cell lines tested stably expressed a protein able to recognize specific origins of replication: HEK293T/SV40 and HEK293E/oriP. Origins of replication were included in the vector sequences in order to test their capacity to increase production titers. HEK293T/SV40 resulted in a decrease of cell density and productivity of 2.3-fold compared to a control plasmid. On the other hand, HEK293E/OriP platform enabled a threefold improvement in HIV-1 VLP production keeping the same cell densities and viabilities compared to a control plasmid.

  12. Variability in expression of antigens responsible for serotype specificity in Candida albicans.

    Science.gov (United States)

    Barturen, B; Bikandi, J; San Millán, R; Moragues, M D; Regulez, P; Quindós, G; Pontón, J

    1995-07-01

    The monoclonal antibody (mAb) B9E, which reacts with a cell wall surface determinant of Candida albicans serotype A, and a polyclonal monospecific antiserum against the antigen 6 (IF6) were used to investigate the expression of the antigens responsible for the serotype specificity in C. albicans under different growth conditions. By indirect immunofluorescence, both antibodies reacted with the cell wall surface of serotype A yeast cells and germ tubes grown in vitro but no reactivity was observed with serotype B yeast cells. In some cases, only a weak reactivity restricted to a zone close to the parent yeast cell was observed in serotype B germ tubes stained with mAb B9E. Both antibodies reacted strongly with yeast cells and germ tubes present in kidney abscesses from rabbits infected with both serotypes, but only serotype A yeast cells and germ tubes present in smears from patients with vulvovaginal candidiasis reacted with B9E and IF6 antibodies. The expression of antigens reactive with both antibodies was modulated by the pH of the environment in which the fungus was grown. Both antibodies showed a similar pattern of reactivity when studied with a spectrofluorometer. Serotype A yeast cells showed maximum reactivity when cells were grown on Sabouraud dextrose broth supplemented with yeast extract at pH 4.6. The lowest reactivity was observed in cells grown at pH 2.0. Conversely, the reactivity of serotype B yeast cells increased at alkaline pH values, the highest being in cells grown at pH values of 7.2 and 9.5.(ABSTRACT TRUNCATED AT 250 WORDS)

  13. Relating Linear and Volumetric Variables Through Body Scanning to Improve Human Interfaces in Space

    Science.gov (United States)

    Margerum, Sarah E.; Ferrer, Mike A.; Young, Karen S.; Rajulu, Sudhakar

    2010-01-01

    Designing space suits and vehicles for the diverse human population present unique challenges for the methods of traditional anthropometry. Space suits are bulky and allow the operator to shift position within the suit and inhibit the ability to identify body landmarks. Limited suit sizing options also cause variability in fit and performance between similarly sized individuals. Space vehicles are restrictive in volume in both the fit and the ability to collect data. NASA's Anthropometric and Biomechanics Facility (ABF) has utilized 3D scanning to shift from traditional linear anthropometry to explore and examine volumetric capabilities to provide anthropometric solutions for design. Overall, the key goals are to improve the human-system performance and develop new processes to aid in the design and evaluation of space systems. Four case studies are presented that illustrate the shift from purely linear analyses to an augmented volumetric toolset to predict and analyze the human within the space suit and vehicle. The first case study involves the calculation of maximal head volume to estimate total free volume in the helmet for proper air exchange. Traditional linear measurements resulted in an inaccurate representation of the head shape, yet limited data exists for the determination of a large head volume. Steps were first taken to identify and classify a maximum head volume and the resulting comparisons to the estimate are presented in this paper. This study illustrates the gap between linear components of anthropometry and the need for overall volume metrics in order to provide solutions. A second case study examines the overlay of the space suit scans and components onto scanned individuals to quantify fit and clearance to aid in sizing the suit to the individual. Restrictions in space suit size availability present unique challenges to optimally fit the individual within a limited sizing range while maintaining performance. Quantification of the clearance and

  14. Expression of RoTat 1.2 cross-reactive variable antigen type in Trypanosoma evansi and T. equiperdum.

    Science.gov (United States)

    Claes, Filip; Verloo, D; De Waal, D T; Urakawa, T; Majiwa, P; Goddeeris, B M; Buscher, P

    2002-10-01

    The variable antigen type (VAT) RoTat 1.2 has been cloned from a T. evansi strain, isolated in 1982 from a water buffalo in Indonesia. All T. evansi isolates hitherto tested express this VAT. In a study on the differential diagnosis of T. equiperdum and T. evansi in horses, we investigated serological evidence for the expression of RoTat 1.2 in 11 T. evansi and six T. equiperdum populations originating from Asia, Europe, Africa, and the Americas. Preinfection sera and sera of days 7, 14, 25, and 35 post-infection (p.i.) were analyzed for the presence of antibodies reactive with RoTat 1.2 in immune trypanolysis, ELISA/T. evansi and CATT/T. evansi. Within the duration of the experiment, all rabbits infected with T. evansi became positive in the three serological tests. Five out of six rabbits infected with T. equiperdum also became positive in the three tests. Only one T. equiperdum strain (the OVI strain from South Africa) did not induce the production of antibodies reactive with RoTat 1.2 and thus might not contain or express a VSG that shares epitopes similar to those on the RoTat 1.2 VSG. The data lead to the conclusion that T. equiperdum can express VSGs containing epitopes serologically similar to those in the T. evansi RoTat 1.2 VAT. This explains, in part, why the antibody detection tests based on Ro Tat 1.2 VSG cannot reliably distinguish between the infections caused by T. evansi and those caused by T. equiperdum. There are no data that contradict the possibility that the putative T. equiperdum strains, which express VSGs with epitopes similar to those on RoTat 1.2, are actually T. evansi.

  15. A Monte Carlo approach for improved estimation of groundwater level spatial variability in poorly gauged basins

    Science.gov (United States)

    Varouchakis, Emmanouil; Hristopulos, Dionissios

    2013-04-01

    Groundwater level is an important source of information in hydrological modelling. In many aquifers the boreholes monitored are scarce and/or sparse in space. In both cases, geostatistical methods can help to visualize the free surface of an aquifer, whereas the use of auxiliary information improves the accuracy of level estimates and maximizes the information gain for the quantification of groundwater level spatial variability. In addition, they allow the exploitation of datasets that cannot otherwise be efficiently used in catchment models. In this presentation, we demonstrate an approach for incorporating auxiliary information in interpolation approaches using a specific case study. In particular, the study area is located on the island of Crete (Greece). The available data consist of 70 hydraulic head measurements for the wet period of the hydrological year 2002-2003, the average pumping rates at the 70 wells, and 10 piezometer readings measured in the preceding hydrological year. We present a groundwater level trend model based on the generalized Thiem's equation for multiple wells. We use the drift term to incorporate secondary information in Residual Kriging (RK) (Varouchakis and Hristopulos 2013). The residuals are then interpolated using Ordinary Kriging and then are added to the drift model. Thiem's equation describes the relationship between the steady-state radial inflow into a pumping well and the drawdown. The generalized form of the equation includes the influence of a number of pumping wells. It incorporates the estimated hydraulic head, the initial hydraulic head before abstraction, the number of wells, the pumping rate, the distance of the estimation point from each well, and the well's radius of influence. We assume that the initial hydraulic head follows a linear trend, which we model based on the preceding hydrological year measurements. The hydraulic conductivity in the study basin varies between 0.0014 and 0.00014 m/s according to geological

  16. Interindividual variability in the expression of surfactant protein A and B in the human lung during development

    Directory of Open Access Journals (Sweden)

    F. Cau

    2016-09-01

    Full Text Available The surfactant complex, thanks to its multiple actions including decrease of surface- tension and antimicrobial activity, plays a fundamental role in newborn survival, lowering the risk of respiratory distress syndrome. The aim of this work was to determine if the synthesis of two surfactant proteins (SP, SPA and pro-SPB, shows some inter-individual variability during lung development in the intrauterine life. Immunoreactivity for SPA and pro-SPB was investigated in the lungs of  40 subjects, including 15 fetuses, ranging from 14 to 22 weeks of gestation, and 25 neonates, from 24 to 41 weeks. Lung samples were formalin fixed, paraffin-embedded and routinely processed. SPA and pro-SPB were detected utilizing commercial antibodies.  A semi-quantitative grading system (1 to 4 was applied, based on the number of reactive cells and the intensity of immunostaining. Surfactant protein immunostaining was found in  three compartments: bronchi, bronchioles and alveoli, starting from 14 weeks of gestation in the bronchial epithelium and from the 21st week in the alveolar spaces. Differences were found regarding SPA and pro-SPB expression in the vast majority of subjects: in some lungs, SPA was more expressed whereas in others pro-SPB showed an higher degree of immunoreactivity. The expression of both surfactant proteins was not strictly correlated with gestational age. Whereas the highest levels of reactivity were detected in at term neonates, on the other hand one case with grade 3 was detected at 22 weeks and one negative case for both proteins was observed at 31 weeks. Our data clearly show a marked inter-individual variability regarding the production of SPA and pro-SPB and suggest the existence of other epigenetic factors, acting during gestation, that might influence surfactant production and, consequently, the survival potential of  neonates at birth. 

  17. Brief Communication: Upper-air relaxation in RACMO2 significantly improves modelled interannual surface mass balance variability in Antarctica

    NARCIS (Netherlands)

    van de Berg, W.J.|info:eu-repo/dai/nl/304831611; Medley, Brooke

    2016-01-01

    The Regional Atmospheric Climate Model (RACMO2) has been a powerful tool for improving surface mass balance (SMB) estimates from GCMs or reanalyses. However, new yearly SMB observations for West Antarctica show that the modelled interannual variability in SMB is poorly simulated by RACMO2, in

  18. Methods for Using Small Non-Coding RNAs to Improve Recombinant Protein Expression in Mammalian Cells

    Directory of Open Access Journals (Sweden)

    Sarah Inwood

    2018-01-01

    Full Text Available The ability to produce recombinant proteins by utilizing different “cell factories” revolutionized the biotherapeutic and pharmaceutical industry. Chinese hamster ovary (CHO cells are the dominant industrial producer, especially for antibodies. Human embryonic kidney cells (HEK, while not being as widely used as CHO cells, are used where CHO cells are unable to meet the needs for expression, such as growth factors. Therefore, improving recombinant protein expression from mammalian cells is a priority, and continuing effort is being devoted to this topic. Non-coding RNAs are RNA segments that are not translated into a protein and often have a regulatory role. Since their discovery, major progress has been made towards understanding their functions. Non-coding RNA has been investigated extensively in relation to disease, especially cancer, and recently they have also been used as a method for engineering cells to improve their protein expression capability. In this review, we provide information about methods used to identify non-coding RNAs with the potential of improving recombinant protein expression in mammalian cell lines.

  19. Improving cellulase production in submerged fermentation by the expression of a Vitreoscilla hemoglobin in Trichoderma reesei.

    Science.gov (United States)

    Lin, Jie; Zhang, Xiamei; Song, Bingran; Xue, Wei; Su, Xiaoyun; Chen, Xiuzhen; Dong, Zhiyang

    2017-11-15

    Trichoderma reesei is well known as an industrial workhorse fungus in cellulase production. The low dissolved oxygen supply in the highly viscous medium of T. reesei remains a major bottleneck that hampers growth and cellulase production in submerged fermentation. Vitreoscilla hemoglobin (VHb) has been demonstrated to improve metabolism and protein production in different heterologous hosts under hypoxic conditions, but the use of VHb in T. reesei remains uninvestigated. This study examines the effect of VHb in improving T. reesei performance in submerged fermentation. The VHb gene (vgb)-expressing cassette was successfully transformed into the TU-6 strain, integrated into the genome of T. reesei, and functionally expressed with biological activity, which was confirmed by carbon monoxide difference analysis. Compared to the parent strain, the expression of VHb increased the glucose consumption rate of the transformant. Moreover, in cellulase-inducing medium total protein secretion of the VHb expressing strain was 2.2-fold of the parental strain and the filter paper cellulase activity was increased by 58% under oxygen-limiting conditions. In summary, our results demonstrate that VHb has beneficial effects on improving total protein secretion and cellulase activity of T. reesei in submerged fermentation.

  20. [Expression of Vitreoscilla hemoglobin improves recombinant lipase production in Pichia pastoris].

    Science.gov (United States)

    Wang, Xiaofeng; Sun, Yongchuan; Shen, Xuguang; Ke, Feng; Xu, Li; Liu, Yun; Yan, Yunjun

    2011-12-01

    Yarrowia lipolytica lipase Lip2 (YlLip2) is an important industrial enzyme with many potential applications. To alleviate the dissolved oxygen (DO) limitation and improve YlLip2 production during high-cell density fermentation, the YlLip2 gene lip2 and Vitreoscilla hemoglobin (VHb) gene vgb were co-expressed in Pichiapastoris under the control of AOX1 and PsADH2 promoter, respectively. The PsADH2 promoter from Pichia stipitis could be activated under oxygen limitation. The SDS-PAGE and CO-difference spectrum analysis indicated that VHb and YlLip2 had successfully co-expressed in recombinant strains. Compared with the control cells (VHb-, GS115/9Klip2), the expression levels of YlLip2 in VHb-expressing cells (VHb+, GS115/9Klip2-pZPVT) under oxygen limitation were improved 25% in shake-flask culture and 83% in a 10 L fermentor. Moreover, the VHb+ cells displayed higher biomass than VHb- cells at lower DO levels in a 10 L fermentor. In this study, we also achieved a VHb-expressing clone harboring multicopy lip2 gene (GS115/9Klip2-pZPVTlip2 49#), which showed the maximum lipolytic activity of 33 900 U/mL in a 10 L fermentor under lower DO conditions. Therefore, it can be seen that expression of VHb with PsADH2 promoter in P. pastoris combined with increasing copies of lip2 gene is an effective strategy to improve YlLip2 production.

  1. Breathing exercise combined with cognitive behavioural intervention improves sleep quality and heart rate variability in major depression.

    Science.gov (United States)

    Chien, Hui-Ching; Chung, Yu-Chu; Yeh, Mei-Ling; Lee, Jia-Fu

    2015-11-01

    The aim of this study was to investigate the effects of a cognitive behavioural intervention combined with a breathing relaxation exercise on sleep quality and heart rate variability in patients with major depression. Depression is a long-lasting illness with significant effects not only in individuals themselves, but on their family, work and social relationships as well. Cognitive behavioural therapy is considered to be an effective treatment for major depression. Breathing relaxation may improve heart rate variability, but few studies have comprehensively examined the effect of a cognitive behavioural intervention combined with relaxing breathing on patients with major depression. An experimental research design with a repeated measure was used. Eighty-nine participants completed this study and entered data analysed. The experimental group (n = 43) received the cognitive behavioural intervention combined with a breathing relaxation exercise for four weeks, whereas the control group (n = 46) did not. Sleep quality and heart rate variability were measured at baseline, posttest1, posttest2 and follow-up. Data were examined by chi-square tests, t-tests and generalised estimating equations. After adjusting for age, socioeconomic status, severity of disease and psychiatric history, the quality of sleep of the experimental group improved, with the results at posttest achieving significance. Heart rate variability parameters were also significantly improved. This study supported the hypothesis that the cognitive behavioural intervention combined with a breathing relaxation exercise could improve sleep quality and heart rate variability in patients with major depression, and the effectiveness was lasting. The cognitive behavioural intervention combined with a breathing relaxation exercise that included muscle relaxation, deep breathing and sleep hygiene could be provided with major depression during hospitalisation. Through group practice and experience sharing

  2. Variable expressivity in Patau syndrome is not all related to trisomy 13 mosaicism.

    Science.gov (United States)

    Hsu, Hui-Fang; Hou, Jia-Woei

    2007-08-01

    Patau syndrome (trisomy 13) is very rare in live-born babies. Individuals with this chromosomal syndrome have a short lifespan and are rarely seen beyond infancy. This study is aimed at the clinical spectrum, natural history, and survival of patients with trisomy 13. We reviewed the detailed data of 13 Patau syndrome live-born babies. Among them two individuals were delivered from continuation of pregnancy even after prenatal diagnosis. The remaining 11 patients were born to younger mothers who did not undergo amniocentesis because no major anomalies except for cleft lip/palate were found on prenatal sonograms. The common features of Patau syndrome including the clinical triad (microphthalmia, cleft lip/palate, and polydactyly) and non-cyanotic heart defects were always found in our series. However, certain serious central defects (holoprosencephaly, omphalocele, and single umbilical artery), which are easily recognized from prenatal sonogram, occurred less frequently than those stated in the literature. The median survival time was 95 days and was longer than that previously reported. There were two infants with trisomic mosaicism with different outcomes in both clinical spectrum and survival. Otherwise, we also found the increased recurrence risks of aneuploidy in two individuals, and the longest survivor (84 months) of non-mosaic trisomy 13 in Taiwan. We thus suggest that long-term survival in our series is strongly correlated with different expressivity after prenatal selection, in addition to cytogenetic mosaicism. Less associated anomalies such as polyhydramnios, oligohydramnios, intrauterine growth retardation, single umbilical artery, eye defects, holoprosencephaly, omphalocele, and polycystic kidney may contribute to their clinical courses. (c) 2007 Wiley-Liss, Inc.

  3. Optimized invertase expression and secretion cassette for improving Yarrowia lipolytica growth on sucrose for industrial applications.

    Science.gov (United States)

    Lazar, Zbigniew; Rossignol, Tristan; Verbeke, Jonathan; Crutz-Le Coq, Anne-Marie; Nicaud, Jean-Marc; Robak, Małgorzata

    2013-11-01

    Yarrowia lipolytica requires the expression of a heterologous invertase to grow on a sucrose-based substrate. This work reports the construction of an optimized invertase expression cassette composed of Saccharomyces cerevisiae Suc2p secretion signal sequence followed by the SUC2 sequence and under the control of the strong Y. lipolytica pTEF promoter. This new construction allows a fast and optimal cleavage of sucrose into glucose and fructose and allows cells to reach the maximum growth rate. Contrary to pre-existing constructions, the expression of SUC2 is not sensitive to medium composition in this context. The strain JMY2593, expressing this new cassette with an optimized secretion signal sequence and a strong promoter, produces 4,519 U/l of extracellular invertase in bioreactor experiments compared to 597 U/l in a strain expressing the former invertase construction. The expression of this cassette strongly improved production of invertase and is suitable for simultaneously high production level of citric acid from sucrose-based media.

  4. Improved heterologous erythromycin A production through expression plasmid re-design.

    Science.gov (United States)

    Jiang, Ming; Fang, Lei; Pfeifer, Blaine A

    2013-01-01

    The production of complex compounds from technically convenient microorganisms is an emerging route to the chemical diversity found in the surrounding environment. In this study, the antibiotic compound erythromycin A is produced from Escherichia coli as an alternative to native production through the soil bacterium Saccharopolyspora erythraea. By doing so, there is an opportunity to apply and refine engineering strategies for the manipulation of the erythromycin biosynthetic pathway and for the overproduction of this and other complex natural compounds. Previously, E. coli-derived production was enabled by the introduction of the entire erythromycin pathway (20 genes total) using separately selectable expression plasmids which demonstrated negative effects on final biosynthesis through metabolic burden and plasmid instability. In this study, improvements to final production were made by altering the design of the expression plasmids needed for biosynthetic pathway introduction. Specifically, the total number of genes and plasmids was pruned to reduce both metabolic burden and plasmid instability. Further, a comparison was conducted between species-specific (E. coli vs. S. coelicolor) protein chaperonins. Results indicate improvements in growth and plasmid retention metrics. The newly designed expression platform also increased erythromycin A production levels 5-fold. In conclusion, the steps outlined in this report were designed to upgrade the E. coli erythromycin A production system, led to improved final compound titers, and suggest additional forms of pathway engineering to further improve results from heterologous production attempts. © 2013 American Institute of Chemical Engineers.

  5. A novel methodology improves reservoir characterization models using geologic fuzzy variables

    Energy Technology Data Exchange (ETDEWEB)

    Soto B, Rodolfo [DIGITOIL, Maracaibo (Venezuela); Soto O, David A. [Texas A and M University, College Station, TX (United States)

    2004-07-01

    One of the research projects carried out in Cusiana field to explain its rapid decline during the last years was to get better permeability models. The reservoir of this field has a complex layered system that it is not easy to model using conventional methods. The new technique included the development of porosity and permeability maps from cored wells following the same trend of the sand depositions for each facie or layer according to the sedimentary facie and the depositional system models. Then, we used fuzzy logic to reproduce those maps in three dimensions as geologic fuzzy variables. After multivariate statistical and factor analyses, we found independence and a good correlation coefficient between the geologic fuzzy variables and core permeability and porosity. This means, the geologic fuzzy variable could explain the fabric, the grain size and the pore geometry of the reservoir rock trough the field. Finally, we developed a neural network permeability model using porosity, gamma ray and the geologic fuzzy variable as input variables. This model has a cross-correlation coefficient of 0.873 and average absolute error of 33% compared with the actual model with a correlation coefficient of 0.511 and absolute error greater than 250%. We tested different methodologies, but this new one showed dramatically be a promiser way to get better permeability models. The use of the models have had a high impact in the explanation of well performance and workovers, and reservoir simulation models. (author)

  6. Cardiac contractility modulation electrical signals improve myocardial gene expression in patients with heart failure.

    Science.gov (United States)

    Butter, Christian; Rastogi, Sharad; Minden, Hans-Heinrich; Meyhöfer, Jürgen; Burkhoff, Daniel; Sabbah, Hani N

    2008-05-06

    The objective of this study was to test whether cardiac contractility modulation (CCM) electric signals induce reverse molecular remodeling in myocardium of patients with heart failure. Heart failure is associated with up-regulation of myocardial fetal and stretch response genes and down-regulation of Ca(2+) cycling genes. Treatment with CCM signals has been associated with improved symptoms and exercise tolerance in heart failure patients. We tested the impact of CCM signals on myocardial gene expression in 11 patients. Endomyocardial biopsies were obtained at baseline and 3 and 6 months thereafter. The CCM signals were delivered in random order of ON for 3 months and OFF for 3 months. Messenger ribonucleic acid expression was analyzed in the core lab by investigators blinded to treatment sequence. Expression of A- and B-type natriuretic peptides and alpha-myosin heavy chain (MHC), the sarcoplasmic reticulum genes SERCA-2a, phospholamban and ryanodine receptors, and the stretch response genes p38 mitogen activated protein kinase and p21 Ras were measured using reverse transcription-polymerase chain reaction and bands quantified in densitometric units. The 3-month therapy OFF phase was associated with increased expression of A- and B-type natriuretic peptides, p38 mitogen activated protein kinase, and p21 Ras and decreased expression of alpha-MHC, SERCA-2a, phospholamban, and ryanodine receptors. In contrast, the 3-month ON therapy phase resulted in decreased expression of A- and B-type natriuretic peptides, p38 mitogen activated protein kinase and p21 Ras and increased expression of alpha-MHC, SERCA-2a, phospholamban, and ryanodine receptors. The CCM signal treatment reverses the cardiac maladaptive fetal gene program and normalizes expression of key sarcoplasmic reticulum Ca(2+) cycling and stretch response genes. These changes may contribute to the clinical effects of CCM.

  7. Exenatide improves glycemic variability assessed by continuous glucose monitoring in subjects with type 2 diabetes.

    Science.gov (United States)

    Irace, Concetta; Fiorentino, Raffaella; Carallo, Claudio; Scavelli, Faustina; Gnasso, Agostino

    2011-12-01

    Daily glycemic fluctuation leads to development of long-term complications. The aim of our pilot study was to determine if exenatide reduces glycemic variability, assessed with a continuous glucose monitoring (CGM) system, compared with glimepiride. We enrolled six consecutive subjects with type 2 diabetes, for whom exenatide was suggested as second-line treatment, and six control subjects, for whom glimepiride was suggested as second-line treatment. CGM was performed at baseline and after 16 weeks of treatment. As measures of glycemic variability we calculated the total daily mean glucose (MG), SD, and mean amplitude of glycemic excursions (MAGE). Exenatide significantly reduced MG, SD, and MAGE, whereas glimepiride did not. Fasting glucose and glycated hemoglobin were lowered in both groups, even if the reduction was not significant. Exenatide can reduce glycemic variability compared with glimepiride, providing additional beneficial effects in controlling glucose homeostasis.

  8. Clinicopathological variables of sporadic schwannomas of peripheral nerve in 291 patients and expression of biologically relevant markers.

    Science.gov (United States)

    Young, Eric D; Ingram, Davis; Metcalf-Doetsch, William; Khan, Dilshad; Al Sannaa, Ghadah; Le Loarer, Francois; Lazar, Alexander J F; Slopis, John; Torres, Keila E; Lev, Dina; Pollock, Raphael E; McCutcheon, Ian E

    2017-09-08

    OBJECTIVE While sporadic peripheral schwannomas (SPSs) are generally well treated with surgery, their biology is not well understood. Consequently, treatment options are limited. The aim of this study was to provide a comprehensive description of SPS. The authors describe clinicopathological features and treatment outcomes of patients harboring these tumors, and they assess expression of biomarkers using a clinically annotated tissue microarray. Together, these data give new insight into the biology and management of SPS. METHODS Patients presenting with a primary SPS between 1993 and 2011 (n = 291) were selected from an institutional registry to construct a clinical database. All patients underwent follow-up, and short- and long-term outcomes were assessed. Expression of relevant biomarkers was assessed using a new tissue microarray (n = 121). RESULTS SPSs were generally large (mean 5.5 cm) and frequently painful at presentation (55%). Most patients were treated with surgery (80%), the majority of whom experienced complete resolution (52%) or improvement (18%) of their symptoms. Tumors that were completely resected (85%) did not recur. Some patients experienced short-term (16%) and long-term (4%) complications postoperatively. Schwannomas expressed higher levels of platelet-derived growth factor receptor-β (2.1) than malignant peripheral nerve sheath tumors (MPNSTs) (1.5, p = 0.004) and neurofibromas (1.33, p = 0.007). Expression of human epidermal growth factor receptor-2 was greater in SPSs (0.91) than in MPNSTs (0.33, p = 0.002) and neurofibromas (0.33, p = 0.026). Epidermal growth factor receptor was expressed in far fewer SPS cells (10%) than in MPNSTs (58%, p SPSs more frequently expressed cytoplasmic survivin (66% of tumor cells) than normal nerve (46% of cells), but SPS expressed nuclear survivin in fewer tumor cells than in MPNSTs (24% and 50%, respectively; p = 0.018). CONCLUSIONS Complete resection is curative for SPS. Left untreated, however, these

  9. Mode choice models' ability to express intention to change travel behaviour considering non-compensatory rules and latent variables

    Directory of Open Access Journals (Sweden)

    Nobuhiro Sanko

    2013-03-01

    Full Text Available Disaggregate behaviour choice models have been improved in many aspects, but they are rarely evaluated from the viewpoint of their ability to express intention to change travel behaviour. This study compared various models, including objective and latent models and compensatory and non-compensatory decision-making models. Latent models contain latent factors calculated using the LISREL (linear structural relations model. Non-compensatory models are based on a lexicographic-semiorder heuristic. This paper proposes ‘probability increment’ and ‘joint probability increment’ as indicators for evaluating the ability of these models to express intention to change travel behaviour. The application to commuting travel data in the Chukyo metropolitan area in Japan showed that the appropriate non-compensatory and latent models outperform other models.

  10. Gene expression during blow fly development: improving the precision of age estimates in forensic entomology.

    Science.gov (United States)

    Tarone, Aaron M; Foran, David R

    2011-01-01

    Forensic entomologists use size and developmental stage to estimate blow fly age, and from those, a postmortem interval. Since such estimates are generally accurate but often lack precision, particularly in the older developmental stages, alternative aging methods would be advantageous. Presented here is a means of incorporating developmentally regulated gene expression levels into traditional stage and size data, with a goal of more precisely estimating developmental age of immature Lucilia sericata. Generalized additive models of development showed improved statistical support compared to models that did not include gene expression data, resulting in an increase in estimate precision, especially for postfeeding third instars and pupae. The models were then used to make blind estimates of development for 86 immature L. sericata raised on rat carcasses. Overall, inclusion of gene expression data resulted in increased precision in aging blow flies. © 2010 American Academy of Forensic Sciences.

  11. Suppression of PC-1/ENPP-1 expression improves insulin sensitivity in vitro and in vivo.

    Science.gov (United States)

    Zhou, Heather H; Chin, Chen-Ni; Wu, Margaret; Ni, Weihua; Quan, Shuo; Liu, Franklin; Dallas-Yang, Qing; Ellsworth, Kenneth; Ho, Thu; Zhang, Aiwu; Natasha, Tajneen; Li, Jing; Chapman, Kevin; Strohl, William; Li, Cai; Wang, I-Ming; Berger, Joel; An, Zhiqiang; Zhang, Bei B; Jiang, Guoqiang

    2009-08-15

    Plasma cell membrane glycoprotein-1, or ectonucleotide pyrophosphatase/phosphodieterase (PC-1/ENPP1) has been shown to inhibit insulin signaling in cultured cells in vitro and in transgenic mice in vivo when overexpressed. Furthermore, both genetic polymorphism and increased expression of PC-1 have been reported to be associated with type 2 diabetes in humans. Thus it was proposed that PC-1 inhibition represents a potential strategy for the treatment of type 2 diabetes. However, it has not been proven that suppression of PC-1 expression or inhibition of its function will actually improve insulin sensitivity. We show in the current study that transient overexpression of PC-1 inhibits insulin-stimulated insulin receptor tyrosine phosphorylation in HEK293 cells, while knockdown of PC-1 with siRNA significantly increases insulin-stimulated Akt phosphorylation in HuH7 human hepatoma cells. Adenoviral vector expressing a short hairpin RNA against mouse PC-1 (PC-1shRNA) was utilized to efficiently knockdown PC-1 expression in the livers of db/db mice. In comparison with db/db mice treated with a control virus, db/db mice treated with the PC-1shRNA adenovirus had approximately 80% lower hepatic PC-1 mRNA levels, approximately 30% lower ambient fed plasma glucose, approximately 25% lower fasting plasma glucose, and significantly improved oral glucose tolerance. Taken together, these results demonstrate that suppression of PC-1 expression improves insulin sensitivity in vitro and in an animal model of diabetes, supporting the proposition that PC-1 inhibition is a potential therapeutic approach for the treatment of type 2 diabetes.

  12. Ethnicity Moderates the Outcomes of Self-Enhancement and Self-Improvement Themes in Expressive Writing

    Science.gov (United States)

    Tsai, William; Lau, Anna S.; Niles, Andrea N.; Coello, Jordan; Lieberman, Matthew D.; Ko, Ahra C.; Hur, Christopher; Stanton, Annette L.

    2014-01-01

    The current study examined whether writing content related to self-enhancing (viz., downward social comparison and situational attributions) and self-improving (viz., upward social comparison and persistence) motivations were differentially related to expressive writing outcomes among 17 Asian American and 17 European American participants. Content analysis of the essays revealed no significant cultural group differences in the likelihood of engaging in self-enhancing vs. self-improving reflections on negative personal experiences. However, cultural group differences were apparent in the relation between self-motivation processes and changes in anxiety and depressive symptoms at 3-month follow-up. Among European Americans, writing that reflected downward social comparison predicted positive outcomes, whereas persistence writing themes were related to poorer outcomes. For Asian Americans, writing about persistence was related to positive outcomes, whereas downward social comparison and situational attributions predicted poorer outcomes. Findings provide evidence suggesting culturally distinct mechanisms for the effects of expressive disclosure. PMID:25111547

  13. A New Improved Variable Frequency Triangular Carrier-PWM with MOPSO Algorithm for Carrier Based PWM Techniques in Inverters

    Directory of Open Access Journals (Sweden)

    Mohammad Sadegh Orfi Yegane

    2017-02-01

    Full Text Available This paper investigates multi-carrier PWM methods in multi-level inverters. Two new MCPWM methods are introduced. This study proposes a new optimized MCPWM method to improve the output voltage characteristics like THD and LOH. The proposed method is based on variable frequency with a specific range. It means each carrier wave has a determined frequency. It is calling Variable Frequency Triangular Carrier-PWM. MOPSO algorithm is used to optimize the answers. This work considers some different levels of inverters like five, seven and nine levels. The results are compared with SPWM method.

  14. Aerobic expression of Vitreoscilla hemoglobin improves the growth performance of CHO-K1 cells.

    Science.gov (United States)

    Juárez, Mariana; González-De la Rosa, Claudia H; Memún, Elisa; Sigala, Juan-Carlos; Lara, Alvaro R

    2017-03-01

    Inefficient carbon metabolism is a relevant issue during the culture of mammalian cells for the production of biopharmaceuticals. Therefore, cell engineering strategies to improve the metabolic and growth performance of cell lines are needed. The expression of Vitreoscilla stercoraria hemoglobin (VHb) has been shown to significantly reduce overflow metabolism and improve the aerobic growth of bacteria. However, the effects of VHb on mammalian cells have been rarely studied. Here, the impact of VHb on growth and lactate accumulation during CHO-K1 cell culture was investigated. For this purpose, CHO-K1 cells were transfected with plasmids carrying the vgb or gfp gene to express VHb or green fluorescence protein (GFP), respectively. VHb expression increased the specific growth rate and biomass yields on glucose and glutamine by 60 %, and reduced the amount of lactate produced per cell by 40 %, compared to the GFP-expression controls. Immunofluorescence microscopy showed that VHb is distributed in the cytoplasm and organelles, which support the hypothesis that VHb could serve as an oxygen carrier, enhancing aerobic respiration. These results are useful for the development of better producing cell lines for industrial applications. Copyright © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Regression mixture models : Does modeling the covariance between independent variables and latent classes improve the results?

    NARCIS (Netherlands)

    Lamont, A.E.; Vermunt, J.K.; Van Horn, M.L.

    2016-01-01

    Regression mixture models are increasingly used as an exploratory approach to identify heterogeneity in the effects of a predictor on an outcome. In this simulation study, we tested the effects of violating an implicit assumption often made in these models; that is, independent variables in the

  16. Improved theory of time domain reflectometry with variable coaxial cable length for electrical conductivity measurements

    Science.gov (United States)

    Although empirical models have been developed previously, a mechanistic model is needed for estimating electrical conductivity (EC) using time domain reflectometry (TDR) with variable lengths of coaxial cable. The goals of this study are to: (1) derive a mechanistic model based on multisection tra...

  17. Acupuncture Alters Expression of Insulin Signaling Related Molecules and Improves Insulin Resistance in OLETF Rats

    Directory of Open Access Journals (Sweden)

    Xin-Yu Huang

    2016-01-01

    Full Text Available To determine effect of acupuncture on insulin resistance in Otsuka Long-Evans Tokushima Fatty (OLETF rats and to evaluate expression of insulin signaling components. Rats were divided into three groups: Sprague-Dawley (SD rats, OLETF rats, and acupuncture+OLETF rats. Acupuncture was subcutaneously applied to Neiguan (PC6, Zusanli (ST36, and Sanyinjiao (SP6; in contrast, acupuncture to Shenshu (BL23 was administered perpendicularly. For Neiguan (PC6 and Zusanli (ST36, needles were connected to an electroacupuncture (EA apparatus. Fasting blood glucose (FPG was measured by glucose oxidase method. Plasma fasting insulin (FINS and serum C peptide (C-P were determined by ELISA. Protein and mRNA expressions of insulin signaling molecules were determined by Western blot and real-time RT-PCR, respectively. OLETF rats exhibit increased levels of FPG, FINS, C-P, and homeostasis model assessment-estimated insulin resistance (HOMA-IR, which were effectively decreased by acupuncture treatment. mRNA expressions of several insulin signaling related molecules IRS1, IRS2, Akt2, aPKCζ, and GLUT4 were decreased in OLETF rats compared to SD controls. Expression of these molecules was restored back to normal levels upon acupuncture administration. PI3K-p85α was increased in OLETF rats; this increase was also reversed by acupuncture treatment. Acupuncture improves insulin resistance in OLETF rats, possibly via regulating expression of key insulin signaling related molecules.

  18. Protein expression and genetic variability of canine Can f 1 in golden and Labrador retriever service dogs.

    Science.gov (United States)

    Breitenbuecher, Christina; Belanger, Janelle M; Levy, Kerinne; Mundell, Paul; Fates, Valerie; Gershony, Liza; Famula, Thomas R; Oberbauer, Anita M

    2016-01-01

    Valued for trainability in diverse tasks, dogs are the primary service animal used to assist individuals with disabilities. Despite their utility, many people in need of service dogs are sensitive to the primary dog allergen, Can f 1, encoded by the Lipocalin 1 gene (LCN1). Several organizations specifically breed service dogs to meet special needs and would like to reduce allergenic potential if possible. In this study, we evaluated the expression of Can f 1 protein and the inherent variability of LCN1 in two breeds used extensively as service dogs. Saliva samples from equal numbers of male and female Labrador retrievers (n = 12), golden retrievers (n = 12), and Labrador-golden crosses (n = 12) were collected 1 h after the morning meal. Can f 1 protein concentrations in the saliva were measured by ELISA, and the LCN1 5' and 3' UTRs and exons sequenced. There was no sex effect (p > 0.2) nor time-of-day effect; however, Can f 1 protein levels varied by breed with Labrador retrievers being lower than golden retrievers (3.18 ± 0.51 and 5.35 ± 0.52 μg/ml, respectively, p service dogs, Labrador retrievers likely have lower allergenic potential and, though there were no DNA sequence differences identified, classical genetic selection on the estimated breeding values associated with salivary Can f 1 expression may further reduce that potential.

  19. High variability of expression profiles of homeologous genes for Wnt, Hh, Notch, and Hippo signaling pathways in Xenopus laevis.

    Science.gov (United States)

    Michiue, Tatsuo; Yamamoto, Takayoshi; Yasuoka, Yuuri; Goto, Toshiyasu; Ikeda, Takafumi; Nagura, Kei; Nakayama, Takuya; Taira, Masanori; Kinoshita, Tsutomu

    2017-06-15

    Cell signaling pathways, such as Wnt, Hedgehog (Hh), Notch, and Hippo, are essential for embryogenesis, organogenesis, and tissue homeostasis. In this study, we analyzed 415 genes involved in these pathways in the allotetraploid frog, Xenopus laevis. Most genes are retained in two subgenomes called L and S (193 homeologous gene pairs and 29 singletons). This conservation rate of homeologs is much higher than that of all genes in the X. laevis genome (86.9% vs 60.2%). Among singletons, 24 genes are retained in the L subgenome, a rate similar to the average for all genes (82.8% vs 74.6%). In addition, as general components of signal transduction, we also analyzed 32 heparan sulfate proteoglycan (HSPG)-related genes and eight TLE/Groucho transcriptional corepressors-related genes. In these gene sets, all homeologous pairs have been retained. Transcriptome analysis using RNA-seq data from developmental stages and adult tissues demonstrated that most homeologous pairs of signaling components have variable expression patterns, in contrast to the conservative expression profiles of homeologs for transcription factors. Our results indicate that homeologous gene pairs for cell signaling regulation have tended to become subfunctionalized after allotetraploidization. Diversification of signaling pathways by subfunctionalization of homeologs may enhance environmental adaptability. These results provide insights into the evolution of signaling pathways after polyploidization. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. Improving the sensitivity of stop searches with on-shell constrained invariant mass variables

    CERN Document Server

    Cho, Won Sang; Kim, Doojin; Matchev, Konstantin T.; Moortgat, Filip; Pape, Luc; Park, Myeonghun

    2015-01-01

    The search for light stops is of paramount importance, both in general as a promising path to the discovery of beyond the standard model physics and more specifically as a way of evaluating the success of the naturalness paradigm. While the LHC experiments have ruled out much of the relevant parameter space, there are "stop gaps", i.e., values of sparticle masses for which existing LHC analyses have relatively little sensitivity to light stops. We point out that techniques involving on-shell constrained M_2 variables can do much to enhance sensitivity in this region and hence help close the stop gaps. We demonstrate the use of these variables for several benchmark points and describe the effect of realistic complications, such as detector effects and combinatorial backgrounds, in order to provide a useful toolkit for light stop searches in particular, and new physics searches at the LHC in general.

  1. Variable-speed wind power system with improved energy capture via multilevel conversion

    Science.gov (United States)

    Erickson, Robert W.; Al-Naseem, Osama A.; Fingersh, Lee Jay

    2005-05-31

    A system and method for efficiently capturing electrical energy from a variable-speed generator are disclosed. The system includes a matrix converter using full-bridge, multilevel switch cells, in which semiconductor devices are clamped to a known constant DC voltage of a capacitor. The multilevel matrix converter is capable of generating multilevel voltage wave waveform of arbitrary magnitude and frequencies. The matrix converter can be controlled by using space vector modulation.

  2. Genetic polymorphisms inside and outside the MHC improve prediction of AS radiographic severity in addition to clinical variables.

    Science.gov (United States)

    Bartolomé, Nerea; Szczypiorska, Magdalena; Sánchez, Alejandra; Sanz, Jesús; Juanola-Roura, Xavier; Gratacós, Jordi; Zarco-Montejo, Pedro; Collantes, Eduardo; Martínez, Antonio; Tejedor, Diego; Artieda, Marta; Mulero, Juan

    2012-08-01

    The aim of this study was to analyse if single nucleotide polymorphisms (SNPs) inside and outside the MHC region might improve the prediction of radiographic severity in AS. A cross-sectional multi-centre study was performed including 473 Spanish AS patients previously diagnosed with AS following the Modified New York Criteria and with at least 10 years of follow-up from the first symptoms of AS. Clinical variables and 384 SNPs were analysed to predict radiographic severity [BASRI-total (BASRI-t) corrected for the duration of AS since first symptoms] using multivariate forward logistic regression. Predictive power was measured by the area under the receiver operating characteristic curve (AUC), specificity, sensitivity, positive predictive value (PPV) and negative predictive value (NPV). The model with the best fit measured radiographic severity as the BASRI-t 60th percentile and combined eight variables: male gender, older age at disease onset and six SNPs at ADRB1 (rs1801253), NELL1 (rs8176785) and MHC (rs1634747, rs9270986, rs7451962 and rs241453) genes. The model predictive power was defined by AUC = 0.76 (95% CI 0.71, 0.80), being significantly better than the model with only clinical variables, AUC = 0.68 (95% CI 0.63, 0.73), P = 0.0004. Internal split-sample analysis proved the validation of the model. Patient genotype for SNPs outside the MHC region, inside the MHC region and clinical variables account for 26, 38 and 36%, respectively, of the explained variability on radiographic severity prediction. Prediction of radiographic severity in AS based on clinical variables can be significantly improved by including SNPs both inside and outside the MHC region.

  3. Development of " Ability of Self-expression and Communication" in Industrial Arts : Exchange of Ideas Improving the Plan.

    OpenAIRE

    Yanagihara, Hironori; Mada, Yasuhiro; Tashima, Shunzo

    2004-01-01

    This is a practical study to increase the students' "ability of self-expression and communication", which is the theme of the study this year. The students showed the figure of a plan which is the basis of manufacturing. They exchanged ideas and advice. It was a good activity for improving manufacturing. They also improved their ability of self-expression.

  4. Non-invasive assessment of inter-and intrapatient variability of integrin expression in metastasized prostate cancer by PET.

    Science.gov (United States)

    Beer, Ambros J; Schwarzenböck, Sarah M; Zantl, Niko; Souvatzoglou, Michael; Maurer, Tobias; Watzlowik, Petra; Kessler, Horst; Wester, Hans-Jürgen; Schwaiger, Markus; Krause, Bernd Joachim

    2016-05-10

    Due to the high expression of the integrin αvβ3 not only on endothelial cells, but also on mature osteoclasts and prostate cancer cells, imaging of osseous metastases with αvβ3-targeted tracers seems promising. However, little is known about the patterns of αvβ3-expression in metastasized prostate cancer lesions in-vivo. Thus we evaluated the uptake of the αvβ3-specific PET tracer [18F]Galacto-RGD for assessment of bone metastases in prostate cancer patients. [18F]Galacto-RGD PET identified 58/74 bone-lesions (detection rate of 78.4%) and lymph node metastases in 2/5 patients. The SUVmean was 2.12+/-0.94 (range 0.70-4.38; tumor/blood 1.36+/-0.53; tumor/muscle 2.82+/-1.31) in bone-lesions and 2.21+/-1.18 (range 0.75-3.56) in lymph node metastases. Good visualization and detection of bone metastases was feasible due to a low background activity of the surrounding normal bone tissue. 12 patients with known metastasized prostate cancer according to conventional staging (including bone-scintigraphy and contrast-enhanced CT; median PSA 68.63 ng/ml, range 3.72-1935) were examined with PET after i.v.-injection of [18F]Galacto-RGD. Two blinded nuclear-medicine physicians evaluated the PET-scans in consensus concerning lesion detectability. Volumes-of-interest were drawn in the PET-scans over all metastases defined by conventional staging (maximum of 11 lesions/patient), over the left ventricle, liver and muscle and standardized-uptake-values (SUVs) were calculated. Our data show generally elevated uptake of [18F]Galacto-RGD in bone metastases from prostate cancer with a marked inter- and intrapatient variability. While [18F]Galacto-RGD PET is inferior to bone scintigraphy for detection of osseous metastases, it might be valuable in patient screening and monitoring of αvβ3-targeted therapies due to the high variability of αvβ3-expression.

  5. Expression of Root Genes in Arabidopsis Seedlings Grown by Standard and Improved Growing Methods

    Directory of Open Access Journals (Sweden)

    Yanli Qu

    2017-05-01

    Full Text Available Roots of Arabidopsis thaliana seedlings grown in the laboratory using the traditional plant-growing culture system (TPG were covered to maintain them in darkness. This new method is based on a dark chamber and is named the improved plant-growing method (IPG. We measured the light conditions in dark chambers, and found that the highest light intensity was dramatically reduced deeper in the dark chamber. In the bottom and side parts of dark chambers, roots were almost completely shaded. Using the high-throughput RNA sequencing method on the whole RNA extraction from roots, we compared the global gene expression levels in roots of seedlings from these two conditions and identified 141 differently expressed genes (DEGs between them. According to the KEGG (Kyoto Encyclopedia of Genes and Genomes enrichment, the flavone and flavonol biosynthesis and flavonoid biosynthesis pathways were most affected among all annotated pathways. Surprisingly, no genes of known plant photoreceptors were identified as DEGs by this method. Considering that the light intensity was decreased in the IPG system, we collected four sections (1.5 cm for each of Arabidopsis roots grown in TPG and IPG conditions, and the spatial-related differential gene expression levels of plant photoreceptors and polar auxin transporters, including CRY1, CRY2, PHYA, PHYB, PHOT1, PHOT2, and UVR8 were analyzed by qRT-PCR. Using these results, we generated a map of the spatial-related expression patterns of these genes under IPG and TPG conditions. The expression levels of light-related genes in roots is highly sensitive to illumination and it provides a background reference for selecting an improved culture method for laboratory-maintained Arabidopsis seedlings.

  6. Brief Communication: Upper Air Relaxation in RACMO2 Significantly Improves Modelled Interannual Surface Mass Balance Variability in Antarctica

    Science.gov (United States)

    van de Berg, W. J.; Medley, B.

    2016-01-01

    The Regional Atmospheric Climate Model (RACMO2) has been a powerful tool for improving surface mass balance (SMB) estimates from GCMs or reanalyses. However, new yearly SMB observations for West Antarctica show that the modelled interannual variability in SMB is poorly simulated by RACMO2, in contrast to ERA-Interim, which resolves this variability well. In an attempt to remedy RACMO2 performance, we included additional upper-air relaxation (UAR) in RACMO2. With UAR, the correlation to observations is similar for RACMO2 and ERA-Interim. The spatial SMB patterns and ice-sheet-integrated SMB modelled using UAR remain very similar to the estimates of RACMO2 without UAR. We only observe an upstream smoothing of precipitation in regions with very steep topography like the Antarctic Peninsula. We conclude that UAR is a useful improvement for regional climate model simulations, although results in regions with steep topography should be treated with care.

  7. pEPito: a significantly improved non-viral episomal expression vector for mammalian cells

    Directory of Open Access Journals (Sweden)

    Ogris Manfred

    2010-03-01

    Full Text Available Abstract Background The episomal replication of the prototype vector pEPI-1 depends on a transcription unit starting from the constitutively expressed Cytomegalovirus immediate early promoter (CMV-IEP and directed into a 2000 bp long matrix attachment region sequence (MARS derived from the human β-interferon gene. The original pEPI-1 vector contains two mammalian transcription units and a total of 305 CpG islands, which are located predominantly within the vector elements necessary for bacterial propagation and known to be counterproductive for persistent long-term transgene expression. Results Here, we report the development of a novel vector pEPito, which is derived from the pEPI-1 plasmid replicon but has considerably improved efficacy both in vitro and in vivo. The pEPito vector is significantly reduced in size, contains only one transcription unit and 60% less CpG motives in comparison to pEPI-1. It exhibits major advantages compared to the original pEPI-1 plasmid, including higher transgene expression levels and increased colony-forming efficiencies in vitro, as well as more persistent transgene expression profiles in vivo. The performance of pEPito-based vectors was further improved by replacing the CMV-IEP with the human CMV enhancer/human elongation factor 1 alpha promoter (hCMV/EF1P element that is known to be less affected by epigenetic silencing events. Conclusions The novel vector pEPito can be considered suitable as an improved vector for biotechnological applications in vitro and for non-viral gene delivery in vivo.

  8. Improved methods for observing Earth's time variable mass distribution with GRACE using spherical cap mascons

    National Research Council Canada - National Science Library

    Watkins, Michael M; Wiese, David N; Yuan, Dah‐Ning; Boening, Carmen; Landerer, Felix W

    2015-01-01

    .... These include both improvements in background geophysical models and orbital parameterization leading to the unconstrained spherical harmonic solution JPL RL05, and an alternate JPL RL05M mass concentration (mascon...

  9. Improved detection of differentially expressed genes in microarray experiments through multiple scanning and image integration

    Science.gov (United States)

    Romualdi, Chiara; Trevisan, Silvia; Celegato, Barbara; Costa, Germano; Lanfranchi, Gerolamo

    2003-01-01

    The variability of results in microarray technology is in part due to the fact that independent scans of a single hybridised microarray give spot images that are not quite the same. To solve this problem and turn it to our advantage, we introduced the approach of multiple scanning and of image integration of microarrays. To this end, we have developed specific software that creates a virtual image that statistically summarises a series of consecutive scans of a microarray. We provide evidence that the use of multiple imaging (i) enhances the detection of differentially expressed genes; (ii) increases the image homogeneity; and (iii) reveals false-positive results such as differentially expressed genes that are detected by a single scan but not confirmed by successive scanning replicates. The increase in the final number of differentially expressed genes detected in a microarray experiment with this approach is remarkable; 50% more for microarrays hybridised with targets labelled by reverse transcriptase, and 200% more for microarrays developed with the tyramide signal amplification (TSA) technique. The results have been confirmed by semi-quantitative RT–PCR tests. PMID:14627839

  10. Probabilistic Requirements (Partial) Verification Methods Best Practices Improvement. Variables Acceptance Sampling Calculators: Derivations and Verification of Plans. Volume 1

    Science.gov (United States)

    Johnson, Kenneth L.; White, K, Preston, Jr.

    2012-01-01

    The NASA Engineering and Safety Center was requested to improve on the Best Practices document produced for the NESC assessment, Verification of Probabilistic Requirements for the Constellation Program, by giving a recommended procedure for using acceptance sampling by variables techniques. This recommended procedure would be used as an alternative to the potentially resource-intensive acceptance sampling by attributes method given in the document. This document contains the outcome of the assessment.

  11. Predicting protein phosphorylation from gene expression: top methods from the IMPROVER Species Translation Challenge.

    Science.gov (United States)

    Dayarian, Adel; Romero, Roberto; Wang, Zhiming; Biehl, Michael; Bilal, Erhan; Hormoz, Sahand; Meyer, Pablo; Norel, Raquel; Rhrissorrakrai, Kahn; Bhanot, Gyan; Luo, Feng; Tarca, Adi L

    2015-02-15

    Using gene expression to infer changes in protein phosphorylation levels induced in cells by various stimuli is an outstanding problem. The intra-species protein phosphorylation challenge organized by the IMPROVER consortium provided the framework to identify the best approaches to address this issue. Rat lung epithelial cells were treated with 52 stimuli, and gene expression and phosphorylation levels were measured. Competing teams used gene expression data from 26 stimuli to develop protein phosphorylation prediction models and were ranked based on prediction performance for the remaining 26 stimuli. Three teams were tied in first place in this challenge achieving a balanced accuracy of about 70%, indicating that gene expression is only moderately predictive of protein phosphorylation. In spite of the similar performance, the approaches used by these three teams, described in detail in this article, were different, with the average number of predictor genes per phosphoprotein used by the teams ranging from 3 to 124. However, a significant overlap of gene signatures between teams was observed for the majority of the proteins considered, while Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were enriched in the union of the predictor genes of the three teams for multiple proteins. Gene expression and protein phosphorylation data are available from ArrayExpress (E-MTAB-2091). Software implementation of the approach of Teams 49 and 75 are available at http://bioinformaticsprb.med.wayne.edu and http://people.cs.clemson.edu/∼luofeng/sbv.rar, respectively. gyanbhanot@gmail.com or luofeng@clemson.edu or atarca@med.wayne.edu Supplementary data are available at Bioinformatics online. Published by Oxford University Press 2014. This work is written by US Government employees and is in the public domain in the US.

  12. A New Strain Collection for Improved Expression of Outer Membrane Proteins

    Directory of Open Access Journals (Sweden)

    Ina Meuskens

    2017-11-01

    Full Text Available Almost all integral membrane proteins found in the outer membranes of Gram-negative bacteria belong to the transmembrane β-barrel family. These proteins are not only important for nutrient uptake and homeostasis, but are also involved in such processes as adhesion, protein secretion, biofilm formation, and virulence. As surface exposed molecules, outer membrane β-barrel proteins are also potential drug and vaccine targets. High production levels of heterologously expressed proteins are desirable for biochemical and especially structural studies, but over-expression and subsequent purification of membrane proteins, including outer membrane proteins, can be challenging. Here, we present a set of deletion mutants derived from E. coli BL21(DE3 designed for the over-expression of recombinant outer membrane proteins. These strains harbor deletions of four genes encoding abundant β-barrel proteins in the outer membrane (OmpA, OmpC, OmpF, and LamB, both single and in all combinations of double, triple, and quadruple knock-outs. The sequences encoding these outer membrane proteins were deleted completely, leaving only a minimal scar sequence, thus preventing the possibility of genetic reversion. Expression tests in the quadruple mutant strain with four test proteins, including a small outer membrane β-barrel protein and variants thereof as well as two virulence-related autotransporters, showed significantly improved expression and better quality of the produced proteins over the parent strain. Differences in growth behavior and aggregation in the presence of high salt were observed, but these phenomena did not negatively influence the expression in the quadruple mutant strain when handled as we recommend. The strains produced in this study can be used for outer membrane protein production and purification, but are also uniquely useful for labeling experiments for biophysical measurements in the native membrane environment.

  13. Intragenic controls utilizing radiation-induced alternative transcript regions improves gene expression biodosimetry.

    Science.gov (United States)

    Forrester, Helen B; Sprung, Carl N

    2014-03-01

    Ionizing-radiation exposure can be life threatening if given to the whole body. In addition, whole body radiation exposure can affect large numbers of people such as after a nuclear reactor accident, a nuclear explosion or a radiological terrorist attack. In these cases, an accurate biodosimeter is essential for triage management. One of the problems for biodosimetry in general is the interindividual variation before and after exposure, which can make it challenging to assign an accurate dose. To begin to address this challenge, lymphocyte cell lines were exposed to 0, 1, 2 and 5 Gy ionizing radiation from a ¹³⁷Cs source at a dose rate of 0.6 Gy/min. Alternative transcripts with regions showing large differential responses to ionizing radiation were determined from exon array data. Gene expression analysis was then performed on isolated mRNA using qRT-PCR with normalization to intergenic (PGK1, GAPDH) and novel intragenic regions for candidate radiation-responsive genes, PPM1D and MDM2. Our studies show that the use of a cis-associated expression reference improved the potential dose prediction approximately 2.3-8.3 fold and provided an advantage for dose prediction compared to distantly or trans-located control ionizing radiation nonresponsive genes. This approach also provides an alternative gene expression normalization method to potentially reduce interindividual variations when untreated basal gene expression levels are unavailable. Using associated noninduced regions of ionizing radiation-induced genes provides a way to estimate basal gene expression in the irradiated sample. This strategy can be utilized as a biodosimeter on its own or to enhance other gene expression candidates for biodosimetry. This normalization strategy may also be generally applicable for other quantitative PCR strategies where normalization is required for a particular response.

  14. The Climate Variability & Predictability (CVP) Program at NOAA - Improved Understanding of Tropical Pacific Processes, Biases, and Climatology

    Science.gov (United States)

    Lucas, S. E.; Todd, J. F.

    2016-02-01

    The Climate Variability & Predictability (CVP) Program at NOAA supports research aimed at providing process-level understanding of the climate system through observation, modeling, analysis, and field studies. This vital knowledge is needed to improve climate models and predictions so that scientists can better anticipate the impacts of future climate variability and change. To achieve its mission, the CVP Program supports research carried out at NOAA and other federal laboratories, NOAA Cooperative Institutes, and academic institutions. The Program also coordinates its sponsored projects with major national and international scientific bodies including the World Climate Research Programme (WCRP), the International and U.S. Climate Variability and Predictability (CLIVAR/US CLIVAR) Program, and the U.S. Global Change Research Program (USGCRP). The CVP program sits within NOAA's Climate Program Office (http://cpo.noaa.gov/CVP). A leading-order issue for improvement of predictions and projections of the El Niño/Southern Oscillation (ENSO), Madden-Julian Oscillation (MJO), Pacific Decadal Oscillation (PDO), and other important climate phenomena is the need for climate models to correctly and consistently produce the seasonally-varying background state. The CVP Program currently supports eleven projects in area of "Improved Understanding of Tropical Pacific Processes, Biases, and Climatology." Recent results from CVP-funded projects will be summarized in this poster and the development of the NOAA CVP Pacific Task Force will be discussed.

  15. Exploration of self-expression to improve L2 writing skills

    Directory of Open Access Journals (Sweden)

    Pfeiffer, Verbra Frances

    2016-12-01

    Full Text Available This article focuses on and explores the issue of teaching students to write with some level of fluency. In light of this, it investigates the use of expressive writing which can develop as the mainstay approach to help students improve their academic writing skills. Teaching students to write with confidence is always a daunting undertaking for any teacher, even more so when they are at a tertiary level. This study was conducted over a semester where a qualitative methodology was used to study autobiographical writing, journal entries and personal-response writing. Our results show that students’ writing improved over a continuum of writing tasks of an evolutionary/daily living nature, through which we explored their self-expression. The study is predicated on the dynamics and fall-outs of L2 writing at a tertiary setting in Cape Town. The data provided by the fourteen participants featured in our study were meant to identify the kinds of strategies that could assist L2 students with English Language writing tasks. By the same token, the study was meant to offer useful insights into the educational practice and prevalence of writing for self-expression.

  16. Constitutive expression of Vitreoscilla haemoglobin in Sphingomonas elodea to improve gellan gum production.

    Science.gov (United States)

    Wu, X C; Chen, Y M; Li, Y D; Li, O; Zhu, L; Qian, C D; Tao, X L; Teng, Y

    2011-02-01

    To improve a commercially used strain for gellan production by exogenous Vitreoscilla haemoglobin (VHb). VHb gene was expressed in Sphingomonas elodea under the control of constitutive bla promoter. Biochemical activity of expressed VHb was confirmed by CO-difference spectra analysis that exhibited a characteristic absorption maximum at 419 nm. During cultivation, not only enhanced cell growth was detected, but also 20% improvement in gellan production was observed after 48 h of incubation, with a maximum yield of 16·82 g l(-1). Moreover, maximum sucrose conversion efficiency (g gellan per g sucrose) was 57·8, 20% higher than that of the parental strain. We further examined the polysaccharide production of VHb-expressing strain at different aeration levels in Erlenmeyer flasks. Again, in all cases, a significant enhancement of gellan production was observed, and the enhancement was more significant under oxygen-limiting conditions (up to 26·8%). VHb exhibited positive effect on cell growth and gellan yield of S. elodea, especially under hypoxic conditions. This is the first application of VHb as an effective metabolic engineering strategy in S. elodea to regulate cell growth and optimize gellan yield. © 2010 The Authors. Journal of Applied Microbiology © 2010 The Society for Applied Microbiology.

  17. A variable hydrophobic surface improves corrosion resistance of electroplating copper coating

    Science.gov (United States)

    Xu, Xiuqing; Zhu, Liqun; Li, Weiping; Liu, Huicong

    2011-04-01

    In this paper, Cu/liquid microcapsule composite coating was prepared by electroplating method. And a variable hydrophobic surface was obtained due to the slow release of microcapsules and the rough surface. The hydrophobic property and corrosion resistance of the composite was investigated by means of water contact angle instrument and electrochemical technique, respectively. The results suggest that the contact angle (CA) of composite increases gradually with the increasing storing time, and the stable super-hydrophobic property was exhibited after storing in air for 15 days. Meanwhile, the excellent corrosion resistance was displayed, which could be ascribed to the good stability of hydrophobic film on composite surface.

  18. Modest weight loss in moderately overweight postmenopausal women improves heart rate variability

    DEFF Research Database (Denmark)

    Mouridsen, Mette Rauhe; Bendsen, Nathalie Tommerup; Astrup, Arne

    2013-01-01

    Purpose: To evaluate the effects of weight loss on heart rate (HR) and heart rate variability (HRV) parameters in overweight postmenopausal women. Design and Methods: Forty-nine overweight postmenopausal women with an average body mass index of 28.8 1.9 kg/m2 underwent a 12-week dietary weight......-to-normal intervals for each 5-min period (SDNNindex). Baseline body fat mass (FM%) and changes in body composition was determined by dual X-ray absorptiometry. Before and after the weight-loss period, total abdominal fat, intra-abdominal fat (IAAT), and subcutaneous abdominal fat (SCAT) were measured by single...

  19. Data-Driven User Feedback: An Improved Neurofeedback Strategy considering the Interindividual Variability of EEG Features

    Directory of Open Access Journals (Sweden)

    Chang-Hee Han

    2016-01-01

    Full Text Available It has frequently been reported that some users of conventional neurofeedback systems can experience only a small portion of the total feedback range due to the large interindividual variability of EEG features. In this study, we proposed a data-driven neurofeedback strategy considering the individual variability of electroencephalography (EEG features to permit users of the neurofeedback system to experience a wider range of auditory or visual feedback without a customization process. The main idea of the proposed strategy is to adjust the ranges of each feedback level using the density in the offline EEG database acquired from a group of individuals. Twenty-two healthy subjects participated in offline experiments to construct an EEG database, and five subjects participated in online experiments to validate the performance of the proposed data-driven user feedback strategy. Using the optimized bin sizes, the number of feedback levels that each individual experienced was significantly increased to 139% and 144% of the original results with uniform bin sizes in the offline and online experiments, respectively. Our results demonstrated that the use of our data-driven neurofeedback strategy could effectively increase the overall range of feedback levels that each individual experienced during neurofeedback training.

  20. Data-Driven User Feedback: An Improved Neurofeedback Strategy considering the Interindividual Variability of EEG Features.

    Science.gov (United States)

    Han, Chang-Hee; Lim, Jeong-Hwan; Lee, Jun-Hak; Kim, Kangsan; Im, Chang-Hwan

    2016-01-01

    It has frequently been reported that some users of conventional neurofeedback systems can experience only a small portion of the total feedback range due to the large interindividual variability of EEG features. In this study, we proposed a data-driven neurofeedback strategy considering the individual variability of electroencephalography (EEG) features to permit users of the neurofeedback system to experience a wider range of auditory or visual feedback without a customization process. The main idea of the proposed strategy is to adjust the ranges of each feedback level using the density in the offline EEG database acquired from a group of individuals. Twenty-two healthy subjects participated in offline experiments to construct an EEG database, and five subjects participated in online experiments to validate the performance of the proposed data-driven user feedback strategy. Using the optimized bin sizes, the number of feedback levels that each individual experienced was significantly increased to 139% and 144% of the original results with uniform bin sizes in the offline and online experiments, respectively. Our results demonstrated that the use of our data-driven neurofeedback strategy could effectively increase the overall range of feedback levels that each individual experienced during neurofeedback training.

  1. Some improved modified ratio estimators based on decile mean of an auxiliary variable

    Directory of Open Access Journals (Sweden)

    Muhammad Abid

    2016-12-01

    Full Text Available The estimators developed so far regarding the study under consideration use the conventional measures of central tendencies, i.e. the mean, the median, the quartile mean etc., and comment on their properties. However, Sohel et al. (2012 have proposed decile mean as a measure of central tendency and have proved that it outperforms the conventional measures of central tendency. In this study, we have attempted to use the decile mean instead of the conventional measures suggested in previous studies. Also, we have used decile mean, population correlation coefficient, coefficient of variation and the linear combinations of auxiliary variable and investigated the properties associated with the proposed estimator. Theoretically, mean square error equations of all proposed ratio estimators are obtained and the efficiency conditions are derived. This study has been verified numerically.

  2. Floral aroma improvement of Muscat spirits by packed column distillation with variable internal reflux.

    Science.gov (United States)

    Matias-Guiu, Pau; Rodríguez-Bencomo, Juan José; Orriols, Ignacio; Pérez-Correa, José Ricardo; López, Francisco

    2016-12-15

    The organoleptic quality of wine distillates depends on raw materials and the distillation process. Previous work has shown that rectification columns in batch distillation with fixed reflux rate are useful to obtain distillates or distillate fractions with enhanced organoleptic characteristics. This study explores variable reflux rate operating strategies to increase the levels of terpenic compounds in specific distillate fractions to emphasize its floral aroma. Based on chemical and sensory analyses, two distillate heart sub-fractions obtained with the best operating strategy found, were compared with a distillate obtained in a traditional alembic. Results have shown that a drastic reduction of the reflux rate at an early stage of the heart cut produced a distillate heart sub-fraction with a higher concentration of terpenic compounds and lower levels of negative aroma compounds. Therefore, this sub-fraction presented a much more noticeable floral aroma than the distillate obtained with a traditional alembic. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. Improved virtual cardiac phantom with variable diastolic filling rates and coronary artery velocities

    Science.gov (United States)

    Sturgeon, Gregory M.; Richards, Taylor W.; Samei, E.; Segars, W. P.

    2017-03-01

    To facilitate studies of measurement uncertainty in computed tomography angiography (CTA), we investigated the cardiac motion profile and resulting coronary artery motion utilizing innovative dynamic virtual and physical phantoms. The four-chamber cardiac finite element (FE) model developed in the Living Heart Project (LHP) served as the computational basis for our virtual cardiac phantom. This model provides deformation or strain information at high temporal and spatial resolution, exceeding that of speckle tracking echocardiography or tagged MRI. This model was extended by fitting its motion profile to left ventricular (LV) volume-time curves obtained from patient echocardiography data. By combining the dynamic patient variability from echo with the local strain information from the FE model, a series of virtual 4D cardiac phantoms were developed. Using the computational phantoms, we characterized the coronary motion and its effect on plaque imaging under a range of heart rates subject to variable diastolic function. The coronary artery motion was sampled at 248 spatial locations over 500 consecutive time frames. The coronary artery velocities were calculated as their average velocity during an acquisition window centered at each time frame, which minimized the discretization error. For the initial set of twelve patients, the diastatic coronary artery velocity ranged from 36.5 mm/s to 2.0 mm/s with a mean of 21.4 mm/s assuming an acquisition time of 75 ms. The developed phantoms have great potential in modeling cardiac imaging, providing a known truth and multiple realistic cardiac motion profiles to evaluate different image acquisition or reconstruction methods.

  4. Candesartan cilexetil attenuated cardiac remodeling by improving expression and function of mitofusin 2 in SHR.

    Science.gov (United States)

    Wang, Zuoguang; Niu, Qiuli; Peng, Xiaoyun; Li, Mei; Liu, Kuo; Liu, Ya; Liu, Jielin; Jin, Fei; Li, Xiao; Wei, Yongxiang

    2016-07-01

    Left ventricular hypotrophy (LVH) is very common in hypertensives even after antihypertensive treatment. Mitofusin 2 (Mfn2) is a critical negative regulator of vascular smooth muscle cell (VSMC) hypertrophy by regulating mitochondrial fusion, ras/raf/MEK signal pathway, et al. The purpose of this study was to investigate whether candesartan attenuated cardiac remodeling by improving expression and function of mitofusin 2 in SHR. Nine weeks old spontaneously hypertensive rats (SHR) were selected and treated with candesartan for eight weeks. Then, heart tissues were investigated for signs of cardiac remodeling, mitochondrial structure and membrane potential, mitochondrial enzyme activities, hydrogen peroxide, mRNA and protein expression of Mfn2/ras/raf/MEK signaling pathway in heart tissues. The results showed that cardiac remodeling was obviously in SHR group: cardiac cell alignment was irregular; cardiac fibers became thick, irregular and enlarged; cell density was reduced in SHR compared to WKY. After candesartan treatment, histopathological structure improved significantly which were consistent with mitochondrial morphology, mitochondrial membrane potential, mitochondrial enzyme activities, hydrogen peroxide, Mfn2/ras/raf/MEK gene and protein expression in cardiac tissues. What's more, although blood pressure was well controlled in a normal range, cardiac remodeling wasn't avoided. In general, candesartan obviously repressed cardiac hypertrophy and cardiac remodeling significantly compared to SHR untreated group, but didn't reverse it. Mfn2 is negatively associated with cardiac remodeling. Candesartan treatment can improve mitochondrial structure and function and regulate Mfn2/ras/raf/MEK signaling pathway. Mfn2 may be used a potential marker for cardiac remodeling and a novel therapeutic target for target organ damage protection. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  5. Over-expressed CmbT multidrug resistance transporter improves the fitness of Lactococcus lactis

    Directory of Open Access Journals (Sweden)

    Filipić Brankica

    2013-01-01

    Full Text Available The influence of the over-expression of CmbT multidrug resistance transporter on the growth rate of Lactococcus lactis NZ9000 was studied. L. lactis is a lactic acid bacteria (LAB widely used as a starter culture in dairy industry. Recently characterized CmbT MDR transporter in L. lactis confers resistance to a wide variety of toxic compounds as well as to some clinically relevant antibiotics. In this study, the cmbT gene was over-expressed in the strain L. lactis NZ9000 in the presence of nisin inducer. Over-expression of the cmbT gene in L. lactis NZ9000 was followed by RT-PCR. The obtained results showed that the cmbT gene was successfully over-expressed by addition of sub-inhibitory amounts of nisin. Growth curves of L. lactis NZ9000/pCT50 over-expressing the cmbT gene and L. lactis NZ9000 control strain were followed in the rich medium as well as in the chemically defined medium in the presence solely of methionine (0.084 mM or mix of methionine and cysteine (8.4 mM and 8.2 mM, respectively. Resulting doubling times revealed that L. lactis NZ9000/pCT50 had higher growth rate comparing to the control strain. This could be a consequence of the CmbT efflux activity, which improves the fitness of the host bacterium through the elimination of toxic compounds from the cell.

  6. Expressive writing for gay-related stress: psychosocial benefits and mechanisms underlying improvement.

    Science.gov (United States)

    Pachankis, John E; Goldfried, Marvin R

    2010-02-01

    This study tested the effectiveness of an expressive writing intervention for gay men on outcomes related to psychosocial functioning. Seventy-seven gay male college students (mean age = 20.19 years, SD = 1.99) were randomly assigned to write for 20 min a day for 3 consecutive days about either (a) the most stressful or traumatic gay-related event in their lives or (b) a neutral topic. We tested an exposure-based hypothesis of written emotional expression by asking half of the participants who were assigned to write about gay-related stress to read their previous day's narrative before writing, whereas the other half did not. Posttest and 3-month follow-up outcomes were assessed with common measures of overall psychological distress, depression, physical health symptoms, and positive and negative affect. Gay-specific social functioning was assessed with measures of gay-related rejection sensitivity, gay-specific self-esteem, and items regarding openness and comfort with one's sexual orientation. Participants who wrote about gay-related stress, regardless of whether they read their previous day's writing, reported significantly greater openness with their sexual orientation 3 months following writing than participants who wrote about a neutral topic, F(1, 74) = 6.66, p writing, severity of the expressed topic, previous disclosure of writing topic, tendency to conceal, and level of perceived social support on mental health outcomes. The findings suggest that an expressive writing task targeting gay-related stress can improve gay men's psychosocial functioning, especially openness with sexual orientation. The intervention seems to be particularly beneficial for those men who write about more severe topics and for those with lower levels of social support. The findings suggest future tests of expressive writing tasks for different aspects of stigma-related stress.

  7. Improved algorithm for the transmittance estimation of spectra obtained with SOIR/Venus Express.

    Science.gov (United States)

    Trompet, Loic; Mahieux, Arnaud; Ristic, Bojan; Robert, Séverine; Wilquet, Valérie; Thomas, Ian R; Vandaele, Ann Carine; Bertaux, Jean-Loup

    2016-11-10

    The Solar Occultation in the InfraRed (SOIR) instrument onboard the ESA Venus Express spacecraft, an infrared spectrometer sensitive from 2.2 to 4.3 μm, probed the atmosphere of Venus from June 2006 until December 2014. During this time, it performed more than 750 solar occultations of the Venus mesosphere and lower thermosphere. A new procedure has been developed for the estimation of the transmittance in order to decrease the number of rejected spectra, to check that the treated spectra are well calibrated, and to improve the quality of the calibrated spectra by reducing the noise and accurately normalizing it to the solar spectrum.

  8. Paper spray mass spectrometry and PLS-DA improved by variable selection for the forensic discrimination of beers.

    Science.gov (United States)

    Pereira, Hebert Vinicius; Amador, Victória Silva; Sena, Marcelo Martins; Augusti, Rodinei; Piccin, Evandro

    2016-10-12

    Paper spray mass spectrometry (PS-MS) combined with partial least squares discriminant analysis (PLS-DA) was applied for the first time in a forensic context to a fast and effective differentiation of beers. Eight different brands of American standard lager beers produced by four different breweries (141 samples from 55 batches) were studied with the aim at performing a differentiation according to their market prices. The three leader brands in the Brazilian beer market, which have been subject to fraud, were modeled as the higher-price class, while the five brands most used for counterfeiting were modeled as the lower-price class. Parameters affecting the paper spray ionization were examined and optimized. The best MS signal stability and intensity was obtained while using the positive ion mode, with PS(+) mass spectra characterized by intense pairs of signals corresponding to sodium and potassium adducts of malto-oligosaccharides. Discrimination was not apparent neither by using visual inspection nor principal component analysis (PCA). However, supervised classification models provided high rates of sensitivity and specificity. A PLS-DA model using full scan mass spectra were improved by variable selection with ordered predictors selection (OPS), providing 100% of reliability rate and reducing the number of variables from 1701 to 60. This model was interpreted by detecting fifteen variables as the most significant VIP (variable importance in projection) scores, which were therefore considered diagnostic ions for this type of beer counterfeit. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. Statistical Analysis of Automatic Seed Word Acquisition to Improve Harmful Expression Extraction in Cyberbullying Detection

    Directory of Open Access Journals (Sweden)

    Suzuha Hatakeyama

    2016-04-01

    Full Text Available We study the social problem of cyberbullying, defined as a new form of bullying that takes place in the Internet space. This paper proposes a method for automatic acquisition of seed words to improve performance of the original method for the cyberbullying detection by Nitta et al. [1]. We conduct an experiment exactly in the same settings to find out that the method based on a Web mining technique, lost over 30% points of its performance since being proposed in 2013. Thus, we hypothesize on the reasons for the decrease in the performance and propose a number of improvements, from which we experimentally choose the best one. Furthermore, we collect several seed word sets using different approaches, evaluate and their precision. We found out that the influential factor in extraction of harmful expressions is not the number of seed words, but the way the seed words were collected and filtered.

  10. Wide Variability in Caloric Density of Expressed Human Milk Can Lead to Major Underestimation or Overestimation of Nutrient Content.

    Science.gov (United States)

    Sauer, Charles W; Boutin, Mallory A; Kim, Jae H

    2017-05-01

    Very-low-birth-weight infants continue to face significant difficulties with postnatal growth. Human milk is the optimal form of nutrition for infants but may exhibit variation in nutrient content. This study aimed to perform macronutrient analysis on expressed human milk from mothers whose babies are hospitalized in the neonatal intensive care unit. Up to five human milk samples per participant were analyzed for protein, carbohydrate, and fat content using reference chemical analyses (Kjeldahl for protein, high pressure liquid chromatography for carbohydrates, and Mojonnier for fat). Calorie content was calculated. A total of 64 samples from 24 participants was analyzed. Wide variability was found in calorie, protein, carbohydrate, and fat composition. The authors found an average of 17.9 kcal/ounce, with only 34% of samples falling within 10% of the expected caloric density. The assumption that human milk contains 20 kcal/ounce is no longer supported based on this study. This supports promoting an individualized nutrition strategy as a crucial aspect to optimal nutrition.

  11. Utilizing multiple state variables to improve the dynamic range of analog switching in a memristor

    Energy Technology Data Exchange (ETDEWEB)

    Jeong, YeonJoo; Kim, Sungho; Lu, Wei D., E-mail: wluee@eecs.umich.edu [Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, 48109 (United States)

    2015-10-26

    Memristors and memristive systems have been extensively studied for data storage and computing applications such as neuromorphic systems. To act as synapses in neuromorphic systems, the memristor needs to exhibit analog resistive switching (RS) behavior with incremental conductance change. In this study, we show that the dynamic range of the analog RS behavior can be significantly enhanced in a tantalum-oxide-based memristor. By controlling different state variables enabled by different physical effects during the RS process, the gradual filament expansion stage can be selectively enhanced without strongly affecting the abrupt filament length growth stage. Detailed physics-based modeling further verified the observed experimental effects and revealed the roles of oxygen vacancy drift and diffusion processes, and how the diffusion process can be selectively enhanced during the filament expansion stage. These findings lead to more desirable and reliable memristor behaviors for analog computing applications. Additionally, the ability to selectively control different internal physical processes demonstrated in the current study provides guidance for continued device optimization of memristor devices in general.

  12. Improved radiological/nuclear source localization in variable NORM background: An MLEM approach with segmentation data

    Energy Technology Data Exchange (ETDEWEB)

    Penny, Robert D., E-mail: robert.d.penny@leidos.com [Leidos Inc., 10260 Campus Point Road, San Diego, CA (United States); Crowley, Tanya M.; Gardner, Barbara M.; Mandell, Myron J.; Guo, Yanlin; Haas, Eric B.; Knize, Duane J.; Kuharski, Robert A.; Ranta, Dale; Shyffer, Ryan [Leidos Inc., 10260 Campus Point Road, San Diego, CA (United States); Labov, Simon; Nelson, Karl; Seilhan, Brandon [Lawrence Livermore National Laboratory, Livermore, CA (United States); Valentine, John D. [Lawrence Berkeley National Laboratory, Berkeley, CA (United States)

    2015-06-01

    A novel approach and algorithm have been developed to rapidly detect and localize both moving and static radiological/nuclear (R/N) sources from an airborne platform. Current aerial systems with radiological sensors are limited in their ability to compensate for variable naturally occurring radioactive material (NORM) background. The proposed approach suppresses the effects of NORM background by incorporating additional information to segment the survey area into regions over which the background is likely to be uniform. The method produces pixelated Source Activity Maps (SAMs) of both target and background radionuclide activity over the survey area. The task of producing the SAMs requires (1) the development of a forward model which describes the transformation of radionuclide activity to detector measurements and (2) the solution of the associated inverse problem. The inverse problem is ill-posed as there are typically fewer measurements than unknowns. In addition the measurements are subject to Poisson statistical noise. The Maximum-Likelihood Expectation-Maximization (MLEM) algorithm is used to solve the inverse problem as it is well suited for under-determined problems corrupted by Poisson noise. A priori terrain information is incorporated to segment the reconstruction space into regions within which we constrain NORM background activity to be uniform. Descriptions of the algorithm and examples of performance with and without segmentation on simulated data are presented.

  13. Improving Continuous-Variable Measurement-Device-Independent Multipartite Quantum Communication with Optical Amplifiers*

    Science.gov (United States)

    Guo, Ying; Zhao, Wei; Li, Fei; Huang, Duan; Liao, Qin; Xie, Cai-Lang

    2017-08-01

    The developing tendency of continuous-variable (CV) measurement-device-independent (MDI) quantum cryptography is to cope with the practical issue of implementing scalable quantum networks. Up to now, most theoretical and experimental researches on CV-MDI QKD are focused on two-party protocols. However, we suggest a CV-MDI multipartite quantum secret sharing (QSS) protocol use the EPR states coupled with optical amplifiers. More remarkable, QSS is the real application in multipartite CV-MDI QKD, in other words, is the concrete implementation method of multipartite CV-MDI QKD. It can implement a practical quantum network scheme, under which the legal participants create the secret correlations by using EPR states connecting to an untrusted relay via insecure links and applying the multi-entangled Greenberger-Horne-Zeilinger (GHZ) state analysis at relay station. Even if there is a possibility that the relay may be completely tampered, the legal participants are still able to extract a secret key from network communication. The numerical simulation indicates that the quantum network communication can be achieved in an asymmetric scenario, fulfilling the demands of a practical quantum network. Additionally, we illustrate that the use of optical amplifiers can compensate the partial inherent imperfections of detectors and increase the transmission distance of the CV-MDI quantum system.

  14. GH replacement in hypopituitarism improves lipid profile and quality of life independently of changes in obesity variables

    DEFF Research Database (Denmark)

    Abrams, P.; Boquete, H.; Fideleff, H.

    2008-01-01

    OBJECTIVE: GH deficiency (GHD) in adults is characterized by elevated body mass index (BMI), increased waist girth (WG) and increased fat mass (FM). Information about how these indicators of obesity affect the lipid profile and quality of life (QoL) of GHD subjects is scarce. It is also unclear how...... with normal WG, n=434 with increased WG) and FM (n=357) and according to changes in these variables after 1 year of GH replacement. Serum IGF-I concentrations, lipid concentrations and QoL using the QoL Assessment of GHD in Adults questionnaire were assessed at baseline and after 1 year of treatment. RESULTS...... replacement, total and LDL cholesterol and QoL improved in all BMI, WG and FM groups. CONCLUSIONS: Variables of obesity adversely affect the already unfavourable lipid profile in GHD subjects by decreasing HDL cholesterol, but do not counteract the positive effect of GH replacement on LDL cholesterol...

  15. Variable geometry gas turbines for improving the part-load performance of marine combined cycles - Combined cycle performance

    DEFF Research Database (Denmark)

    Haglind, Fredrik

    2011-01-01

    The part-load performance of combined cycles intended for naval use is of great importance, and it is influenced by the gas turbine configuration and load control strategy. This paper is aimed at quantifying the effects of variable geometry gas turbines on the part-load efficiency for combined...... cycles used for ship propulsion. Moreover, the paper is aimed at developing methodologies and deriving models for part-load simulations suitable for energy system analysis of various components within combined cycle power plants. Two different gas turbine configurations are studied, a two-shaft aero......-derivative configuration and a single-shaft industrial configuration. The results suggest that by the use of variable geometry gas turbines, the combined cycle part-load performance can be improved. In order to minimise the voyage fuel consumption, a combined cycle featuring two-shaft gas turbines with VAN control...

  16. Reduced TDP-43 Expression Improves Neuronal Activities in a Drosophila Model of Perry Syndrome

    Directory of Open Access Journals (Sweden)

    Yuka Hosaka

    2017-07-01

    Full Text Available Parkinsonian Perry syndrome, involving mutations in the dynein motor component dynactin or p150Glued, is characterized by TDP-43 pathology in affected brain regions, including the substantia nigra. However, the molecular relationship between p150Glued and TDP-43 is largely unknown. Here, we report that a reduction in TDP-43 protein levels alleviates the synaptic defects of neurons expressing the Perry mutant p150G50R in Drosophila. Dopaminergic expression of p150G50R, which decreases dopamine release, disrupts motor ability and reduces the lifespan of Drosophila. p150G50R expression also causes aggregation of dense core vesicles (DCVs, which contain monoamines and neuropeptides, and disrupts the axonal flow of DCVs, thus decreasing synaptic strength. The above phenotypes associated with Perry syndrome are improved by the removal of a copy of Drosophila TDP-43 TBPH, thus suggesting that the stagnation of axonal transport by dynactin mutations promotes TDP-43 aggregation and interferes with the dynamics of DCVs and synaptic activities.

  17. Modeling and Performance Improvement of the Constant Power Regulator Systems in Variable Displacement Axial Piston Pump

    Directory of Open Access Journals (Sweden)

    Sung Hwan Park

    2013-01-01

    Full Text Available An irregular performance of a mechanical-type constant power regulator is considered. In order to find the cause of an irregular discharge flow at the cut-off pressure area, modeling and numerical simulations are performed to observe dynamic behavior of internal parts of the constant power regulator system for a swashplate-type axial piston pump. The commercial numerical simulation software AMESim is applied to model the mechanical-type regulator with hydraulic pump and simulate the performance of it. The validity of the simulation model of the constant power regulator system is verified by comparing simulation results with experiments. In order to find the cause of the irregular performance of the mechanical-type constant power regulator system, the behavior of main components such as the spool, sleeve, and counterbalance piston is investigated using computer simulation. The shape modification of the counterbalance piston is proposed to improve the undesirable performance of the mechanical-type constant power regulator. The performance improvement is verified by computer simulation using AMESim software.

  18. Modeling and performance improvement of the constant power regulator systems in variable displacement axial piston pump.

    Science.gov (United States)

    Park, Sung Hwan; Lee, Ji Min; Kim, Jong Shik

    2013-01-01

    An irregular performance of a mechanical-type constant power regulator is considered. In order to find the cause of an irregular discharge flow at the cut-off pressure area, modeling and numerical simulations are performed to observe dynamic behavior of internal parts of the constant power regulator system for a swashplate-type axial piston pump. The commercial numerical simulation software AMESim is applied to model the mechanical-type regulator with hydraulic pump and simulate the performance of it. The validity of the simulation model of the constant power regulator system is verified by comparing simulation results with experiments. In order to find the cause of the irregular performance of the mechanical-type constant power regulator system, the behavior of main components such as the spool, sleeve, and counterbalance piston is investigated using computer simulation. The shape modification of the counterbalance piston is proposed to improve the undesirable performance of the mechanical-type constant power regulator. The performance improvement is verified by computer simulation using AMESim software.

  19. Determining variables of plyometric training for improving vertical jump height performance: a meta-analysis.

    Science.gov (United States)

    de Villarreal, Eduardo Saéz-Saez; Kellis, Eleftherios; Kraemer, William J; Izquierdo, Mikel

    2009-03-01

    Plyometric training improves vertical jump height (VJH). However, the effectiveness of plyometric training depends on various factors. A meta-analysis of 56 studies with a total of 225 effect sizes (ESs) was carried out to analyze the role of various factors on the effects of plyometrics on VJH performance. The inclusion criteria for the analysis were a) studies using plyometric programs for lower-limb muscles, b) studies employing true experimental designs and valid and reliable measurements, and c) studies including enough data to calculate ESs. Subjects with more experience in sport obtained greater enhancements in VJH performance (p performance, training volumes of more than 10 weeks and more than 20 sessions, using high-intensity programs (with more than 50 jumps per session), were the strategies that seemed to maximize the probability of obtaining significantly greater improvements in performance (p < 0.05). To optimize jumping enhancement, the combination of different types of plyometrics (squat jump + countermovement jump + drop jump) is recommended rather than using only 1 form (p < 0.05). However, no extra benefits were found to be gained from doing plyometrics with added weight. The responses identified in this analysis are essential and should be considered by strength and conditioning professionals with regard to the most appropriate dose-response trends for optimizing plyometric-induced gains.

  20. Variable phase dark-field contrast--a variant illumination technique for improved visualizations of transparent specimens.

    Science.gov (United States)

    Piper, Timm; Piper, Jörg

    2012-04-01

    Variable phase dark-field contrast has been developed as an illumination technique in light microscopy, which promises significant improvements and a higher variability in imaging of several transparent specimens. In this method, a phase contrast image is optically superimposed on a dark-field image so that a partial image based on the principal zeroth-order maximum (phase contrast) interferes with an image that is based on the secondary maxima (dark field). The background brightness and character of the resulting image can be continuously modulated from a phase-contrast-dominated to a dark-field-dominated character. The condenser aperture diaphragm can be used for modulations of the image's appearance. Specimens can either be illuminated concentrically or obliquely (eccentrically) when parts of the illuminating light beams are covered and blocked. Moreover, a bright-field-like partial image can be added. In this way, the illumination can be optimally adjusted to the specific properties of the specimen. The techniques described can lead to improved visual information especially in biological specimens consisting of phase structures and additional light-absorbing or -reflecting components. Moreover, the specimen's three-dimensionality can be accentuated with improved clarity because the illuminating light beams associated with phase contrast and dark field run to the specimen at different angles of incidence.

  1. Ethnicity moderates the outcomes of self-enhancement and self-improvement themes in expressive writing.

    Science.gov (United States)

    Tsai, William; Lau, Anna S; Niles, Andrea N; Coello, Jordan; Lieberman, Matthew D; Ko, Ahra C; Hur, Christopher; Stanton, Annette L

    2015-10-01

    The current study examined whether writing content related to self-enhancing (viz., downward social comparison and situational attributions) and self-improving (viz., upward social comparison and persistence) motivations were differentially related to expressive writing outcomes among 17 Asian American and 17 European American participants. Content analysis of the essays revealed no significant cultural group differences in the likelihood of engaging in self-enhancing versus self-improving reflections on negative personal experiences. However, cultural group differences were apparent in the relation between self-motivation processes and changes in anxiety and depressive symptoms at 3-month follow-up. Among European Americans, writing that reflected downward social comparison predicted positive outcomes, whereas persistence writing themes were related to poorer outcomes. For Asian Americans, writing about persistence was related to positive outcomes, whereas downward social comparison and situational attributions predicted poorer outcomes. Findings provide evidence suggesting culturally distinct mechanisms for the effects of expressive disclosure. (PsycINFO Database Record (c) 2015 APA, all rights reserved).

  2. Vitamin B12 supplementation improves heart rate variability in healthy elderly Indian subjects.

    Science.gov (United States)

    Sucharita, S; Thomas, T; Antony, B; Vaz, M

    2012-05-21

    While vitamin B(12) deficiency is global, data in elderly Indians are lacking. The problem in India is likely to be higher because of vegetarianism and malabsorption related to gastro-intestinal parasites. Autonomic dysfunction is known to occur much earlier in pernicious anemia. However, what is not known is whether these changes are reflected in healthy elderly individuals. This study assessed cardiac sympathetic and parasympathetic activity using heart rate variability (HRV) in healthy elderly individuals of low and high vitamin B(12) status and evaluated the effect of vitamin B(12) supplementation in those with low vitamin B(12) status. 140 elderly subjects aged ≥60 years were screened; 47 healthy subjects were assessed. They underwent blood sampling, anthropometry, HRV and nerve conduction assessment. Subjects were classified based on vitamin B(12) level (148 pmol/L) into deplete vitamin B(12) and replete vitamin B(12) groups. Elderly subjects with low vitamin B(12) status underwent cyanocobalamin supplementation (100 μg) for 3 months. Low frequency (LF) HRV in absolute units was significantly lower in the low vitamin B(12) group. Following supplementation, LF HRV in absolute units and total power rose significantly as compared to pre-supplementation values for the entire supplemented group. In conclusion, elderly with lower vitamin B(12) status have reduced low frequency HRV suggestive of sympathetic involvement. Supplementation with vitamin B(12) for 3 months results in a significant increase in low frequency HRV to values comparable with unsupplemented, but vitamin B(12) replete elderly. Copyright © 2012 Elsevier B.V. All rights reserved.

  3. BDNF expression in perirhinal cortex is associated with exercise-induced improvement in object recognition memory.

    Science.gov (United States)

    Hopkins, Michael E; Bucci, David J

    2010-09-01

    Physical exercise induces widespread neurobiological adaptations and improves learning and memory. Most research in this field has focused on hippocampus-based spatial tasks and changes in brain-derived neurotrophic factor (BDNF) as a putative substrate underlying exercise-induced cognitive improvements. Chronic exercise can also be anxiolytic and causes adaptive changes in stress-reactivity. The present study employed a perirhinal cortex-dependent object recognition task as well as the elevated plus maze to directly test for interactions between the cognitive and anxiolytic effects of exercise in male Long Evans rats. Hippocampal and perirhinal cortex tissue was collected to determine whether the relationship between BDNF and cognitive performance extends to this non-spatial and non-hippocampal-dependent task. We also examined whether the cognitive improvements persisted once the exercise regimen was terminated. Our data indicate that 4weeks of voluntary exercise every-other-day improved object recognition memory. Importantly, BDNF expression in the perirhinal cortex of exercising rats was strongly correlated with object recognition memory. Exercise also decreased anxiety-like behavior, however there was no evidence to support a relationship between anxiety-like behavior and performance on the novel object recognition task. There was a trend for a negative relationship between anxiety-like behavior and hippocampal BDNF. Neither the cognitive improvements nor the relationship between cognitive function and perirhinal BDNF levels persisted after 2weeks of inactivity. These are the first data demonstrating that region-specific changes in BDNF protein levels are correlated with exercise-induced improvements in non-spatial memory, mediated by structures outside the hippocampus and are consistent with the theory that, with regard to object recognition, the anxiolytic and cognitive effects of exercise may be mediated through separable mechanisms. Copyright 2010 Elsevier

  4. Improved emotional stability in experienced meditators with concentrative meditation based on electroencephalography and heart rate variability.

    Science.gov (United States)

    Lee, Yu-Hao; Shiah, Yung-Jong; Chen, Sharon Chia-Ju; Wang, Shih-Feng; Young, Ming-Shing; Lin, Chih-Lung

    2015-01-01

    To determine whether emotional stability distinguishes how experienced and novice meditators react to visual stimuli. PARTICIPANTS practiced concentrative meditation and then responded to visual stimuli while continuing to meditate. Ten experienced and 10 novice meditators responded to sequences of visual stimuli after concentrative meditation. As predicted, both groups had increased parasympathetic activities during concentrative meditation. Experienced meditators had increased low-frequency electroencephalography (EEG) rhythms in response to visual stimulation, whereas novices had increased high-frequency EEG rhythms. Correlational analyses revealed that novice meditators changed from a meditative state to a nonrelaxed state when the visual stimuli were presented, whereas experienced meditators maintained the meditative state. The study provides evidence that regular concentrative meditation can improve emotional stability and that recording physiologic responses to visual stimuli can be a good method for identifying the effects of long-term concentrative meditation practice.

  5. PTEN overexpression improves cisplatin-resistance of human ovarian cancer cells through upregulating KRT10 expression

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Huijuan; Wang, Ke; Liu, Wenxin; Hao, Quan, E-mail: quan_haotj@126.com

    2014-02-07

    Highlights: • Overexpression of PTEN enhanced the sensitivity of C13K cells to cisplatin. • KRT10 is a downstream molecule of PTEN involved in the resistance-reversing effect. • Overexpression of KRT10 enhanced the chemosensitivity of C13K cells to cisplatin. - Abstract: Multi-drug resistance (MDR) is a common cause of the failure of chemotherapy in ovarian cancer. PTEN, a tumor suppressor gene, has been demonstrated to be able to reverse cisplatin-resistance in ovarian cancer cell line C13K. However, the downstream molecules of PTEN involved in the resistance-reversing effect have not been completely clarified. Therefore, we screened the downstream molecules of PTEN and studied their interactions in C13K ovarian cancer cells using a 3D culture model. Firstly, we constructed an ovarian cancer cell line stably expressing PTEN, C13K/PTEN. MTT assay showed that overexpression of PTEN enhanced the sensitivity of C13K cells to cisplatin, but not to paclitaxel. Then we examined the differently expressed proteins that interacted with PTEN in C13K/PTEN cells with or without cisplatin treatment by co-immunoprecipitation. KRT10 was identified as a differently expressed protein in cisplatin-treated C13K/PTEN cells. Further study confirmed that cisplatin could induce upregulation of KRT10 mRNA and protein in C13K/PTEN cells and there was a directly interaction between KRT10 and PTEN. Forced expression of KRT10 in C13K cells also enhanced cisplatin-induced proliferation inhibition and apoptosis of C13K cells. In addition, KRT10 siRNA blocked cisplatin-induced proliferation inhibition of C13K/PTEN cells. In conclusion, our data demonstrate that KRT10 is a downstream molecule of PTEN which improves cisplatin-resistance of ovarian cancer and forced KRT10 overexpression may also act as a therapeutic method for overcoming MDR in ovarian cancer.

  6. Improved adhesive properties of recombinant bifidobacteria expressing the Bifidobacterium bifidum-specific lipoprotein BopA.

    Science.gov (United States)

    Gleinser, Marita; Grimm, Verena; Zhurina, Daria; Yuan, Jing; Riedel, Christian U

    2012-06-13

    Bifidobacteria belong to one of the predominant bacterial groups in the intestinal microbiota of infants and adults. Several beneficial effects on the health status of their human hosts have been demonstrated making bifidobacteria interesting candidates for probiotic applications. Adhesion of probiotics to the intestinal epithelium is discussed as a prerequisite for colonisation of and persistence in the gastrointestinal tract. In the present study, 15 different strains of bifidobacteria were tested for adhesion. B. bifidum was identified as the species showing highest adhesion to all tested intestinal epithelial cell (IEC) lines. Adhesion of B. bifidum S17 to IECs was strongly reduced after treatment of bacteria with pronase. These results strongly indicate that a proteinaceous cell surface component mediates adhesion of B. bifidum S17 to IECs. In silico analysis of the currently accessible Bifidobacterium genomes identified bopA encoding a lipoprotein as a B. bifidum-specific gene previously shown to function as an adhesin of B. bifidum MIMBb75. The in silico results were confirmed by Southern Blot analysis. Furthermore, Northern Blot analysis demonstrated that bopA is expressed in all B. bifidum strains tested under conditions used to cultivate bacteria for adhesion assays. The BopA gene was successfully expressed in E. coli and purified by Ni-NTA affinity chromatography as a C-terminal His6-fusion. Purified BopA had an inhibitory effect on adhesion of B. bifidum S17 to IECs. Moreover, bopA was successfully expressed in B. bifidum S17 and B. longum/infantis E18. Strains overexpressing bopA showed enhanced adhesion to IECs, clearly demonstrating a role of BopA in adhesion of B. bifidum strains. BopA was identified as a B. bifidum-specific protein involved in adhesion to IECs. Bifidobacterium strains expressing bopA show enhanced adhesion. Our results represent the first report on recombinant bifidobacteria with improved adhesive properties.

  7. Improved adhesive properties of recombinant bifidobacteria expressing the Bifidobacterium bifidum-specific lipoprotein BopA

    Directory of Open Access Journals (Sweden)

    Gleinser Marita

    2012-06-01

    Full Text Available Abstract Background Bifidobacteria belong to one of the predominant bacterial groups in the intestinal microbiota of infants and adults. Several beneficial effects on the health status of their human hosts have been demonstrated making bifidobacteria interesting candidates for probiotic applications. Adhesion of probiotics to the intestinal epithelium is discussed as a prerequisite for colonisation of and persistence in the gastrointestinal tract. Results In the present study, 15 different strains of bifidobacteria were tested for adhesion. B. bifidum was identified as the species showing highest adhesion to all tested intestinal epithelial cell (IEC lines. Adhesion of B. bifidum S17 to IECs was strongly reduced after treatment of bacteria with pronase. These results strongly indicate that a proteinaceous cell surface component mediates adhesion of B. bifidum S17 to IECs. In silico analysis of the currently accessible Bifidobacterium genomes identified bopA encoding a lipoprotein as a B. bifidum-specific gene previously shown to function as an adhesin of B. bifidum MIMBb75. The in silico results were confirmed by Southern Blot analysis. Furthermore, Northern Blot analysis demonstrated that bopA is expressed in all B. bifidum strains tested under conditions used to cultivate bacteria for adhesion assays. The BopA gene was successfully expressed in E. coli and purified by Ni-NTA affinity chromatography as a C-terminal His6-fusion. Purified BopA had an inhibitory effect on adhesion of B. bifidum S17 to IECs. Moreover, bopA was successfully expressed in B. bifidum S17 and B. longum/infantis E18. Strains overexpressing bopA showed enhanced adhesion to IECs, clearly demonstrating a role of BopA in adhesion of B. bifidum strains. Conclusions BopA was identified as a B. bifidum-specific protein involved in adhesion to IECs. Bifidobacterium strains expressing bopA show enhanced adhesion. Our results represent the first report on recombinant

  8. Beyond clay: Towards an improved set of variables for predicting soil organic matter content

    Science.gov (United States)

    Rasmussen, Craig; Heckman, Katherine; Wieder, William R.; Keiluweit, Marco; Lawrence, Corey R.; Berhe, Asmeret Asefaw; Blankinship, Joseph C.; Crow, Susan E.; Druhan, Jennifer; Hicks Pries, Caitlin E.; Marin-Spiotta, Erika; Plante, Alain F.; Schadel, Christina; Schmiel, Joshua P.; Sierra, Carlos A.; Thompson, Aaron; Wagai, Rota

    2018-01-01

    Improved quantification of the factors controlling soil organic matter (SOM) stabilization at continental to global scales is needed to inform projections of the largest actively cycling terrestrial carbon pool on Earth, and its response to environmental change. Biogeochemical models rely almost exclusively on clay content to modify rates of SOM turnover and fluxes of climate-active CO2 to the atmosphere. Emerging conceptual understanding, however, suggests other soil physicochemical properties may predict SOM stabilization better than clay content. We addressed this discrepancy by synthesizing data from over 5,500 soil profiles spanning continental scale environmental gradients. Here, we demonstrate that other physicochemical parameters are much stronger predictors of SOM content, with clay content having relatively little explanatory power. We show that exchangeable calcium strongly predicted SOM content in water-limited, alkaline soils, whereas with increasing moisture availability and acidity, iron- and aluminum-oxyhydroxides emerged as better predictors, demonstrating that the relative importance of SOM stabilization mechanisms scales with climate and acidity. These results highlight the urgent need to modify biogeochemical models to better reflect the role of soil physicochemical properties in SOM cycling.

  9. Suppression of Tla1 gene expression for improved solar conversion efficiency and photosynthetic productivity in plants and algae

    Science.gov (United States)

    Melis, Anastasios; Mitra, Mautusi

    2010-06-29

    The invention provides method and compositions to minimize the chlorophyll antenna size of photosynthesis by decreasing TLA1 gene expression, thereby improving solar conversion efficiencies and photosynthetic productivity in plants, e.g., green microalgae, under bright sunlight conditions.

  10. Total and High Molecular Weight Adiponectin Expression Is Decreased in Patients with Common Variable Immunodeficiency: Correlation with Ig Replacement Therapy

    Directory of Open Access Journals (Sweden)

    Antonio Pecoraro

    2017-07-01

    Full Text Available Adiponectin (Acrp30 is an adipokine widely studied for its beneficial metabolic properties. It circulates as low molecular weight (LMW, medium molecular weight (MMW, and high molecular weight (HMW oligomers. The latter exerts the most potent biological effects. Acrp30 attracted renewed interest with the finding that it was associated with the development and progression of immune disorders. The mechanisms underlying this association and the role of Acrp30 in the pathophysiology of immune-mediated conditions remain unknown. Common variable immunodeficiency (CVID is a primary immunodeficiency characterized by chronic activation of the immune system, impaired antibody production, and imbalanced cytokine production. In the attempt to shed light on the expression of Acrp30 in CVID, we: (a investigated total Acrp30 and its oligomerization state in CVID patients undergoing maintenance Ig replacement therapy; (b assessed the effects of Ig replacement therapy on Acrp30 expression in treatment-naïve CVID patients, namely, patients not treated before diagnosis, before and after the first Ig administration; and (c evaluated the correlation between Acrp30 levels and clinical phenotypes of the disease. As controls, we analyzed healthy subjects and patients affected by a non-immunodeficiency chronic inflammatory demyelinating polyneuropathy (CIDP, before and after Ig infusion. We found that total Acrp30 and HMW oligomers were decreased in CVID but not in CIDP patients versus controls. Moreover, Acrp30 levels were correlated with IgA levels and were associated with two CVID phenotypes, namely, autoimmune cytopenia and enteropathy. Receiver operating characteristic curve analysis indicated that Acrp30 modulation is specific for CVID patients. Acrp30 and HMW levels quickly and dramatically increased after Ig infusion only in eight treatment-naïve CVID patients but not in five CIDP patients. This finding indicates that Ig administration per se is not able to

  11. Expression of variable viruses as herpes simplex glycoprotein D and varicella zoster gE glycoprotein using a novel plasmid based expression system in insect cell

    Directory of Open Access Journals (Sweden)

    A.M. Al-Sulaiman

    2017-11-01

    Full Text Available Several prokaryotic and eukaryotic expression systems have been used for in vitro production of viruses’ proteins. However eukaryotic expression system was always the first choice for production of proteins that undergo post-translational modification such as glycosylation. Recombinant baculoviruses have been widely used as safe vectors to express heterologous genes in the culture of insect cells, but the manipulation involved in creating, titrating, and amplifying viral stocks make it time consuming and laborious. Therefore, to facilitate rapid expression in insect cell, a plasmid based expression system was used to express herpes simplex type 1 glycoprotein D (HSV-1 gD and varicella zoster glycoprotein E (VZV gE. Recombinant plasmids were generated, transfected into insect cells (SF9, and both glycoproteins were expressed 48 h post-infection. A protein with approximately molecular weight of 64-kDa and 98-kDa for HSV-1 gD and VZV gE respectively was expressed and confirmed by SDS. Proteins were detected in insect cells cytoplasm and outer membrane by immunofluorescence. The antigenicity and immunoreactivity of each protein were confirmed by immunoblot and ELISA. Results suggest that this system can be an alternative to the traditional baculovirus expression for small scale expression system in insect cells.

  12. Revised cloud processes to improve the mean and intraseasonal variability of Indian summer monsoon in climate forecast system: Part 1

    Science.gov (United States)

    Abhik, S.; Krishna, R. P. M.; Mahakur, M.; Ganai, Malay; Mukhopadhyay, P.; Dudhia, J.

    2017-06-01

    The National Centre for Environmental Prediction (NCEP) Climate Forecast System (CFS) is being used for operational monsoon prediction over the Indian region. Recent studies indicate that the moist convective process in CFS is one of the major sources of uncertainty in monsoon predictions. In this study, the existing simple cloud microphysics of CFS is replaced by the six-class Weather Research Forecasting (WRF) single moment (WSM6) microphysical scheme. Additionally, a revised convective parameterization is employed to improve the performance of the model in simulating the boreal summer mean climate and intraseasonal variability over the Indian summer monsoon (ISM) region. The revised version of the model (CFSCR) exhibits a potential to improve shortcomings in the seasonal mean precipitation distribution relative to the standard CFS (CTRL), especially over the ISM region. Consistently, notable improvements are also evident in other observed ISM characteristics. These improvements are found to be associated with a better simulation of spatial and vertical distributions of cloud hydrometeors in CFSCR. A reasonable representation of the subgrid-scale convective parameterization along with cloud hydrometeors helps to improve the convective and large-scale precipitation distribution in the model. As a consequence, the simulated low-frequency boreal summer intraseasonal oscillation (BSISO) exhibits realistic propagation and the observed northwest-southeast rainband is well reproduced in CFSCR. Additionally, both the high and low-frequency BSISOs are better captured in CFSCR. The improvement of low and high-frequency BSISOs in CFSCR is shown to be related to a realistic phase relationship of clouds.Plain Language SummaryThis study attempts to demonstrate the impact of better representation of cloud processes on simulating the mean and intraseasonal variability of Indian summer monsoon in a revised version of CFSv2 called CFSCR. The CFSCR shows better fidelity in

  13. Improved methods and resources for paramecium genomics: transcription units, gene annotation and gene expression.

    Science.gov (United States)

    Arnaiz, Olivier; Van Dijk, Erwin; Bétermier, Mireille; Lhuillier-Akakpo, Maoussi; de Vanssay, Augustin; Duharcourt, Sandra; Sallet, Erika; Gouzy, Jérôme; Sperling, Linda

    2017-06-26

    The 15 sibling species of the Paramecium aurelia cryptic species complex emerged after a whole genome duplication that occurred tens of millions of years ago. Given extensive knowledge of the genetics and epigenetics of Paramecium acquired over the last century, this species complex offers a uniquely powerful system to investigate the consequences of whole genome duplication in a unicellular eukaryote as well as the genetic and epigenetic mechanisms that drive speciation. High quality Paramecium gene models are important for research using this system. The major aim of the work reported here was to build an improved gene annotation pipeline for the Paramecium lineage. We generated oriented RNA-Seq transcriptome data across the sexual process of autogamy for the model species Paramecium tetraurelia. We determined, for the first time in a ciliate, candidate P. tetraurelia transcription start sites using an adapted Cap-Seq protocol. We developed TrUC, multi-threaded Perl software that in conjunction with TopHat mapping of RNA-Seq data to a reference genome, predicts transcription units for the annotation pipeline. We used EuGene software to combine annotation evidence. The high quality gene structural annotations obtained for P. tetraurelia were used as evidence to improve published annotations for 3 other Paramecium species. The RNA-Seq data were also used for differential gene expression analysis, providing a gene expression atlas that is more sensitive than the previously established microarray resource. We have developed a gene annotation pipeline tailored for the compact genomes and tiny introns of Paramecium species. A novel component of this pipeline, TrUC, predicts transcription units using Cap-Seq and oriented RNA-Seq data. TrUC could prove useful beyond Paramecium, especially in the case of high gene density. Accurate predictions of 3' and 5' UTR will be particularly valuable for studies of gene expression (e.g. nucleosome positioning, identification of cis

  14. Impact of Narrative Expressive Writing on Heart Rate, Heart Rate Variability, and Blood Pressure After Marital Separation.

    Science.gov (United States)

    Bourassa, Kyle J; Allen, John J B; Mehl, Matthias R; Sbarra, David A

    Divorce is a common stressor that is associated with increased risk for poor long-term physical and mental health. Using an experimental design, the current study examined the impact of expressive writing (EW) on average heart rate (HR), HR variability (HRV), and blood pressure (BP) 7.5 months later. Participants from a community sample of recently separated adults (N = 109) were assigned to one of three conditions: traditional EW, narrative EW, or a control writing condition, and were assessed three times for an average of 7.5 months. Each study visit included 27 minutes of physiological assessment; the primary outcomes at each assessment were mean-level HR, HRV, BP scores averaged across six different tasks. Participants in the traditional EW condition did not significantly differ from control participants in their later HR, HRV, or BP. However, relative to control participants, those in the narrative EW condition had significantly lower HR (B = -3.41, 95% confidence interval = -5.76 to -1.06, p = .004) and higher HRV 7.5 months later (B = 0.41, 95% confidence interval = 0.16 to 0.74, p = .001). When comparing narrative EW participants to those in the traditional EW and control writing as a single group, these effects remained and were moderately sized, Cohen d values of -0.61 and 0.60, respectively, and durable across all task conditions when analyzed in independent models. The writing condition groups did not differ in their later BP. Narrative EW decreased HR and increased HRV after marital separation but did not affect BP. We discuss the possible disconnect between psychology and physiology in response to EW, as well as possible future clinical applications after marital separation.

  15. The expression of RoTat 1.2 variable surface glycoprotein (VSG) in Trypanosoma evansi and T. equiperdum.

    Science.gov (United States)

    Claes, F; Verloo, D; De Waal, D T; Majiwa, P A O; Baltz, T; Goddeeris, B M; Büscher, P

    2003-10-20

    In order to define whether the variable antigenic type RoTat 1.2 is restricted to Trypansoma evansi and could be used as antigen in serological tests to differentiate T. evansi from Trypansoma equiperdum, the appearance of RoTat 1.2-specific antibodies in rabbits, experimentally infected with T. evansi and T. equiperdum, respectively, was analyzed. Ten strains of T. evansi and 11 strains of T. equiperdum originating from Asia, Europe, Africa and Latin America were tested. Rabbit pre-infection sera and sera of days 7, 14, 25, 35 post-infection (p.i.) were analyzed for the presence of antibodies reactive with RoTat 1.2 in immune trypanolysis, ELISA/T. evansi and CATT/T. evansi. Within the duration of the infection (maximum 35 days), all T. evansi as well as 9 out of 11 T. equiperdum infected rabbits became positive in all these tests. The rabbits infected with T. equiperdum OVI (South Africa) and BoTat 1.1 (Morocco) remained negative in the immune trypanolysis test although the latter rabbit became positive in the CATT/T. evansi and ELISA/T. evansi. On the contrary, both rabbits were positive in immune trypanolysis when tested against their respective infecting population. From these data, we conclude that most T. equiperdum strains express isoVATs of RoTat 1.2. This explains, in part, why antibody tests based on T. evansi RoTat 1.2 cannot reliably distinguish between infections caused by T. evansi and those caused by T. equiperdum unless it can be proven that most described T. equiperdum are actually misclassified T. evansi.

  16. Improvement of the R-SWAT-FME framework to support multiple variables and multi-objective functions

    Science.gov (United States)

    Wu, Yiping; Liu, Shu-Guang

    2014-01-01

    Application of numerical models is a common practice in the environmental field for investigation and prediction of natural and anthropogenic processes. However, process knowledge, parameter identifiability, sensitivity, and uncertainty analyses are still a challenge for large and complex mathematical models such as the hydrological/water quality model, Soil and Water Assessment Tool (SWAT). In this study, the previously developed R program language-SWAT-Flexible Modeling Environment (R-SWAT-FME) was improved to support multiple model variables and objectives at multiple time steps (i.e., daily, monthly, and annually). This expansion is significant because there is usually more than one variable (e.g., water, nutrients, and pesticides) of interest for environmental models like SWAT. To further facilitate its easy use, we also simplified its application requirements without compromising its merits, such as the user-friendly interface. To evaluate the performance of the improved framework, we used a case study focusing on both streamflow and nitrate nitrogen in the Upper Iowa River Basin (above Marengo) in the United States. Results indicated that the R-SWAT-FME performs well and is comparable to the built-in auto-calibration tool in multi-objective model calibration. Overall, the enhanced R-SWAT-FME can be useful for the SWAT community, and the methods we used can also be valuable for wrapping potential R packages with other environmental models.

  17. Collaborative Proposal: Improving Decadal Prediction of Arctic Climate Variability and Change Using a Regional Arctic System Model (RASM)

    Energy Technology Data Exchange (ETDEWEB)

    Maslowski, Wieslaw [Naval Postgraduate School, Monterey, CA (United States)

    2016-10-17

    This project aims to develop, apply and evaluate a regional Arctic System model (RASM) for enhanced decadal predictions. Its overarching goal is to advance understanding of the past and present states of arctic climate and to facilitate improvements in seasonal to decadal predictions. In particular, it will focus on variability and long-term change of energy and freshwater flows through the arctic climate system. The project will also address modes of natural climate variability as well as extreme and rapid climate change in a region of the Earth that is: (i) a key indicator of the state of global climate through polar amplification and (ii) which is undergoing environmental transitions not seen in instrumental records. RASM will readily allow the addition of other earth system components, such as ecosystem or biochemistry models, thus allowing it to facilitate studies of climate impacts (e.g., droughts and fires) and of ecosystem adaptations to these impacts. As such, RASM is expected to become a foundation for more complete Arctic System models and part of a model hierarchy important for improving climate modeling and predictions.

  18. Variable-speed belt conveyor systems improve economy in operation; Drehzahlgeregelte Bandanlagen verbessern die betriebswirtschaftlichen Kennzahlen

    Energy Technology Data Exchange (ETDEWEB)

    Keller, C.; Neuffer, I.; Weber, D. [Siemens AG, Erlangen (Germany). Bereich Anlagenbau und Technische Dienstleistungen (ATD)

    1999-03-01

    Previous large conveyor system solutions were a compromise between mechanical design and electrical drive technology, usually based on slipring motors for cost reasons. Today`s power electronics systems now make it possible to use medium-voltage frequency converters in large conveyor systems. This new technology opens up design solutions with torque control that yield distinctly better behaviour under load fluctuation conditions, thereby reducing wear and tear. Experience gained from completed projects has shown that a higher-level load-dependent conveyor speed control can achieve energy savings of up to 20%, since material flows tend to be stochastic rather than constant. Maximum speed is required for short periods only and can therefore be obtained by means of field weakening, a higher gear ratio and short-time overshooting of the rated motor current. This permits the use of motors with smaller frame sizes. Furthermore, in view of the controlled torque and shorter belt runs, it is conceivable that built-in safety margins could be reduced. The solution presented here shows how a distinct improvement in cost efficiency can be attained. (orig.) [Deutsch] Bisherige Loesungen fuer grosse Bandanlagen sind ein Kompromiss zwischen mechanischer Konstruktion und elektrischer Antriebstechnik, bei der aus Kostengruenden meist Schleifringlaeufermotoren eingesetzt werden. Aufgrund der Moeglichkeiten, die die Leistungselektronik heute bietet, ist ein Einsatz von Mittelspannungsumrichtern auch auf diesem Gebiet realisierbar. Damit sind Loesungen moeglich, die besonders durch ein gefuehrtes Moment ein deutlich verbessertes Verhalten bei Momenten- oder Lastaenderungen herbeifuehren und damit eine materialschonende Betriebsweise ermoeglichen. Ausserdem hat sich bei ausgefuehrten Anlagen gezeigt, dass sich durch eine uebergeordnete foerderleistungsabhaengige Bandgeschwindigkeitsregelung auch Energie bis zu 20% einsparen laesst, da der Materialfluss nicht stetig, sondern eher

  19. Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes

    Directory of Open Access Journals (Sweden)

    Eils Roland

    2005-11-01

    Full Text Available Abstract Background The extensive use of DNA microarray technology in the characterization of the cell transcriptome is leading to an ever increasing amount of microarray data from cancer studies. Although similar questions for the same type of cancer are addressed in these different studies, a comparative analysis of their results is hampered by the use of heterogeneous microarray platforms and analysis methods. Results In contrast to a meta-analysis approach where results of different studies are combined on an interpretative level, we investigate here how to directly integrate raw microarray data from different studies for the purpose of supervised classification analysis. We use median rank scores and quantile discretization to derive numerically comparable measures of gene expression from different platforms. These transformed data are then used for training of classifiers based on support vector machines. We apply this approach to six publicly available cancer microarray gene expression data sets, which consist of three pairs of studies, each examining the same type of cancer, i.e. breast cancer, prostate cancer or acute myeloid leukemia. For each pair, one study was performed by means of cDNA microarrays and the other by means of oligonucleotide microarrays. In each pair, high classification accuracies (> 85% were achieved with training and testing on data instances randomly chosen from both data sets in a cross-validation analysis. To exemplify the potential of this cross-platform classification analysis, we use two leukemia microarray data sets to show that important genes with regard to the biology of leukemia are selected in an integrated analysis, which are missed in either single-set analysis. Conclusion Cross-platform classification of multiple cancer microarray data sets yields discriminative gene expression signatures that are found and validated on a large number of microarray samples, generated by different laboratories and

  20. Aerobic exercise + weight loss decreases skeletal muscle myostatin expression and improves insulin sensitivity in older adults.

    Science.gov (United States)

    Ryan, A S; Li, G; Blumenthal, J B; Ortmeyer, H K

    2013-07-01

    To determine whether aerobic exercise training + weight loss (AEX + WL) would affect the expression of myostatin and its relationship with insulin sensitivity in a longitudinal, clinical intervention study. Thirty-three obese sedentary postmenopausal women and men (n = 17 and 16, age: 61 ± 1 years, body mass index: 31 ± 1 kg/m(2) , VO2 max: 21.9 ± 1.0 mL/kg/min, X ± Standard error of the mean (SEM)) completed 6 months of 3 days/week AEX + WL. During an 80 mU m(-2) min(-1) hyperinsulinemic-euglycemic clamp, we measured glucose utilization (M), myostatin, myogenin, and MyoD gene expression by real-time RT-PCR in vastus lateralis muscle at baseline and 2 h. Body weight (-8%) and fat mass (-17%) decreased after AEX + WL (P Fat-free mass (FFM) and mid-thigh muscle area by computed tomography did not change but muscle attenuation increased (P weight loss results in a downregulation of myostatin mRNA and an improvement in insulin sensitivity in obese older men and women. Copyright © 2012 The Obesity Society.

  1. An improved method for purification and refolding of recombinant HIV Vif expressed in Escherichia coli.

    Science.gov (United States)

    Duarte, Carlos A; Palomino, Mickel

    2017-02-08

    Virion infectivity factor (Vif) is a 23 kDa protein that protects HIV-1 from deamination of its proviral DNA by APOBEC3G. The active form of Vif is a multimer that interacts simultaneously with CBF-beta, the elongin B and C subunits, Cullin 5, and APOBEC3G to form a ubiquitin ligase complex targeting the latter for degradation. Vif clearly represents an attractive target for developing novel antiviral drugs for the therapy of HIV/AIDS, and this goal requires a source of well folded, readily available protein. For that purpose, we have cloned Vif in the pET28a expression vector, expressing the resulting His-tagged recombinant protein in the BL21(DE3) Escherichia coli strain. After lysis, Vif was solubilized from the insoluble fraction with 6 M guanidinium chloride and purified by denaturing immobilized-metal affinity chromatography, refolding the protein afterwards by dialysis. The use of 2-(N-morpholino)ethanesulfonic acid buffer at pH 6.2 and the presence of EDTA improved Vif refolding yields by reducing the formation of insoluble aggregates. The purified protein was bound by two monoclonal antibodies against sequential and conformational epitopes located at the C and N terminus, respectively. © 2017 International Union of Biochemistry and Molecular Biology, Inc.

  2. The Use of Chromatin Insulators to Improve the Expression and Safety of Integrating Gene Transfer Vectors

    Science.gov (United States)

    2011-01-01

    Abstract The therapeutic application of recombinant retroviruses and other integrating gene transfer vectors has been limited by problems of vector expression and vector-mediated genotoxicity. These problems arise in large part from the interactions between vector sequences and the genomic environment surrounding sites of integration. Strides have been made in overcoming both of these problems through the modification of deleterious vector sequences, the inclusion of better enhancers and promoters, and the use of alternative virus systems. However, these modifications often add other restrictions on vector design, which in turn can further limit therapeutic applications. As an alternative, several groups have been investigating a class of DNA regulatory elements known as chromatin insulators. These elements provide a means of blocking the interaction between an integrating vector and the target cell genome in a manner that is independent of the vector transgene, regulatory elements, or virus of origin. This review outlines the background, rationale, and evidence for using chromatin insulators to improve the expression and safety of gene transfer vectors. Also reviewed are topological factors that constrain the use of insulators in integrating gene transfer vectors, alternative sources of insulators, and the role of chromatin insulators as one of several components for optimal vector design. PMID:21247248

  3. Improved microarray gene expression profiling of virus-infected cells after removal of viral RNA

    Directory of Open Access Journals (Sweden)

    Rottier Peter JM

    2008-05-01

    Full Text Available Abstract Background Sensitivity and accuracy are key points when using microarrays to detect alterations in gene expression under different conditions. Critical to the acquisition of reliable results is the preparation of the RNA. In the field of virology, when analyzing the host cell's reaction to infection, the often high representation of viral RNA (vRNA within total RNA preparations from infected cells is likely to interfere with microarray analysis. Yet, this effect has not been investigated despite the many reports that describe gene expression profiling of virus-infected cells using microarrays. Results In this study we used coronaviruses as a model to show that vRNA indeed interferes with microarray analysis, decreasing both sensitivity and accuracy. We also demonstrate that the removal of vRNA from total RNA samples, by means of virus-specific oligonucleotide capturing, significantly reduced the number of false-positive hits and increased the sensitivity of the method as tested on different array platforms. Conclusion We therefore recommend the specific removal of vRNA, or of any other abundant 'contaminating' RNAs, from total RNA samples to improve the quality and reliability of microarray analyses.

  4. A Link-Based Cluster Ensemble Approach For Improved Gene Expression Data Analysis

    Directory of Open Access Journals (Sweden)

    P.Balaji

    2015-01-01

    Full Text Available Abstract It is difficult from possibilities to select a most suitable effective way of clustering algorithm and its dataset for a defined set of gene expression data because we have a huge number of ways and huge number of gene expressions. At present many researchers are preferring to use hierarchical clustering in different forms this is no more totally optimal. Cluster ensemble research can solve this type of problem by automatically merging multiple data partitions from a wide range of different clusterings of any dimensions to improve both the quality and robustness of the clustering result. But we have many existing ensemble approaches using an association matrix to condense sample-cluster and co-occurrence statistics and relations within the ensemble are encapsulated only at raw level while the existing among clusters are totally discriminated. Finding these missing associations can greatly expand the capability of those ensemble methodologies for microarray data clustering. We propose general K-means cluster ensemble approach for the clustering of general categorical data into required number of partitions.

  5. Using Improved Entropy-Cloud Model to Select High-Speed Railway Express Freight Train Service Sites

    Directory of Open Access Journals (Sweden)

    Wencheng Huang

    2017-01-01

    Full Text Available High-speed railway (HSR express freight train service sites selection is critical to the development of China’s Third Party Logistics market. In this paper, we formulate an improved entropy-cloud model based approach to solve the HSR express sites selection problem for the first time. The basic data of the indicators, for example, existing railway network conditions, traffic environment, express freight market demand, and policy, will be used as the inputs. We apply improved entropy method to obtain each subindicator’s weight. The cloud model will be used to select and classify each station under evaluation.

  6. A jasmonic acid derivative improves skin healing and induces changes in proteoglycan expression and glycosaminoglycan structure.

    Science.gov (United States)

    Henriet, Elodie; Jäger, Sibylle; Tran, Christian; Bastien, Philippe; Michelet, Jean-François; Minondo, Anne-Marie; Formanek, Florian; Dalko-Csiba, Maria; Lortat-Jacob, Hugues; Breton, Lionel; Vivès, Romain R

    2017-09-01

    Jasmonates are plant hormones that exhibit anti-cancer and anti-inflammatory properties and have therefore raised interest for human health applications. The molecular basis of these activities remains poorly understood, although increasing evidence suggests that a variety of mechanisms may be involved. Recently, we have reported that a jasmonate derivative (JAD) displayed anti-aging effects on human skin by inducing extracellular matrix (ECM) remodeling. Based on this observation, we have investigated here the effects of JAD on proteoglycans and glycosaminoglycan (GAG) polysaccharides, which are major cell-surface/ECM components and are involved in a multitude of biological processes. In parallel, we have examined the ability of JAD to promote growth factor activities and improve skin wound healing. Proteoglycan expression was analyzed on epidermal primary keratinocytes and reconstituted skin epidermis, using electron/immunofluorescence microscopy, western blotting and flow cytometry. GAG composition was determined by disaccharide analysis. Finally, biological activities of JAD were assessed in cellulo, in FGF-7 induced migration/proliferation assays, as well as in vivo, using a suction blister model performed on 24 healthy volunteers. JAD was found to induce expression of major skin proteoglycans and to induce subtle changes in GAG structure. In parallel, we showed that JAD promoted FGF-7 and improved skin healing by accelerating epithelial repair in vivo. This study highlights JAD as a promising compound for investigating GAG structure-function relationships and for applications in skin cosmetic /corrective strategies. We propose here a novel mechanism, by which jasmonate derivatives may elicit biological activities in mammals. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Expression

    Directory of Open Access Journals (Sweden)

    Wang-Xia Wang

    2014-02-01

    Full Text Available The miR-15/107 family comprises a group of 10 paralogous microRNAs (miRNAs, sharing a 5′ AGCAGC sequence. These miRNAs have overlapping targets. In order to characterize the expression of miR-15/107 family miRNAs, we employed customized TaqMan Low-Density micro-fluid PCR-array to investigate the expression of miR-15/107 family members, and other selected miRNAs, in 11 human tissues obtained at autopsy including the cerebral cortex, frontal cortex, primary visual cortex, thalamus, heart, lung, liver, kidney, spleen, stomach and skeletal muscle. miR-103, miR-195 and miR-497 were expressed at similar levels across various tissues, whereas miR-107 is enriched in brain samples. We also examined the expression patterns of evolutionarily conserved miR-15/107 miRNAs in three distinct primary rat brain cell preparations (enriched for cortical neurons, astrocytes and microglia, respectively. In primary cultures of rat brain cells, several members of the miR-15/107 family are enriched in neurons compared to other cell types in the central nervous system (CNS. In addition to mature miRNAs, we also examined the expression of precursors (pri-miRNAs. Our data suggested a generally poor correlation between the expression of mature miRNAs and their precursors. In summary, we provide a detailed study of the tissue and cell type-specific expression profile of this highly expressed and phylogenetically conserved family of miRNA genes.

  8. Combined strategies for improving expression of Citrobacter amalonaticus phytase in Pichia pastoris.

    Science.gov (United States)

    Li, Cheng; Lin, Ying; Zheng, Xueyun; Pang, Nuo; Liao, Xihao; Liu, Xiaoxiao; Huang, Yuanyuan; Liang, Shuli

    2015-09-26

    Phytase is used as an animal feed additive that degrades phytic acid and reduces feeding costs and pollution caused by fecal excretion of phosphorus. Some phytases have been expressed in Pichia pastoris, among which the phytase from Citrobacter amalonaticus CGMCC 1696 had high specific activity (3548 U/mg). Improvement of the phytase expression level will contribute to facilitate its industrial applications. To improve the phytase expression, we use modification of P AOX1 and the α-factor signal peptide, increasing the gene copy number, and overexpressing HAC1 (i) to enhance folding and secretion of the protein in the endoplasmic reticulum. The genetic stability and fermentation in 10-L scaled-up fed-batch fermenter was performed to prepare for the industrial production. The phytase gene from C. amalonaticus CGMCC 1696 was cloned under the control of the AOX1 promoter (P AOX1 ) and expressed in P. pastoris. The phytase activity achieved was 414 U/mL. Modifications of P AOX1 and the α-factor signal peptide increased the phytase yield by 35 and 12%, respectively. Next, on increasing the copy number of the Phy gene to six, the phytase yield was 141% higher than in the strain containing only a single gene copy. Furthermore, on overexpression of HAC1 (i) (i indicating induced), a gene encoding Hac1p that regulates the unfolded protein response, the phytase yield achieved was 0.75 g/L with an activity of 2119 U/mL, 412% higher than for the original strain. The plasmids in this high-phytase expression strain were stable during incubation at 30 °C in Yeast Extract Peptone Dextrose (YPD) Medium. In a 10-L scaled-up fed-batch fermenter, the phytase yield achieved was 9.58 g/L with an activity of 35,032 U/mL. The production of a secreted protein will reach its limit at a specific gene copy number where further increases in transcription and translation due to the higher abundance of gene copies will not enhance the secretion process any further. Enhancement of protein

  9. Improvement of desulfurizing activity of haloalkaliphilic Thialkalivibrio versutus SOB306 with the expression of Vitreoscilla hemoglobin gene.

    Science.gov (United States)

    Mu, Tingzhen; Yang, Maohua; Zhao, Jixiang; Sharshar, Moustafa Mohammed; Tian, Jiangnan; Xing, Jianmin

    2017-03-01

    To construct efficient transformation and expression system and further improve desulfurizing activity of cells through expression of Vitreoscilla hemoglobin (VHb) in haloalkaliphilic Thialkalivibrio versutus SOB306. We transferred plasmids pKT230 and pBBR-smr into T. versutus SOB306 via a conjugation method. We identified four promoters from among several predicted promoters by scoring for streptomycin resistance, and finally selected tac and p3 based on the efficiency of expression of red fluorescent protein (RFP). Expression of RFP when regulated by tac was more than three times that of p3 in SOB306. Further, we expressed VHb under the control of tac promoter in SOB306. Expression of VHb was verified using CO-difference spectra. The results showed that VHb expression can boost sulfur metabolism, as evidenced by an increase of about 11.7 ± 1.8% in the average rate of thiosulfate removal in the presence of VHb. A conjugation transfer and an expression system for Thialkalivibrio, has been developed for the first time and used for expression of VHb to improve desulfurizing activity.

  10. N-Glycosylation Engineering to Improve the Constitutive Expression of Rhizopus oryzae Lipase in Komagataella phaffii.

    Science.gov (United States)

    Yu, Xiao-Wei; Yang, Min; Jiang, Chuanhuan; Zhang, Xiaofeng; Xu, Yan

    2017-07-26

    Our previous studies demonstrated that the N-glycans in Rhizopus chinensis lipase (RCL) was important for its secretion. In order to improve the secretion of Rhizopus oryzae lipase (ROL) under the control of the GAP promoter in Komagataella phaffii, two extra N-glycosylation sites were introduced in ROL according to the position of the N-glycosylation sites of RCL by sequence alignment. The results indicated that the secretion level of ROL was strongly improved by N-glycosylation engineering, and the highest value of extracellular enzyme activity was increased from 0.4 ± 0.2 U/mL to 207 ± 6 U/mL in a shake flask. In the 7-L fermenter, the extracellular enzyme activity of the mutant (2600 ± 43 U/mL) and the total protein concentration (2.5 ± 0.2 g/L) were 218- and 6.25-fold higher than these of the parent, respectively. This study presents a strategy for constitutive recombinant expression of ROL using the GAP promoter combined with N-glycosylation engineering, providing a potential enzyme for application in the food industry.

  11. Water-deficit inducible expression of a cytokinin biosynthetic gene IPT improves drought tolerance in cotton.

    Directory of Open Access Journals (Sweden)

    Sundaram Kuppu

    Full Text Available Water-deficit stress is a major environmental factor that limits agricultural productivity worldwide. Recent episodes of extreme drought have severely affected cotton production in the Southwestern USA. There is a pressing need to develop cotton varieties with improved tolerance to water-deficit stress for sustainable production in water-limited regions. One approach to engineer drought tolerance is by delaying drought-induced senescence via up-regulation of cytokinin biosynthesis. The isopentenyltransferase gene (IPT that encodes a rate limiting enzyme in cytokinin biosynthesis, under the control of a water-deficit responsive and maturation specific promoter P(SARK was introduced into cotton and the performance of the P(SARK::IPT transgenic cotton plants was analyzed in the greenhouse and growth chamber conditions. The data indicate that P(SARK::IPT-transgenic cotton plants displayed delayed senescence under water deficit conditions in the greenhouse. These plants produced more root and shoot biomass, dropped fewer flowers, maintained higher chlorophyll content, and higher photosynthetic rates under reduced irrigation conditions in comparison to wild-type and segregated non-transgenic lines. Furthermore, P(SARK::IPT-transgenic cotton plants grown in growth chamber condition also displayed greater drought tolerance. These results indicate that water-deficit induced expression of an isopentenyltransferase gene in cotton could significantly improve drought tolerance.

  12. Improving starch yield in cereals by over-expression of ADPglucose pyrophosphorylase: expectations and unanticipated outcomes.

    Science.gov (United States)

    Tuncel, Aytug; Okita, Thomas W

    2013-10-01

    Significant improvements in crop productivity are required to meet the nutritional requirements of a growing world population. This challenge is magnified by an increased demand for bioenergy as a means to mitigate carbon inputs into the environment. Starch is a major component of the harvestable organs of many crop plants, and various endeavors have been taken to improve the yields of starchy organs through the manipulation of starch synthesis. Substantial efforts have centered on the starch regulatory enzyme ADPglucose pyrophosphorylase (AGPase) due to its pivotal role in starch biosynthesis. These efforts include over-expression of this enzyme in cereal plants such as maize, rice and wheat as well as potato and cassava, as they supply the bulk of the staple food worldwide. In this perspective, we describe efforts to increase starch yields in cereal grains by first providing an introduction about the importance of source-sink relationship and the motives behind the efforts to alter starch biosynthesis and turnover in leaves. We then discuss the catalytic and regulatory properties of AGPase and the molecular approaches used to enhance starch synthesis by manipulation of this process during grain filling using seed-specific promoters. Several studies have demonstrated increases in starch content per seed using endosperm-specific promoters, but other studies have demonstrated an increase in seed number with only marginal impact on seed weight. Potential mechanisms that may be responsible for this paradoxical increase in seed number will also be discussed. Finally, we describe current efforts and future prospects to improve starch yield in cereals. These efforts include further enhancement of starch yield in rice by augmenting the process of ADPglucose transport into amyloplast as well as other enzymes involved in photoassimilate partitioning in seeds. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  13. Improvements in Force Variability and Structure from Vision- to Memory-Guided Submaximal Isometric Knee Extension in Subacute Stroke.

    Science.gov (United States)

    Chow, John W; Stokic, Dobrivoje S

    2017-11-02

    We examined changes in variability, accuracy, frequency composition, and temporal regularity of force signal from vision-guided to memory-guided force-matching tasks in 17 subacute stroke and 17 age-matched healthy subjects. Subjects performed a unilateral isometric knee extension at 10%, 30%, and 50% of peak torque (MVC) for 10 s (3 trials each). Visual feedback was removed at the 5s-mark in the first 2 trials (feedback withdrawal), and 30 s after the second trial the subjects were asked to produce the target force without visual feedback (force recall). The coefficient of variation and constant error were used to quantify force variability and accuracy. Force structure was assessed by the median frequency, relative spectral power in the 0-3 Hz band, and sample entropy of the force signal. At 10% MVC, the force signal in subacute stroke subjects became steadier, more broadband, and temporally more irregular after the withdrawal of visual feedback, with progressively larger error at higher contraction levels. Also, the lack of modulation in the spectral frequency at higher force levels with visual feedback persisted in both the withdrawal and recall conditions. In terms of changes from the visual feedback condition, the feedback withdrawal produced a greater difference between the paretic, non-paretic, and control legs than the force recall. The overall results suggest improvements in force variability and structure from vision- to memory-guided force control in subacute stroke despite decreased accuracy. Different sensory-motor memory retrieval mechanisms seem to be involved in the feedback withdrawal and force recall conditions, which deserves further studies.

  14. Using an improved understanding of current climate variability to develop increased drought resilience in UK irrigated agriculture

    Science.gov (United States)

    Holman, I.; Rey Vicario, D.

    2016-12-01

    Improving community preparedness for climate change can be supported by developing resilience to past events, focused on those changes of particular relevance (such as floods and droughts). However, communities' perceptions of impacts and risk can be influenced by an incomplete appreciation of historical baseline climate variability. This can arise from a number of factors including individual's age, access to long term data records and availability of local knowledge. For example, the most significant recent drought in the UK occurred in 1976/77 but does it represent the worst drought that did occur (or could have occurred) without climate change? We focus on the east of England where most irrigated agriculture is located and where many local farmers interviewed were either not in business then or have an incomplete memory of the impacts of the drought. This paper describes a comparison of an annual agroclimatic indicator closely linked to irrigation demand (maximum Potential Soil Moisture Deficit) calculated from three sources of long term observational and simulated historical weather data with recent data. These long term datasets include gridded measured / calculated datasets of precipitation and reference evapotranspiration; a dynamically downscaled 20th Century Re-analysis dataset, and two Regional Climate Model ensemble datasets (FutureFlows and the MaRIUS event set) which each provide between 110 and 3000 years of baseline weather. The comparison shows that the long term datasets provide a wider characterisation of current climate variability and affect the perception of current drought frequency and severity. The paper will show that using a more comprehensive understanding of current climate variability and drought risk as a basis for adapting irrigated systems to droughts can provide substantial increased resilience to (uncertain) climate change.

  15. Genetic variability in the regulation of the expression cluster of MDR genes in patients with breast cancer.

    Science.gov (United States)

    Tsyganov, Matvey M; Freidin, Maxim B; Ibragimova, Marina K; Deryusheva, Irina V; Kazantseva, Polina V; Slonimskaya, Elena M; Cherdyntseva, Nadezhda V; Litviakov, Nikolai V

    2017-08-01

    We aimed to investigate the association between the polymorphism and expression patterns of multiple drug resistance genes (MDR) in breast cancer (BC). The MDR gene expression levels were measured in tumor tissues of 106 breast cancer patients using quantitative real-time PCR. Affymetrix CytoScan™ HD Array chips were used to assess genotypes. Pairwise correlation analysis for ABCB1, ABCC1, ABCC2 and ABCG2 gene expression levels was carried out to reveal co-expression clusters. Associations between SNPs of MDR genes and their preoperative expression levels were assessed using analysis of covariance adjusting for covariates. The SNPs associated with the expression of the ABCB1, ABCC1, ABCC2 and ABCG2 genes before NAC were detected. In addition, 21 SNPs associated with the expression of four ABC-transporter genes and involved in the expression regulation were identified. Validation in an independent sample confirmed the association between the MDR cluster genes and 11 SNPs. Four MDR genes: ABCB1, ABCC1, ABCC2 and ABCG2 were shown to form the functional expression cluster in breast tumor. Further studies are required to discover precise mechanisms of the cluster regulation, thereby providing new approaches and targets to combat the development of the MDR phenotype during chemotherapy.

  16. Improvement of groundwater level prediction in sparsely gauged basins using physical laws and local geographic features as auxiliary variables

    Science.gov (United States)

    Varouchakis, E. A.; Hristopulos, D. T.

    2013-02-01

    This work aims to present new modeling tools that help to better monitor and predict the groundwater level in sparsely gauged basins. The working area is the Mires basin of Mesara valley in the island of Crete (Greece). Efficient groundwater management in the basin is crucial in light of regional climate change model estimates showing a substantial risk of desertification for Crete. We propose that the prediction of the hydraulic head spatial variability in Mires basin can be improved by incorporating in the trend the distance of the prediction points from a temporary river crossing the basin and a component based on the generalized Thiem's equation for multiple wells as well as using the flexible Spartan semivariogram family to perform Residual Kriging. Our proposal is supported by the results of cross validation analysis. Our results are applicable to other unconfined aquifers.

  17. Options to Improve the Quality of Wind Generation Output Forecasting with the Use of Available Information as Explanatory Variables

    Directory of Open Access Journals (Sweden)

    Rafał Magulski

    2015-06-01

    Full Text Available Development of wind generation, besides its positive aspects related to the use of renewable energy, is a challenge from the point of view of power systems’ operational security and economy. The uncertain and variable nature of wind generation sources entails the need for the for the TSO to provide adequate reserves of power, necessary to maintain the grid’s stable operation, and the actors involved in the trading of energy from these sources incur additional of balancing unplanned output deviations. The paper presents the results of analyses concerning the options to forecast a selected wind farm’s output exercised by means of different methods of prediction, using a different range of measurement and forecasting data available on the farm and its surroundings. The analyses focused on the evaluation of forecast errors, and selection of input data for forecasting models and assessment of their impact on prediction quality improvement.

  18. Constraining spatial variability in recharge and discharge in an arid environment through modeling carbon-14 with improved boundary conditions

    Science.gov (United States)

    Wood, Cameron; Cook, Peter G.; Harrington, Glenn A.; Knapton, Anthony

    2017-01-01

    Carbon-14 (14C) has been widely used to estimate groundwater recharge rates in arid regions, and is increasingly being used as a tool to assist numerical model calibration. However, lack of knowledge on 14C inputs to groundwater potentially limits its reliability for constraining spatial variability in recharge. In this study, we use direct measurements of 14C in the unsaturated zone to develop a 14C input map for a regional scale unconfined aquifer in the Ti Tree Basin in central Australia. The map is used as a boundary condition for a 3-D groundwater flow and solute transport model for the basin. The model is calibrated to both groundwater 14C activity and groundwater level, and calibration is achieved by varying recharge rates in 18 hydrogeological zones. We test the sensitivity of the calibration to both the 14C boundary condition, and the number or recharge zones used. The calibrated recharge rates help resolve the conceptual model for the basin, and demonstrate that spatially distributed discharge (through evapotranspiration) is an important part of the water balance. This approach demonstrates the importance of boundary conditions for 14C transport modeling (14C input activity), for improving estimates of spatial variability in recharge and discharge.

  19. Improving actuation efficiency through variable recruitment hydraulic McKibben muscles: modeling, orderly recruitment control, and experiments.

    Science.gov (United States)

    Meller, Michael; Chipka, Jordan; Volkov, Alexander; Bryant, Matthew; Garcia, Ephrahim

    2016-11-03

    Hydraulic control systems have become increasingly popular as the means of actuation for human-scale legged robots and assistive devices. One of the biggest limitations to these systems is their run time untethered from a power source. One way to increase endurance is by improving actuation efficiency. We investigate reducing servovalve throttling losses by using a selective recruitment artificial muscle bundle comprised of three motor units. Each motor unit is made up of a pair of hydraulic McKibben muscles connected to one servovalve. The pressure and recruitment state of the artificial muscle bundle can be adjusted to match the load in an efficient manner, much like the firing rate and total number of recruited motor units is adjusted in skeletal muscle. A volume-based effective initial braid angle is used in the model of each recruitment level. This semi-empirical model is utilized to predict the efficiency gains of the proposed variable recruitment actuation scheme versus a throttling-only approach. A real-time orderly recruitment controller with pressure-based thresholds is developed. This controller is used to experimentally validate the model-predicted efficiency gains of recruitment on a robot arm. The results show that utilizing variable recruitment allows for much higher efficiencies over a broader operating envelope.

  20. Cytokeratin immunohistochemistry improves interobserver variability between unskilled pathologists in the evaluation of tumor budding in T1 colorectal cancer.

    Science.gov (United States)

    Kai, Keita; Aishima, Shinichi; Aoki, Shigehisa; Takase, Yukari; Uchihashi, Kazuyoshi; Masuda, Masanori; Nishijima-Matsunobu, Aki; Yamamoto, Mihoko; Ide, Kousuke; Nakayama, Atsushi; Yamasaki, Makiko; Toda, Shuji

    2016-02-01

    Tumor budding is a major risk factor for T1 colorectal cancer. Quality control of the pathological diagnosis of budding is crucial, irrespective of the pathologist's experience. This study examines the interobserver variability according to pathologists' experience and evaluates the influence of cytokeratin (CK) immunostaining in the assessment of budding. Hematoxylin-eosin (HE) and CK-immunostained slides of 40 cases with T1 primary colorectal cancer were examined. Budding grades were individually evaluated by 12 pathologists who we categorized into three groups by their experience (expert, with >10 years of experience (n = 4), senior, with 5-10 years (n = 4), and junior, budding grades compared to the less-experienced pathologists. In the junior group, the interobserver variability obtained with HE slides was poor, but it was markedly improved in the evaluation using CK-immunostained slides. The benefit of CK immunostaining was only slight in the expert group. CK immunostaining would be useful when a pathologist is not experienced enough or does not have enough confidence in the assessment of budding. © 2016 Japanese Society of Pathology and John Wiley & Sons Australia, Ltd.

  1. Mediation of social cognitive theory variables in the relationship of exercise and improved eating in sedentary adults with severe obesity.

    Science.gov (United States)

    Annesi, James J; Tennant, Gisèle A

    2013-01-01

    Results from behavioral treatments for obesity have been disappointing due to an inability to sustain healthy eating. The concurrent use of theory, research, and practical application has the potential of reducing overeating through innovative treatments. When overweight individuals begin an exercise program their eating tends to improve, however, the basis of this relationship is not determined. If the psychosocial mediators of the relationship between exercise and improved eating are better understood, supported exercise may be a key component for improving the efficacy of behavioral weight management treatments. In Phase 1 of this research, psychosocial variables derived from social cognitive theory were tested as possible mediators of the relationship of exercise participation with increased fruit and vegetable intake in severely obese adults initiating a 26-week treatment of supported exercise and standard nutrition education (n = 161). Change in self-regulation for healthy eating and self-regulation at treatment end was a strong mediator; with the addition of mood and self-efficacy for healthy eating being additional mediators that notably increased effect ratios. In Phase 2, participants in a cognitive-behavioral nutrition treatment tailored to improve the identified mediators (n = 163) were contrasted with the original group. The cognitive-behavioral nutrition treatment was associated with significantly greater increases than standard nutrition education in self-regulation, p = 0.023, CIs [4.69, 6.48], and [3.19, 5.02], respectively; self-efficacy, p = 0.013, CIs [19.72, 29.41], and [11.70, 20.71], respectively; and a marginally significant decrease in negative mood, p = 0.062, CIs [-14.26, -9.36], and [-10.90, -6.45], respectively. Findings served to inform treatment designs concerning the use of supported exercise and cognitive-behavioral means to derive better outcomes related to nutrition and weight loss in individuals with severe

  2. iHeartLift: a closed loop system with bio-feedback that uses music tempo variability to improve heart rate variability.

    Science.gov (United States)

    Ho, Thomas C T; Chen, Xiang

    2011-01-01

    "Musica delenit bestiam feram" translates into "Music soothes the savage beast". There is a hidden truth in this ancient quip passed down from generations. Besides soothing the heart, it also incites the heart to a healthier level of heart rate variability (HRV). In this paper, an approach to use and test music and biofeedback to increase the heart rate variability for people facing daily stress is discussed. By determining the music tempo variability (MTV) of a piece of music and current heart rate variability, iHeartLift is able to compare the 2 trends and locate a musical piece that is suited to increase the user's heart rate variability to a healthier level. With biofeedback, the 2 trends are continuously compared in real-time and the musical piece is changed in accordance with the current comparisons. A study was conducted and it was generally found that HRV can be uplifted by music regardless of language and meaning of musical lyrics but with limitations to musical genre.

  3. Allogeneic Stem Cells Alter Gene Expression and Improve Healing of Distal Limb Wounds in Horses

    Science.gov (United States)

    Textor, Jamie A.; Clark, Kaitlin C.; Walker, Naomi J.; Aristizobal, Fabio A.; Kol, Amir; LeJeune, Sarah S.; Bledsoe, Andrea; Davidyan, Arik; Gray, Sarah N.; Bohannon‐Worsley, Laurie K.; Woolard, Kevin D.

    2017-01-01

    Abstract Distal extremity wounds are a significant clinical problem in horses and humans and may benefit from mesenchymal stem cell (MSC) therapy. This study evaluated the effects of direct wound treatment with allogeneic stem cells, in terms of gross, histologic, and transcriptional features of healing. Three full‐thickness cutaneous wounds were created on each distal forelimb in six healthy horses, for a total of six wounds per horse. Umbilical cord‐blood derived equine MSCs were applied to each wound 1 day after wound creation, in one of four forms: (a) normoxic‐ or (b) hypoxic‐preconditioned cells injected into wound margins, or (c) normoxic‐ or (d) hypoxic‐preconditioned cells embedded in an autologous fibrin gel and applied topically to the wound bed. Controls were one blank (saline) injected wound and one blank fibrin gel‐treated wound per horse. Data were collected weekly for 6 weeks and included wound surface area, thermography, gene expression, and histologic scoring. Results indicated that MSC treatment by either delivery method was safe and improved histologic outcomes and wound area. Hypoxic‐preconditioning did not offer an advantage. MSC treatment by injection resulted in statistically significant increases in transforming growth factor beta and cyclooxygenase‐2 expression at week 1. Histologically, significantly more MSC‐treated wounds were categorized as pro‐healing than pro‐inflammatory. Wound area was significantly affected by treatment: MSC‐injected wounds were consistently smaller than gel‐treated or control wounds. In conclusion, MSC therapy shows promise for distal extremity wounds in horses, particularly when applied by direct injection into the wound margin. stem cells translational medicine 2018;7:98–108 PMID:29063737

  4. Bioelectrical signals improve cardiac function and modify gene expression of extracellular matrix components.

    Science.gov (United States)

    Macfelda, Karin; Kapeller, Barbara; Holly, Alexander; Podesser, Bruno K; Losert, Udo; Brandes, Kersten; Goettel, Peter; Mueller, Johannes

    2017-08-01

    Beyond the influence of stimulating devices on cardiac excitation, their use in treating patients with heart failure has positive effects on the myocardium at the molecular level. Electrical signals can induce a wide spectrum of effects in living tissue. Therefore, we sought to determine whether applying electrical microcurrent directly to failing hearts leads to functional improvement. Sixteen male spontaneously hypertensive rats (SHRs) with heart failure underwent application of a patch electrode to the left ventricular epicardium and placement of a subcutaneous counter electrode. The electrode delivered a 0.35 μA microcurrent to nine of the SHRs for 45 ± 3 days; the other seven SHRs were used as controls. At baseline and before the SHRs were humanely put to death, we measured the left ventricular ejection fraction (LVEF) and the thickness of the LV posterior wall during systole and diastole (LVPWs/d). We used quantitative PCR to determine extracellular matrix parameters [collagen I-III, matrix metalloproteinase (MMP)-2, MMP-9, tissue inhibitor of metalloproteinases 3 (TIMP3), TIMP4, connexins (Cxs) 40/43/45, transforming growth factor (TGF)-β, and interleukin (IL)-6]. Among SHRs undergoing microcurrent application, LVEF normalized (mean decrease, 22.8%; P = 0.009), and LVPWs decreased (mean, 35.3%; P = 0.001). Compared with the control group, the SHRs receiving microcurrent exhibited a mean decrease in the gene expression of collagen I (10.6%, P = 0.003), TIMP3 (18.5%, P = 0.005), Cx43 (14.3%, P = 0.003), Cx45 (12.7%, P = 0.020), TGF-β (13.0%, P = 0.005), and IL-6 (53.7%, P = 0.000). Microcurrent application induced no changes in the expression of collagen III, MMP-2, MMP-9, TIMP4, or Cx40. Applying microcurrent to the LV epicardium of SHRs leads to statistically significant functional improvement and alterations in the levels of inflammatory and extracellular matrix components. © 2017 The Authors. ESC Heart Failure published by John

  5. Can survival prediction be improved by merging gene expression data sets?

    Directory of Open Access Journals (Sweden)

    Haleh Yasrebi

    Full Text Available BACKGROUND: High-throughput gene expression profiling technologies generating a wealth of data, are increasingly used for characterization of tumor biopsies for clinical trials. By applying machine learning algorithms to such clinically documented data sets, one hopes to improve tumor diagnosis, prognosis, as well as prediction of treatment response. However, the limited number of patients enrolled in a single trial study limits the power of machine learning approaches due to over-fitting. One could partially overcome this limitation by merging data from different studies. Nevertheless, such data sets differ from each other with regard to technical biases, patient selection criteria and follow-up treatment. It is therefore not clear at all whether the advantage of increased sample size outweighs the disadvantage of higher heterogeneity of merged data sets. Here, we present a systematic study to answer this question specifically for breast cancer data sets. We use survival prediction based on Cox regression as an assay to measure the added value of merged data sets. RESULTS: Using time-dependent Receiver Operating Characteristic-Area Under the Curve (ROC-AUC and hazard ratio as performance measures, we see in overall no significant improvement or deterioration of survival prediction with merged data sets as compared to individual data sets. This apparently was due to the fact that a few genes with strong prognostic power were not available on all microarray platforms and thus were not retained in the merged data sets. Surprisingly, we found that the overall best performance was achieved with a single-gene predictor consisting of CYB5D1. CONCLUSIONS: Merging did not deteriorate performance on average despite (a The diversity of microarray platforms used. (b The heterogeneity of patients cohorts. (c The heterogeneity of breast cancer disease. (d Substantial variation of time to death or relapse. (e The reduced number of genes in the merged data

  6. Performance improvement of continuous-variable quantum key distribution with an entangled source in the middle via photon subtraction

    Science.gov (United States)

    Guo, Ying; Liao, Qin; Wang, Yijun; Huang, Duan; Huang, Peng; Zeng, Guihua

    2017-03-01

    A suitable photon-subtraction operation can be exploited to improve the maximal transmission of continuous-variable quantum key distribution (CVQKD) in point-to-point quantum communication. Unfortunately, the photon-subtraction operation faces solving the improvement transmission problem of practical quantum networks, where the entangled source is located in the third part, which may be controlled by a malicious eavesdropper, instead of in one of the trusted parts, controlled by Alice or Bob. In this paper, we show that a solution can come from using a non-Gaussian operation, in particular, the photon-subtraction operation, which provides a method to enhance the performance of entanglement-based (EB) CVQKD. Photon subtraction not only can lengthen the maximal transmission distance by increasing the signal-to-noise rate but also can be easily implemented with existing technologies. Security analysis shows that CVQKD with an entangled source in the middle (ESIM) from applying photon subtraction can well increase the secure transmission distance in both direct and reverse reconciliations of the EB-CVQKD scheme, even if the entangled source originates from an untrusted part. Moreover, it can defend against the inner-source attack, which is a specific attack by an untrusted entangled source in the framework of ESIM.

  7. Human carboxylesterases HCE1 and HCE2: ontogenic expression, inter-individual variability and differential hydrolysis of oseltamivir, aspirin, deltamethrin and permethrin.

    Science.gov (United States)

    Yang, Dongfang; Pearce, Robin E; Wang, Xiliang; Gaedigk, Roger; Wan, Yu-Jui Yvonne; Yan, Bingfang

    2009-01-15

    Carboxylesterases hydrolyze chemicals containing such functional groups as a carboxylic acid ester, amide and thioester. The liver contains the highest carboxylesterase activity and expresses two major carboxylesterases: HCE1 and HCE2. In this study, we analyzed 104 individual liver samples for the expression patterns of both carboxylesterases. These samples were divided into three age groups: adults (>or= 18 years of age), children (0 days-10 years) and fetuses (82-224 gestation days). In general, the adult group expressed significantly higher HCE1 and HCE2 than the child group, which expressed significantly higher than the fetal group. The age-related expression was confirmed by RT-qPCR and Western immunoblotting. To determine whether the expression patterns reflected the hydrolytic activity, liver microsomes were pooled from each group and tested for the hydrolysis of drugs such as oseltamivir and insecticides such as deltamethrin. Consistent with the expression patterns, adult microsomes were approximately 4 times as active as child microsomes and 10 times as active as fetal microsomes in hydrolyzing these chemicals. Within the same age group, particularly in the fetal and child groups, a large inter-individual variability was detected in mRNA (430-fold), protein (100-fold) and hydrolytic activity (127-fold). Carboxylesterases are recognized to play critical roles in drug metabolism and insecticide detoxication. The findings on the large variability among different age groups or even within the same age group have important pharmacological and toxicological implications, particularly in relation to pharmacokinetic alterations of ester drugs in children and vulnerability of fetuses and children to pyrethroid insecticides.

  8. Improving the Expression and Purification of Soluble, Recombinant Native-Like HIV-1 Envelope Glycoprotein Trimers by Targeted Sequence Changes.

    Science.gov (United States)

    Ringe, Rajesh P; Ozorowski, Gabriel; Yasmeen, Anila; Cupo, Albert; Cruz Portillo, Victor M; Pugach, Pavel; Golabek, Michael; Rantalainen, Kimmo; Holden, Lauren G; Cottrell, Christopher A; Wilson, Ian A; Sanders, Rogier W; Ward, Andrew B; Klasse, P J; Moore, John P

    2017-06-15

    Soluble, recombinant native-like envelope glycoprotein (Env) trimers of various human immunodeficiency virus type 1 (HIV-1) genotypes are being developed for structural studies and as vaccine candidates aimed at the induction of broadly neutralizing antibodies (bNAbs). The prototypic design is designated SOSIP.664, but many HIV-1 env genes do not yield fully native-like trimers efficiently. One such env gene is CZA97.012 from a neutralization-resistant (tier 2) clade C virus. As appropriately purified, native-like CZA97.012 SOSIP.664 trimers induce autologous neutralizing antibodies (NAbs) efficiently in immunized rabbits, we sought to improve the efficiency with which they can be produced and to better understand the limitations to the original design. By using structure- and antigenicity-guided mutagenesis strategies focused on the V2 and V3 regions and the gp120-gp41 interface, we developed the CZA97 SOSIP.v4.2-M6.IT construct. Fully native-like, stable trimers that display multiple bNAb epitopes could be expressed from this construct in a stable CHO cell line and purified at an acceptable yield using either a PGT145 or a 2G12 bNAb affinity column. We also show that similar mutagenesis strategies can be used to improve the yields and properties of SOSIP.664 trimers of the DU422, 426c, and 92UG037 genotypes.IMPORTANCE Recombinant trimeric proteins based on HIV-1 env genes are being developed for future vaccine trials in humans. A feature of these proteins is their mimicry of the envelope glycoprotein (Env) structure on virus particles that is targeted by neutralizing antibodies, i.e., antibodies that prevent cells from becoming infected. The vaccine concept under exploration is that recombinant trimers may be able to elicit virus-neutralizing antibodies when delivered as immunogens. Because HIV-1 is extremely variable, a practical vaccine may need to incorporate Env trimers derived from multiple different virus sequences. Accordingly, we need to understand how to

  9. Optical Molecular Imaging of Epidermal Growth Factor Receptor Expression to Improve Detection of Oral Neoplasia

    Directory of Open Access Journals (Sweden)

    Nitin Nitin

    2009-06-01

    Full Text Available Background: The development of noninvasive molecular imaging approaches has the potential to improve management of cancer. Methods: In this study, we demonstrate the potential of noninvasive topical delivery of an epidermal growth factor-Alexa 647 (EGF-Alexa 647 conjugate to image changes in epidermal growth factor receptor expression associated with oral neoplasia. We report a series of preclinical analyses to evaluate the optical contrast achieved after topical delivery of EGF-Alexa 647 in a variety of model systems, including cells, three-dimensional tissue cultures, and intact human tissue specimens using wide-field and high-resolution fluorescence imaging. Data were collected from 17 different oral cancer patients: eight pairs of normal and abnormal biopsies and nine resected tumors were examined. Results: The EGF-dye conjugate can be uniformly delivered throughout the oral epithelium with a penetration depth exceeding 500 µm and incubation time of less than 30 minutes. After EGF-Alexa 647 incubation, the presence of oral neoplasia is associated with a 1.5- to 6.9-fold increase in fluorescence contrast compared with grossly normal mucosa from the same patient with both wide-field and high-resolution fluorescence imaging. Conclusions: Results illustrate the potential of EGF-targeted fluorescent agents for in vivo molecular imaging, a technique that may aid in the diagnosis and characterization of oral neoplasia and allow real-time detection of tumor margins.

  10. Physical Exercise Improves Total Antioxidant Capacity and Gene Expression in Rat Hippocampal Tissue.

    Science.gov (United States)

    Franzoni, F; Federighi, G; Fusi, J; Agosta, V; Cerri, E; Banducci, R; Petrocchi, A; Bernardi, R; Innocenti, A; Pruneti, C; Daniele, S; Pellegrini, S; Martini, C; Scuri, R; Galetta, F

    2017-07-01

    Exercise may exert beneficial effects on cognitive functions and play an important role in the prevention of neurodegenerative diseases. Such effects seem to be mediated by changes in anti-oxidative status, but limited information is available on the nature of molecular pathways supporting the antioxidant effects of exercise in the brain. In this study 3-5-month-old male Wistar albino rats were subjected to three times/week moderate intensity exercise on a rodent treadmill for a period of 6 weeks. The tissue antioxidant activity towards various reactive oxygen species (ROS) was determined in the hippocampus. In addition, to identify the molecular pathways that may be involved in ROS metabolism, the expression of nerve growth factor (NGF) and sirtuins (SIRT1 and SIRT3) were measured. Our results showed a higher antioxidant activity in the hippocampus of physically trained rats compared to sedentary controls. Furthermore, exercise induced an up-regulation of NGF, possibly related to an improved redox balance in the hippocampus. These results suggest that physical exercise might prevent age-induced oxidative damage in the hippocampus.

  11. A breast cancer meta-analysis of two expression measures of chromosomal instability reveals a relationship with younger age at diagnosis and high risk histopathological variables

    DEFF Research Database (Denmark)

    Endesfelder, David; McGranahan, Nicholas; Birkbak, Nicolai Juul

    2011-01-01

    , assessed by the two independently derived CIN expression signatures, is significantly associated with increased tumour size, ER negative or HER2 positive disease, higher tumour grade and younger age at diagnosis in ER negative breast cancer. These data support the hypothesis that chromosomal instability......Breast cancer in younger patients often presents with adverse histopathological features, including increased frequency of estrogen receptor negative and lymph node positive disease status. Chromosomal instability (CIN) is increasingly recognised as an important prognostic variable in solid tumours...

  12. Variable 18F-fluorodeoxyglucose uptake in gastric cancer is associated with different levels of GLUT-1 expression.

    Science.gov (United States)

    Alakus, Hakan; Batur, Mert; Schmidt, Matthias; Drebber, Uta; Baldus, Stephan E; Vallböhmer, Daniel; Prenzel, Klaus L; Metzger, Ralf; Bollschweiler, Elfriede; Hölscher, Arnulf H; Mönig, Stefan P

    2010-06-01

    Detection rates of gastric cancer in F-fluorodeoxyglucose (FDG)-PET depend on the histopathological characteristics of the primary tumor. To clarify this observation, FDG uptake in gastric carcinoma was analyzed by focusing on histopathology and on the expression of the glucose transporter (GLUT-1) in the primary tumor. Thirty-five patients with the diagnosis of gastric cancer underwent FDG-PET with visual image analysis and measurement of maximum standardized uptake value (SUV(max)) before surgical treatment. Resected tumor samples were categorized according to Union internationale contre le cancer, WHO, and Laurén classification and tumor differentiation. GLUT-1 expression was graded semiquantitatively by immunohistochemistry. Statistical analysis was done for the correlation of histology, different classifications, and tumor grading with SUV(max) and GLUT-1 expression. SUV(max) significantly correlated with histopathological classifications according to the WHO (P=0.009) and Laurén classification (P=0.034). Signet-ring cell carcinoma had a median SUV(max) of only 3.0 (range, 1.0-11.5). Median SUV(max) for papillary and tubular carcinoma was 7.8 (range, 1.8-14.4). In 21 (60%) cases, GLUT-1 expression in the primary tumor was positive. GLUT-1 expression correlated significantly with tumor differentiation (P=0.018) and the classification according to Laurén (P=0.023) and WHO (PGLUT-1 expression. SUV(max) in relation to GLUT-1 expression showed a significant correlation (P=0.002). For cases with detectable GLUT-1 expression the median SUV(max) was 6.9 (range, 2.3-14.1) versus a median of 3.1 (range, 1-8.8) for cases without GLUT-1 expression. FDG uptake in gastric cancer depends on GLUT-1 expression. One major reason for low FDG uptake in signet-ring cell carcinoma is the low GLUT-1 expression in this histological subtype of gastric cancer.

  13. MYT1L mutations cause intellectual disability and variable obesity by dysregulating gene expression and development of the neuroendocrine hypothalamus.

    Science.gov (United States)

    Blanchet, Patricia; Bebin, Martina; Bruet, Shaam; Cooper, Gregory M; Thompson, Michelle L; Duban-Bedu, Benedicte; Gerard, Benedicte; Piton, Amelie; Suckno, Sylvie; Deshpande, Charu; Clowes, Virginia; Vogt, Julie; Turnpenny, Peter; Williamson, Michael P; Alembik, Yves; Glasgow, Eric; McNeill, Alisdair

    2017-08-01

    Deletions at chromosome 2p25.3 are associated with a syndrome consisting of intellectual disability and obesity. The smallest region of overlap for deletions at 2p25.3 contains PXDN and MYT1L. MYT1L is expressed only within the brain in humans. We hypothesized that single nucleotide variants (SNVs) in MYT1L would cause a phenotype resembling deletion at 2p25.3. To examine this we sought MYT1L SNVs in exome sequencing data from 4, 296 parent-child trios. Further variants were identified through a genematcher-facilitated collaboration. We report 9 patients with MYT1L SNVs (4 loss of function and 5 missense). The phenotype of SNV carriers overlapped with that of 2p25.3 deletion carriers. To identify the transcriptomic consequences of MYT1L loss of function we used CRISPR-Cas9 to create a knockout cell line. Gene Ontology analysis in knockout cells demonstrated altered expression of genes that regulate gene expression and that are localized to the nucleus. These differentially expressed genes were enriched for OMIM disease ontology terms "mental retardation". To study the developmental effects of MYT1L loss of function we created a zebrafish knockdown using morpholinos. Knockdown zebrafish manifested loss of oxytocin expression in the preoptic neuroendocrine area. This study demonstrates that MYT1L variants are associated with syndromic obesity in humans. The mechanism is related to dysregulated expression of neurodevelopmental genes and altered development of the neuroendocrine hypothalamus.

  14. The Use Of Cartoon Movie In Improving Students Speaking Ability In Using Expression Of Asking For And Giving Help

    OpenAIRE

    Puspitasari, Herwinda; Bunau, Eusabinus; Novita, Dewi

    2014-01-01

    This research is focused on the use of cartoon movie in improving students speaking ability in using expression of asking for and giving help. The aim of this research is to know whether or not cartoon movie can improve the ability in using expression of asking for and giving to the seventh grade students of SMP Negeri 6 Pontianak in the academic year 2012/2013. It is a pre-experimental study where the form used is one group of pretest and posttest design. The population in this research was...

  15. Reduced Penetrance and Variable Expression of SCN5A Mutations and the Importance of Co-inherited Genetic Variants: Case Report and Review of the Literature

    Directory of Open Access Journals (Sweden)

    T. Robyns, MD.

    2014-05-01

    Full Text Available Mutations in the SCN5A gene are responsible for multiple phenotypical presentations including Brugada syndrome, long QT syndrome, progressive familial heart block, sick sinus syndrome, dilated cardiomyopathy, lone atrial fibrillation and multiple overlap syndromes. These different phenotypic expressions of a mutation in a single gene can be explained by variable expression and reduced penetrance. One of the possible explanations of these phenomena is the co-inheritance of genetic variants. We describe a family where the individuals exhibit a compound heterozygosity in the SCN5A gene including a mutation (R1632H and a new variant (M858L. Individuals with both the mutation and new variant present with a more severe phenotype including spontaneous atrial tachyarrhythmia at young age. We give an overview of the different phenotypes of "SCN5A disease" and discuss the importance of co-inherited genetic variants in the expression of SCN5A disease.

  16. [Cloning, ligation and expression of the variable region genes of the monoclonal antibody against human HnRNPA2/B1].

    Science.gov (United States)

    Wang, Xia; Peng, Xiao-dong; Li, Guang; Hu, Li-juan; Bi, Jian-hong

    2004-12-01

    To clone the variable region genes of the monoclonal antibody (McAb) against human heterogeneous nuclear ribonucleoprotein A2/B1 (HnRNPA2/B1), ligate them to assemble single chain Fv (ScFv) gene and express in Escherichia coli. The specificity of the anti-HnRNPA2/B1 McAb 3E8 to synthetic HnRNPA2/B1 peptide, HnRNPA2/B1 protein in lung cancer cells were examined by dot-immunobinding assay, Western blot and immunohistochemistry. The variable region genes of heavy chain (VH) and light chain (VL) were amplified from hybridoma cell by reverse transcription-polymerase chain reaction(RT-PCR), and then were linked by a linker peptide using SOE-PCR (splicing by overlap extension-PCR) to construct recombination ScFv gene. The latter was cloned into the expression vector pET28 (a+) and expressed in E coli BL21. The expressed product was identified by SDS-PAGE and competitive ELISA inhibition test. It was shown that the McAb combined specifically with synthetic HnRNPA2/B1 peptide and HnRNPA2/B1 protein in three lung cancer cells. The cloned VH gene and VL gene were 345 bp and 309 bp respectively and were linked successfully to obtain ScFv gene. The ScFv protein was expressed in the form of inclusion body, with molecular weight of 28,000 and immunoreactivity to HnRNPA2/B1. VH gene, VL gene and ScFv gene of anti-HnRNPA2/B1 antibody were cloned, constructed and functionally expressed in E coli. These results provide the experimental basis for elucidating the role of HnRNPA2/B1 in lung cancer.

  17. Determination of supplier-to-supplier and lot-to-lot variability in glycation of recombinant human serum albumin expressed in Oryza sativa.

    Science.gov (United States)

    Frahm, Grant E; Smith, Daryl G S; Kane, Anita; Lorbetskie, Barry; Cyr, Terry D; Girard, Michel; Johnston, Michael J W

    2014-01-01

    The use of different expression systems to produce the same recombinant human protein can result in expression-dependent chemical modifications (CMs) leading to variability of structure, stability and immunogenicity. Of particular interest are recombinant human proteins expressed in plant-based systems, which have shown particularly high CM variability. In studies presented here, recombinant human serum albumins (rHSA) produced in Oryza sativa (Asian rice) (OsrHSA) from a number of suppliers have been extensively characterized and compared to plasma-derived HSA (pHSA) and rHSA expressed in yeast (Pichia pastoris and Saccharomyces cerevisiae). The heterogeneity of each sample was evaluated using size exclusion chromatography (SEC), reversed-phase high-performance liquid chromatography (RP-HPLC) and capillary electrophoresis (CE). Modifications of the samples were identified by liquid chromatography-mass spectrometry (LC-MS). The secondary and tertiary structure of the albumin samples were assessed with far U/V circular dichroism spectropolarimetry (far U/V CD) and fluorescence spectroscopy, respectively. Far U/V CD and fluorescence analyses were also used to assess thermal stability and drug binding. High molecular weight aggregates in OsrHSA samples were detected with SEC and supplier-to-supplier variability and, more critically, lot-to-lot variability in one manufactures supplied products were identified. LC-MS analysis identified a greater number of hexose-glycated arginine and lysine residues on OsrHSA compared to pHSA or rHSA expressed in yeast. This analysis also showed supplier-to-supplier and lot-to-lot variability in the degree of glycation at specific lysine and arginine residues for OsrHSA. Both the number of glycated residues and the degree of glycation correlated positively with the quantity of non-monomeric species and the chromatographic profiles of the samples. Tertiary structural changes were observed for most OsrHSA samples which correlated well

  18. Determination of supplier-to-supplier and lot-to-lot variability in glycation of recombinant human serum albumin expressed in Oryza sativa.

    Directory of Open Access Journals (Sweden)

    Grant E Frahm

    Full Text Available The use of different expression systems to produce the same recombinant human protein can result in expression-dependent chemical modifications (CMs leading to variability of structure, stability and immunogenicity. Of particular interest are recombinant human proteins expressed in plant-based systems, which have shown particularly high CM variability. In studies presented here, recombinant human serum albumins (rHSA produced in Oryza sativa (Asian rice (OsrHSA from a number of suppliers have been extensively characterized and compared to plasma-derived HSA (pHSA and rHSA expressed in yeast (Pichia pastoris and Saccharomyces cerevisiae. The heterogeneity of each sample was evaluated using size exclusion chromatography (SEC, reversed-phase high-performance liquid chromatography (RP-HPLC and capillary electrophoresis (CE. Modifications of the samples were identified by liquid chromatography-mass spectrometry (LC-MS. The secondary and tertiary structure of the albumin samples were assessed with far U/V circular dichroism spectropolarimetry (far U/V CD and fluorescence spectroscopy, respectively. Far U/V CD and fluorescence analyses were also used to assess thermal stability and drug binding. High molecular weight aggregates in OsrHSA samples were detected with SEC and supplier-to-supplier variability and, more critically, lot-to-lot variability in one manufactures supplied products were identified. LC-MS analysis identified a greater number of hexose-glycated arginine and lysine residues on OsrHSA compared to pHSA or rHSA expressed in yeast. This analysis also showed supplier-to-supplier and lot-to-lot variability in the degree of glycation at specific lysine and arginine residues for OsrHSA. Both the number of glycated residues and the degree of glycation correlated positively with the quantity of non-monomeric species and the chromatographic profiles of the samples. Tertiary structural changes were observed for most OsrHSA samples which

  19. Bootstrapping of gene-expression data improves and controls the false discovery rate of differentially expressed genes

    Directory of Open Access Journals (Sweden)

    Goddard Mike E

    2004-03-01

    Full Text Available Abstract The ordinary-, penalized-, and bootstrap t-test, least squares and best linear unbiased prediction were compared for their false discovery rates (FDR, i.e. the fraction of falsely discovered genes, which was empirically estimated in a duplicate of the data set. The bootstrap-t-test yielded up to 80% lower FDRs than the alternative statistics, and its FDR was always as good as or better than any of the alternatives. Generally, the predicted FDR from the bootstrapped P-values agreed well with their empirical estimates, except when the number of mRNA samples is smaller than 16. In a cancer data set, the bootstrap-t-test discovered 200 differentially regulated genes at a FDR of 2.6%, and in a knock-out gene expression experiment 10 genes were discovered at a FDR of 3.2%. It is argued that, in the case of microarray data, control of the FDR takes sufficient account of the multiple testing, whilst being less stringent than Bonferoni-type multiple testing corrections. Extensions of the bootstrap simulations to more complicated test-statistics are discussed.

  20. MYT1L mutations cause intellectual disability and variable obesity by dysregulating gene expression and development of the neuroendocrine hypothalamus.

    Directory of Open Access Journals (Sweden)

    Patricia Blanchet

    2017-08-01

    Full Text Available Deletions at chromosome 2p25.3 are associated with a syndrome consisting of intellectual disability and obesity. The smallest region of overlap for deletions at 2p25.3 contains PXDN and MYT1L. MYT1L is expressed only within the brain in humans. We hypothesized that single nucleotide variants (SNVs in MYT1L would cause a phenotype resembling deletion at 2p25.3. To examine this we sought MYT1L SNVs in exome sequencing data from 4, 296 parent-child trios. Further variants were identified through a genematcher-facilitated collaboration. We report 9 patients with MYT1L SNVs (4 loss of function and 5 missense. The phenotype of SNV carriers overlapped with that of 2p25.3 deletion carriers. To identify the transcriptomic consequences of MYT1L loss of function we used CRISPR-Cas9 to create a knockout cell line. Gene Ontology analysis in knockout cells demonstrated altered expression of genes that regulate gene expression and that are localized to the nucleus. These differentially expressed genes were enriched for OMIM disease ontology terms "mental retardation". To study the developmental effects of MYT1L loss of function we created a zebrafish knockdown using morpholinos. Knockdown zebrafish manifested loss of oxytocin expression in the preoptic neuroendocrine area. This study demonstrates that MYT1L variants are associated with syndromic obesity in humans. The mechanism is related to dysregulated expression of neurodevelopmental genes and altered development of the neuroendocrine hypothalamus.

  1. [Expression of single chain fragment variable P1D3 antibody against shrimp white spot syndrome virus in Pichia pastoris].

    Science.gov (United States)

    Yang, Yi; Zhang, Min; Yuan, Li; Zhang, Xiao-Hua; Dai, He-Ping

    2006-11-01

    White spot syndrome virus (WSSV) is a major pathogen in aquaculture penaeid shrimp, which caused catastrophic economic losses in the worldwide. No adequate treatments against WSSV are available. In order to study infection mechanism of WSSV, a phage display scFv cDNA library against WSSV was constructed and a neutralizing antibody of scFv P1D3 was selected in our lab previously. In this study, scFv P1D3 was expressed successfully in yeast. Firstly, the original expression vector of P1D3, M13 phagmid, was used as a template to design primers with restriction sites of SnaB I and EcoR I . Then the gene of P1D3 was amplified by PCR. After digested by SnaB I and EcoR I , the fragment of scFv P1D3 with E-tag was inserted into yeast and E. coli shuttle plasmid pPIC9k. The recombinant plasmid pPIC9k-scFv P1D3-Etag was linearized with Bgl II and then transformed into Pichia pastoris GS115 by electroporation. Positive clones were selected and verified by PCR and DNA sequencing. The scFv PID3 was induced to express in yeast by methanol. The results of ELISA demonstrate that scFv P1D3 expressed in yeast still has high specificity to bind on WSSV and the binding activity is higher than that expressed in E. coli TG1. After several optimizing experiments, the results show that the expression amount of scFv P1D3 can reach to 302 mg/L in yeast culture supernatant. This experiment has offered a new source of antibody for the researches on passive immunology for shrimp.

  2. Estimating annoyance to calculated wind turbine shadow flicker is improved when variables associated with wind turbine noise exposure are considered.

    Science.gov (United States)

    Voicescu, Sonia A; Michaud, David S; Feder, Katya; Marro, Leonora; Than, John; Guay, Mireille; Denning, Allison; Bower, Tara; van den Berg, Frits; Broner, Norm; Lavigne, Eric

    2016-03-01

    The Community Noise and Health Study conducted by Health Canada included randomly selected participants aged 18-79 yrs (606 males, 632 females, response rate 78.9%), living between 0.25 and 11.22 km from operational wind turbines. Annoyance to wind turbine noise (WTN) and other features, including shadow flicker (SF) was assessed. The current analysis reports on the degree to which estimating high annoyance to wind turbine shadow flicker (HAWTSF) was improved when variables known to be related to WTN exposure were also considered. As SF exposure increased [calculated as maximum minutes per day (SFm)], HAWTSF increased from 3.8% at 0 ≤ SFm wind turbine-related features, concern for physical safety, and noise sensitivity. Reported dizziness was also retained in the final model at p = 0.0581. Study findings add to the growing science base in this area and may be helpful in identifying factors associated with community reactions to SF exposure from wind turbines.

  3. Variable phase bright-field contrast--an alternative illumination technique for improved imaging in transparent specimens.

    Science.gov (United States)

    Piper, Timm; Piper, Jörg

    2013-02-01

    In variable phase bright-field contrast, a bright-field image based on axial or concentric-peripheral light is optically superimposed with a phase-contrast image, so that typical details that are imminent in one or the other technique contribute to the resulting composite image. In particular, complex structured specimens consisting of high-density light absorbing details and additional low-density phase shifting components can be observed with improved clarity. As both partial images interfere with each other, fine details within thin specimens can be highlighted further by additional contrast effects based on interference. Haloing and shade-off are significantly reduced when compared with phase contrast carried out stand-alone. Our method is characterized by several technical means that are relevant for the high image quality that can be achieved: both illuminating light components associated with bright field and phase contrast are filtered at different colors and separated from each other so that they meet the specimen at different angles of incidence. The intensities of the phase-contrast- and bright-field-producing light can be selectively regulated so that the final image can be dominated by phase contrast or bright field, or be equalized. The condenser aperture diaphragm can be used for modulations of the image's appearance.

  4. The verbal facilitation effect: re-reading person descriptions as a system variable to improve identification performance.

    Science.gov (United States)

    Sporer, Siegfried L; Kaminski, Kristina S; Davids, Maike C; McQuiston, Dawn

    2016-11-01

    When witnesses report a crime, police usually ask for a description of the perpetrator. Several studies suggested that verbalising faces leads to a detriment in identification performance (verbal overshadowing effect [VOE]) but the effect has been difficult to replicate. Here, we sought to reverse the VOE by inducing context reinstatement as a system variable through re-reading one's own description before an identification task. Participants (N = 208) watched a video film and were then dismissed (control group), only described the perpetrator, or described and later re-read their own descriptions before identification in either target-present or target-absent lineups after a 2-day or a 5-week delay. Identification accuracy was significantly higher after re-reading (85.0%) than in the no description control group (62.5%) irrespective of target presence. Data were internally replicated using a second target and corroborated by several small meta-analyses. Identification accuracy was related to description quality. Moreover, there was a tendency towards a verbal facilitation effect (VFE) rather than a VOE. Receiver operating characteristic (ROC) curve analyses confirm that our findings are not due to a shift in response bias but truly reflect improvement of recognition performance. Differences in the ecological validity of study paradigms are discussed.

  5. Over-Expression of SlSHN1 Gene Improves Drought Tolerance by Increasing Cuticular Wax Accumulation in Tomato

    Directory of Open Access Journals (Sweden)

    Ayed M. Al-Abdallat

    2014-10-01

    Full Text Available Increasing cuticular wax accumulation in plants has been associated with improving drought tolerance in plants. In this study, a cDNA clone encoding the SlSHN1 transcription factor, the closest ortholog to WIN/SHN1 gene in Arabidopsis, was isolated from tomato plant. Expression analysis of SlSHN1 indicated that it is induced in response to drought conditions. The over-expression of SlSHN1 in tomato under the control of the constitutive CaMV 35S promoter produced plants that showed mild growth retardation phenotype with shiny and dark green leaves. Scanning electron microscopy showed that the over-expression of SlSHN1 in tomato resulted in higher cuticular wax deposition on leaf epidermial tissue when compared to non-transformed plants. Expression analysis in transgenic lines over-expressing SlSHN1 indicated that several wax-related synthesis genes were induced. Transgenic tomato plants over-expressing SlSHN1 showed higher drought tolerance when compared with wild type plants; this was reflected in delayed wilting of transgenic lines, improved water status and reduced water loss rate when compared with wild type plants. In conclusion, the SlSHN1 gene can modulate wax accumulation and could be utilized to enhance drought tolerance in tomato plant.

  6. Changes in heart rate variability are associated with expression of short-term and long-term contextual and cued fear memories.

    Directory of Open Access Journals (Sweden)

    Jun Liu

    Full Text Available Heart physiology is a highly useful indicator for measuring not only physical states, but also emotional changes in animals. Yet changes of heart rate variability during fear conditioning have not been systematically studied in mice. Here, we investigated changes in heart rate and heart rate variability in both short-term and long-term contextual and cued fear conditioning. We found that while fear conditioning could increase heart rate, the most significant change was the reduction in heart rate variability which could be further divided into two distinct stages: a highly rhythmic phase (stage-I and a more variable phase (stage-II. We showed that the time duration of the stage-I rhythmic phase were sensitive enough to reflect the transition from short-term to long-term fear memories. Moreover, it could also detect fear extinction effect during the repeated tone recall. These results suggest that heart rate variability is a valuable physiological indicator for sensitively measuring the consolidation and expression of fear memories in mice.

  7. Improvement of water use efficiency in rice by expression of HARDY, an Arabidopsis drought and salt tolerance gene

    NARCIS (Netherlands)

    Karaba, A.; Dixit, S.A.; Greco, Raffaella; Aharoni, A.; Trijatmiko, K.R.; Marsch-Martinez, N.; Krishnan, A.; Nataraja, K.N.; Udayakumar, M.; Pereira, A.B.

    2007-01-01

    Freshwater is a limited and dwindling global resource; therefore, efficient water use is required for food crops that have high water demands, such as rice, or for the production of sustainable energy biomass. We show here that expression of the Arabidopsis HARDY (HRD) gene in rice improves water

  8. Can geometric indices of heart rate variability predict improvement in autonomic modulation after resistance training in chronic obstructive pulmonary disease?

    Science.gov (United States)

    Santos, Ana Alice Soares Dos; Ricci-Vitor, Ana Laura; Bragatto, Vanessa Santa Rosa; Santos, Ana Paula Soares Dos; Ramos, Ercy Mara Cipulo; Vanderlei, Luiz Carlos Marques

    2017-03-01

    Chronic obstructive pulmonary disease (COPD) is associated with autonomic dysfunctions that can be evaluated through heart rate variability (HRV). Resistance training promotes improvement in autonomic modulation; however, studies that evaluate this scenario using geometric indices, which include nonlinear evaluation, thus providing more accurate information for physiological interpretation of HRV, are unknown. This study aimed to investigate the influence of resistance training on autonomic modulation, using geometric indices of HRV, and peripheral muscle strength in individuals with COPD. Fourteen volunteers with COPD were submitted to resistance training consisting of 24 sessions lasting 60 min each, with a frequency of three times a week. The intensity was determined as 60% of one maximum repetition and was progressively increased until 80% for the upper and lower limbs. The HRV and dynamometry were performed at two moments, the beginning and the end of the experimental protocol. Significant increases were observed in the RRtri (4·81 ± 1·60 versus 6·55 ± 2·69, P = 0·033), TINN (65·36 ± 35·49 versus 101·07 ± 63·34, P = 0·028), SD1 (7·48 ± 3·17 versus 11·04 ± 6·45, P = 0·038) and SD2 (22·30 ± 8·56 versus 32·92 ± 18·78, P = 0·022) indices after the resistance training. Visual analysis of the Poincare plot demonstrated greater dispersion beat-to-beat and in the long-term interval between consecutive heart beats. Regarding muscle strength, there was a significant increase in the shoulder abduction and knee flexion. In conclusion, geometric indices of HRV can predict improvement in autonomic modulation after resistance training in individuals with COPD; improvement in peripheral muscle strength in patients with COPD was also observed. © 2015 Scandinavian Society of Clinical Physiology and Nuclear Medicine. Published by John Wiley & Sons Ltd.

  9. Improvements on a simple muscle-based 3D face for realistic facial expressions

    NARCIS (Netherlands)

    Bui, T.D.; Heylen, Dirk K.J.; Nijholt, Antinus; Badler, N.; Thalmann, D.

    2003-01-01

    Facial expressions play an important role in face-to-face communication. With the development of personal computers capable of rendering high quality graphics, computer facial animation has produced more and more realistic facial expressions to enrich human-computer communication. In this paper, we

  10. Design-Based Learning for Biology: Genetic Engineering Experience Improves Understanding of Gene Expression

    Science.gov (United States)

    Ellefson, Michelle R.; Brinker, Rebecca A.; Vernacchio, Vincent J.; Schunn, Christian D.

    2008-01-01

    Gene expression is a difficult topic for students to learn and comprehend, at least partially because it involves various biochemical structures and processes occurring at the microscopic level. Designer Bacteria, a design-based learning (DBL) unit for high-school students, applies principles of DBL to the teaching of gene expression. Throughout…

  11. Benign breast tissue composition in breast cancer patients: association with risk factors, clinical variables, and gene expression.

    Science.gov (United States)

    Sun, Xuezheng; Sandhu, Rupninder; Figueroa, Jonine D; Gierach, Gretchen L; Sherman, Mark E; Troester, Melissa A

    2014-12-01

    Breast tissue composition (epithelium, non-fatty stroma, and adipose) changes qualitatively and quantitatively throughout the lifespan, and may mediate relationships between risk factors and breast cancer initiation. We sought to identify relationships between tissue composition, risk factors, tumor characteristics, and gene expression. Participants were 146 patients from the Polish Breast Cancer Study, with data on risk factor and clinicopathological characteristics. Benign breast tissue composition was evaluated using digital image analysis of histologic sections. Whole-genome microarrays were performed on the same tissue blocks. Mean epithelial, non-fatty stromal, and adipose proportions were 8.4% (SD = 4.9%), 27.7% (SD = 24.0%), and 64.0% (SD = 24.0%), respectively. Among women associated with obesity (7.6% in nonobese vs. 10.1% in obese; P = 0.02) and with poorly differentiated tumors (7.8% in well/moderate vs. 9.9% in poor; P = 0.05). Gene expression signatures associated with epithelial and stromal proportion were identified and validated. Stroma-associated genes were in metabolism and stem cell maintenance pathways, whereas epithelial genes were enriched for cytokine and immune response pathways. Breast tissue composition was associated with age, body mass index, and tumor grade, with consequences for breast gene expression. Breast tissue morphologic factors may influence breast cancer etiology. Composition and gene expression may act as biomarkers of breast cancer risk and progression. ©2014 American Association for Cancer Research.

  12. IMP3 expression in human ovarian cancer is associated with improved survival

    DEFF Research Database (Denmark)

    Noske, Aurelia; Faggad, Areeg; Wirtz, Ralph

    2009-01-01

    The insulin-like growth factor-II mRNA-binding protein IMP3 plays an important role in embryogenesis and recent reports suggest an involvement in tumorigenesis. Although IMP3 expression has been well studied in mouse and human fetal and adult gonads, its role in ovarian cancer is unknown. We...... investigated the expression of IMP3 at protein and mRNA levels in a cohort of primary ovarian carcinomas and in 11 ovarian cancer cell lines. Western blot analysis revealed an expression of IMP3 in all ovarian cancer cell lines and immunohistochemistry demonstrated a positive cytoplasmic staining in 32 of 68...... carcinomas (47%). In contrast, epithelium of borderline tumors, as well as, benign ovarian lesions and normal ovaries exhibited only weak or no IMP3 expression. In univariate Kaplan-Meier analysis, IMP3 protein expression was significantly associated with better overall survival (P=0.048). To confirm...

  13. Intranasal insulin improves cerebral blood flow, Nrf-2 expression and BDNF in STZ (ICV)-induced memory impaired rats.

    Science.gov (United States)

    Rajasekar, N; Nath, Chandishwar; Hanif, Kashif; Shukla, Rakesh

    2017-03-15

    Insulin/insulin receptor signaling is involved in cognitive functions. Clinical studies have shown that intranasal insulin administration improves memory functions. However, the molecular mechanisms associated with improvement in memory functions are largely unexplored. Therefore, we investigated the protective effect of intranasal insulin in intracerebroventricular (ICV) streptozotocin (STZ) induced memory impairment in rats. Rats were injected with STZ (3mg/kg, ICV) bilaterally twice, on days 1 and 3 and intranasal insulin (2IU/rat/day) was given for 14days. Memory was assessed by Morris water maze test. Cerebral blood flow (CBF) was measured by laser-Doppler flowmetry. The biochemical and molecular studies were done in cortex and hippocampus of rat brain. STZ (ICV) administration caused memory impairment along with the reduction of CBF, ATP level, and Nrf-2 expression. Treatment with intranasal insulin significantly improved memory functions as well as restored CBF, ATP content and Nrf-2 expression in STZ injected rats. STZ administration stimulated oxidative-nitrosative stress as evidenced by a significant increase in ROS, malondialdehyde, NO level and inducible nitric oxide synthase expression and the decrease in glutathione level; which was normalized by intranasal insulin delivery. STZ-induced cholinergic dysfunction (AChE activity and α7-nAChR expression), and mitochondrial hypofunction was largely prevented by treatment with intranasal insulin. Intranasal insulin delivery successfully restored BDNF level and pCREB expression in STZ injected rats. The study shows the beneficial effects of intranasal insulin against STZ-induced memory impairment, which attributed to improved CBF, cholinergic function, brain energy metabolism, BDNF, Nrf-2 expression and antioxidative action. Copyright © 2016. Published by Elsevier Inc.

  14. Variable stromal periductular expression of CD34 and smooth muscle actin (SMA in intraductal carcinoma of the breast.

    Directory of Open Access Journals (Sweden)

    Xavier Catteau

    Full Text Available In breast carcinoma, the stromal loss of CD34 expression and acquisition of SMA myofibroblastic features may constitute a prerequisite for tumor invasiveness. However, this hypothesis remains controversial, with some authors describing the loss of CD34 fibrocytes in the absence of SMA myofibroblastic-like cells in the stroma of invasive carcinoma. Others have also described the disappearance of CD34 fibrocytes from in situ carcinoma. To clarify this issue, we compared the distribution of CD34 fibrocytes and SMA reactive myofibroblasts between stromal areas of tumor-free mammary tissue, ductal carcinoma in situ (DCIS and invasive ductal carcinoma (IDC. In addition to 28 IDC, 300 normal duct-lobular units and 600 ducts with DCIS (158 low-grade, 266 intermediate, and 176 high-grade were scored. The relationships between staining patterns and different histological features (grade of DCIS and presence or absence of necrosis were compared. Loss of CD34 expression and acquisition of SMA expression were more frequent in high-grade in situ lesions than in intermediate and low-grade lesions (p<0.001. When necrosis was found in association with grade 2 or 3 DCIS, the decrease in CD34 expression was higher than in lesions without necrosis and that independently of the grade of DCIS (p<0.05. Necrosis did not appear to play a significant role in the expression of SMA (p = 0.35. In all cases, the stroma of invasive carcinomas showed a complete loss of CD34 fibrocytes. Future research on both CD34 fibrocytes and mechanisms stromal changes are essential in the future and may potentially lead to new treatment approaches.

  15. Comparison of factor VIII transgenes bioengineered for improved expression in gene therapy of hemophilia A.

    Science.gov (United States)

    Dooriss, Kerry L; Denning, Gabriela; Gangadharan, Bagirath; Javazon, Elisabeth H; McCarty, David A; Spencer, H Trent; Doering, Christopher B

    2009-05-01

    Successful gene therapy of hemophilia A depends on the sustained expression of therapeutic levels of factor VIII (fVIII). Because of mRNA instability, interactions with resident endoplasmic reticulum (ER) chaperones, and the requirement for carbohydrate-facilitated transport from the ER to the Golgi apparatus, fVIII is expressed at much lower levels from mammalian cells than other proteins of similar size and complexity. A number of bioengineered forms of B domain-deleted (BDD) human fVIII have been generated and shown to have enhanced expression. Previously, we demonstrated that recombinant BDD porcine fVIII exhibits high-level expression due to specific sequence elements that increase biosynthesis via enhanced posttranslational transit through the secretory pathway. In the current study, high-expression recombinant fVIII constructs were compared directly in order to determine the relative expression of the various bioengineered fVIII transgenes. The data demonstrate that BDD porcine fVIII expression is superior to that of any of the human fVIII variant constructs tested. Mean fVIII expression of 18 units/10(6) cells/24 hr was observed from HEK-293 cells expressing a single copy of the porcine fVIII transgene, which was 36- to 225-fold greater than that of any human fVIII transgene tested. Furthermore, greater than 10-fold higher expression was observed in human cells transduced with BDD porcine fVIII versus BDD human fVIII-encoding lentiviral vectors, even at low proviral copy numbers, supporting its use over other human fVIII variants in future hemophilia A gene therapy clinical trials.

  16. Quantitative assessment of prevalence of pre-analytical variables and their effect on coagulation assay. Can intervention improve patient safety?

    Science.gov (United States)

    Bhushan, Ravi; Sen, Arijit

    2017-04-01

    Very few Indian studies exist on evaluation of pre-analytical variables affecting "Prothrombin Time" the commonest coagulation assay performed. The study was performed in an Indian tertiary care setting with an aim to assess quantitatively the prevalence of pre-analytical variables and their effects on the results (patient safety), for Prothrombin time test. The study also evaluated their effects on the result and whether intervention, did correct the results. The firstly evaluated the prevalence for various pre-analytical variables detected in samples sent for Prothrombin Time testing. These samples with the detected variables wherever possible were tested and result noted. The samples from the same patients were repeated and retested ensuring that no pre-analytical variable is present. The results were again noted to check for difference the intervention produced. The study evaluated 9989 samples received for PT/INR over a period of 18 months. The prevalence of different pre-analytical variables was found to be 862 (8.63%). The proportion of various pre-analytical variables detected were haemolysed samples 515 (5.16%), over filled vacutainers 62 (0.62%), under filled vacutainers 39 (0.39%), low values 205 (2.05%), clotted samples 11 (0.11%), wrong labeling 4 (0.04%), wrong vacutainer use 2 (0.02%), chylous samples 7 (0.07%) and samples with more than one variable 17 (0.17%). The comparison of percentage of samples showing errors were noted for the first variables since they could be tested with and without the variable in place. The reduction in error percentage was 91.5%, 69.2%, 81.5% and 95.4% post intervention for haemolysed, overfilled, under filled and samples collected with excess pressure at phlebotomy respectively. Correcting the variables did reduce the error percentage to a great extent in these four variables and hence the variables are found to affect "Prothrombin Time" testing and can hamper patient safety.

  17. Blocking gp130 signaling suppresses autotaxin expression in adipocytes and improves insulin sensitivity in diet-induced obesity.

    Science.gov (United States)

    Sun, Shuhong; Wang, Ran; Song, Jianwen; Guan, Ming; Li, Na; Zhang, Xiaotian; Zhao, Zhenwen; Zhang, Junjie

    2017-11-01

    Autotaxin (ATX), which is highly expressed and secreted by adipocytes, functions as the key enzyme to generate lysophosphatidic acid (LPA) from lysophosphatidylcholine. Adipose tissue is the main source of circulating ATX that modulates plasma LPA levels. Upregulation of ATX expression in obese patients and mice is closely related with insulin resistance and impaired glucose tolerance. However, the mechanism of ATX expression in adipocytes remains largely unknown. In this study, we found that glycoprotein 130 (gp130)-mediated Janus kinase (JAK)-signal transducer and activator of transcription 3 (STAT3) activation was required for abundant ATX expression in adipocytes. Through gp130, the interleukin 6 (IL-6) family cytokines, such as IL-6, leukemia inhibitory factor, cardiotrophin-1, and ciliary neurotrophic factor, upregulated ATX expression in adipocytes. ATX contributes to the induction of insulin resistance and lipolysis in IL-6-stimulated adipocytes. Oral administration of gp130 inhibitor SC144 suppressed ATX expression in adipose tissue, decreased plasma ATX, LPA, and FFA levels, and significantly improved insulin sensitivity and glucose tolerance in high-fat diet-fed obese mice. In summary, our results indicate that the activation of gp130-JAK-STAT3 pathway by IL-6 family cytokines has an important role in regulating ATX expression in adipocytes and that gp130 is a promising target in the management of obesity-associated glucose metabolic diseases. Copyright © 2017 by the American Society for Biochemistry and Molecular Biology, Inc.

  18. Generation and expression in plants of a single-chain variable fragment antibody against the immunodominant membrane protein of Candidatus phytoplasma aurantifolia.

    Science.gov (United States)

    Shahryari, F; Safarnejad, M R; Shams-Bakhsh, M; Schillberg, S; Nölke, G

    2013-08-01

    Witches' broom of lime is a disease caused by Candidatus Phytoplasma aurantifolia, which represents the most significant global threat to the production of lime trees (Citrus aurantifolia). Conventional disease management strategies have shown little success, and new approaches based on genetic engineering need to be considered. The expression of recombinant antibodies and fragments thereof in plant cells is a powerful approach that can be used to suppress plant pathogens. We have developed a single-chain variable fragment antibody (scFvIMP6) against the immunodominant membrane protein (IMP) of witches' broom phytoplasma and expressed it in different plant cell compartments. We isolated scFvIMP6 from a naïve scFv phage display library and expressed it in bacteria to demonstrate its binding activity against both recombinant IMP and intact phytoplasma cells. The expression of scFvIMP6 in plants was evaluated by transferring the scFvIMP6 cDNA to plant expression vectors featuring constitutive or phloem specific promoters in cassettes with or without secretion signals, therefore causing the protein to accumulate either in the cytosol or apoplast. All constructs were transiently expressed in Nicotiana benthamiana by agroinfiltration, and antibodies of the anticipated size were detected by immunoblotting. Plant-derived scFvIMP6 was purified by affinity chromatography, and specific binding to recombinant IMP was demonstrated by enzyme-linked immunosorbent assay. Our results indicate that scFvIMP6 binds with high activity and can be used for the detection of Ca. Phytoplasma aurantifolia and is also a suitable candidate for stable expression in lime trees to suppress witches' broom of lime.

  19. Expression of heterologous transporters in Saccharomyces kudriavzevii: A strategy for improving yeast salt tolerance and fermentation performance.

    Science.gov (United States)

    Dibalova-Culakova, Hana; Alonso-Del-Real, Javier; Querol, Amparo; Sychrova, Hana

    2018-03-02

    S. kudriavzevii has potential for fermentations and other biotechnological applications, but is sensitive to many types of stress. We tried to increase its tolerance and performance via the expression of various transporters from different yeast species. Whereas the overexpression of Z. rouxii fructose uptake systems (ZrFfz1 and ZrFsy1) or a glycerol importer (ZrStl1) did not improve the ability of S. kudriavzevii to consume fructose and survive osmotic stress, the expression of alkali-metal-cation exporters (ScEna1, ScNha1, YlNha2) improved S. kudriavzevii salt tolerance, and that of ScNha1 also the fermentation performance. The level of improvement depended on the type and activity of the transporter suggesting that the natural sensitivity of S. kudriavzevii cells to salts is based on a non-optimal functioning of its own transporters. Copyright © 2018. Published by Elsevier B.V.

  20. Evaluation and improvement of the regulatory inference for large co-expression networks with limited sample size.

    Science.gov (United States)

    Guo, Wenbin; Calixto, Cristiane P G; Tzioutziou, Nikoleta; Lin, Ping; Waugh, Robbie; Brown, John W S; Zhang, Runxuan

    2017-06-19

    Co-expression has been widely used to identify novel regulatory relationships using high throughput measurements, such as microarray and RNA-seq data. Evaluation studies on co-expression network analysis methods mostly focus on networks of small or medium size of up to a few hundred nodes. For large networks, simulated expression data usually consist of hundreds or thousands of profiles with different perturbations or knock-outs, which is uncommon in real experiments due to their cost and the amount of work required. Thus, the performances of co-expression network analysis methods on large co-expression networks consisting of a few thousand nodes, with only a small number of profiles with a single perturbation, which more accurately reflect normal experimental conditions, are generally uncharacterized and unknown. We proposed a novel network inference methods based on Relevance Low order Partial Correlation (RLowPC). RLowPC method uses a two-step approach to select on the high-confidence edges first by reducing the search space by only picking the top ranked genes from an intial partial correlation analysis and, then computes the partial correlations in the confined search space by only removing the linear dependencies from the shared neighbours, largely ignoring the genes showing lower association. We selected six co-expression-based methods with good performance in evaluation studies from the literature: Partial correlation, PCIT, ARACNE, MRNET, MRNETB and CLR. The evaluation of these methods was carried out on simulated time-series data with various network sizes ranging from 100 to 3000 nodes. Simulation results show low precision and recall for all of the above methods for large networks with a small number of expression profiles. We improved the inference significantly by refinement of the top weighted edges in the pre-inferred partial correlation networks using RLowPC. We found improved performance by partitioning large networks into smaller co-expressed

  1. Naturally occurring genetic variability in expression of Gsta4 is associated with differential survival of axotomized rat motoneurons

    DEFF Research Database (Denmark)

    Mikael, Ström; Al Nimer, Faiez; Lindblom, Rickard

    2012-01-01

    A large number of molecular pathways have been implicated in the degeneration of axotomized motoneurons. We previously have demonstrated substantial differences in the survival rate of axotomized motoneurons across different rat strains. Identification of genetic differences underlying...... to regulate motoneuron survival after ventral root avulsion. The smallest genetic fragment, R5, contains 35 genes and displays a highly significant regulatory effect on motoneuron survival. Furthermore, expression profiling in a F2(DAxPVG) intercross demonstrates one single cis-regulated gene within the R5......, with a strong cytoplasmic labeling of motoneurons. These results demonstrate and map naturally occurring genetic differences in the expression of Gsta4 is associated both with a highly significant increase in the survival of axotomized motoneurons and with a trans-regulation of several molecular pathways...

  2. Variable metastatic potentials correlate with differential plectin and vimentin expression in syngeneic androgen independent prostate cancer cells.

    Directory of Open Access Journals (Sweden)

    Tanya C Burch

    Full Text Available Prostate cancer is a clinically heterogeneous disease, ranging from indolent asymptomatic disease to very aggressive metastatic and life threatening forms of the disease. Distant metastasis represents the major lethal cause of prostate cancer. The most critical clinical challenge in the management of the patients is identifying those individuals at risk of developing metastatic disease. To understand the molecular mechanisms of prostate cancer metastasis and identify markers with metastatic potential, we have analyzed protein expression in two syngeneic prostate cancer cells lines PC3-N2 and PC3-ML2 using isobaric tags for relative and absolute quantitation labeling and multi-dimensional protein identification technology liquid chromatography matrix assisted laser desorption ionization tandem mass spectrometry. PC3-N2 is lowly metastatic while PC3-ML2 highly metastatic. A total of 1,756 proteins were identified in the analyses with 130 proteins showing different expression levels (p<0.01 in the two cell lines. Out of these, 68 proteins were found to be significantly up-regulated while 62 are significantly down-regulated in PC3-ML2 cells compared with PC3-N2 cells. The upregulation of plectin and vimentin which were the most significantly differentially expressed were validated by Western blot and their functional relevance with respect to invasion and migration was determined by siRNA gene silencing. To our knowledge, this study is the first to demonstrate that up-regulation of vimentin and plectin expression positively correlates with the invasion and metastasis of androgen-independent PCA.

  3. Recombinant Escherichia coli strains with inducible Campylobacter jejuni single domain hemoglobin CHb expression exhibited improved cell growth in bioreactor culture.

    Directory of Open Access Journals (Sweden)

    Li Xu

    Full Text Available Maintaining an appropriate concentration of dissolved oxygen in aqueous solution is critical for efficient operation of a bioreactor, requiring sophisticated engineering design and a system of regulation to maximize oxygen transfer from the injected air bubbles to the cells. Bacterial hemoglobins are oxygen-binding proteins that transfer oxygen from the environment to metabolic processes and allow bacteria to grow even under microaerophilic conditions. To improve the oxygen utilization efficiency of cells and overcome the oxygen shortage in bioreactors, the gene coding for the Campylobacter jejuni single domain hemoglobin (CHb gene was artificially synthesized and functionally expressed under the control of inducible expression promoters PT7 and Pvgh in Escherichia coli. The effects of the recombinants PT7-CHb and Pvgh-CHb on cell growth were evaluated in aerobic shake flasks, anaerobic capped bottles and a 5-L bioreactor, and a pronounced improvement in cell biomass was observed for CHb-expressing cells. To determine the growth curves, CHb gene expression, and CHb oxygen-binding capacity of specific recombinants with different promoters, we determined the time course of CHb gene expression in the two recombinants by semi-quantitative RT-PCR and CO differential spectrum assays. Based on the growth patterns of the two recombinants in the bioreactor, we proposed different recombinant types with optimal performance under specific culture conditions.

  4. Improvement of cognitive function and physical activity of aging mice by human neural stem cells over-expressing choline acetyltransferase.

    Science.gov (United States)

    Park, Dongsun; Yang, Yun-Hui; Bae, Dae Kwon; Lee, Sun Hee; Yang, Goeun; Kyung, Jangbeen; Kim, Dajeong; Choi, Ehn-Kyoung; Lee, Seong Won; Kim, Gon Hyung; Hong, Jin Tae; Choi, Kyung-Chul; Lee, Hong Jun; Kim, Seung U; Kim, Yun-Bae

    2013-11-01

    Aging is characterized by progressive loss of cognitive and memory functions as well as decrease in physical activities. In the present study, a human neural stem cell line (F3 NSC) over-expressing choline acetyltransferase (F3.ChAT), an enzyme responsible for acetylcholine synthesis, was generated and transplanted in the brain of 18-month-old male ICR mice. Four weeks post-transplantation, neurobehavioral functions, expression of ChAT enzyme, production of acetylcholine and neurotrophic factors, and expression of cholinergic nervous system markers in transplanted animals were investigated. F3.ChAT NSCs markedly improved both the cognitive function and physical activity of aging animals, in parallel with the elevation of brain acetylcholine level. Transplanted F3 and F3.ChAT cells were found to differentiate into neurons and astrocytes, and to produce ChAT proteins. Transplantation of the stem cells increased brain-derived neurotrophic factor (BDNF) and nerve growth factor (NGF), enhanced expression of Trk B, and restored host microtubule-associated protein 2 and cholinergic nervous system. The results demonstrate that human NSCs over-expressing ChAT improve cognitive function and physical activity of aging mice, not only by producing ACh directly but also by restoring cholinergic neuronal integrity, which might be mediated by neurotrophins BDNF and NGF. Copyright © 2013 Elsevier Inc. All rights reserved.

  5. New Frontiers in Heart Rate Variability and Social Coherence Research: Techniques, Technologies, and Implications for Improving Group Dynamics and Outcomes.

    Science.gov (United States)

    McCraty, Rollin

    2017-01-01

    Concepts embraced by the term coherence have been identified as central to fields such as quantum physics, physiology, and social science. There are different types of coherence, although the term always implies a harmonious relationship, correlations and connections between the various parts of a system. A specific measure derived from heart rate variability (HRV) provides a measure of physiological coherence. Another type of coherence, social coherence, relates to the harmonious alignment between couples or pairs, family units, small groups, or larger organizations in which a network of relationships exists among individuals who share common interests and objectives. A high degree of social coherence is reflected by stable and harmonious relationships, which allows for the efficient flow and utilization of energy and communication required for optimal collective cohesion and action. Social coherence requires that group members are attuned and are emotionally connected with each other, and that the group's emotional energy is organized and regulated by the group as a whole. A number of studies are reviewed which have explored various types of synchronization in infants, pairs and groups, indicating that feelings of cooperation, trust, compassion and increased prosocial behaviors depends largely on the establishment of a spontaneous synchronization of various physiological rhythms between individuals. This article discusses a new application using HRV monitoring in social coherence research and the importance of physiological synchronization in group developmental processes and dynamics. Building on the extensive body of research showing that providing feedback of HRV coherence level at the individual level can improve self-regulation, we suggest the following hypotheses: (1) providing feedback of individual and collective HRV coherence and the degree of heart rhythm synchronization will increase group coherence, and heart rhythm synchronization among group members

  6. New Frontiers in Heart Rate Variability and Social Coherence Research: Techniques, Technologies, and Implications for Improving Group Dynamics and Outcomes

    Directory of Open Access Journals (Sweden)

    Rollin McCraty

    2017-10-01

    Full Text Available Concepts embraced by the term coherence have been identified as central to fields such as quantum physics, physiology, and social science. There are different types of coherence, although the term always implies a harmonious relationship, correlations and connections between the various parts of a system. A specific measure derived from heart rate variability (HRV provides a measure of physiological coherence. Another type of coherence, social coherence, relates to the harmonious alignment between couples or pairs, family units, small groups, or larger organizations in which a network of relationships exists among individuals who share common interests and objectives. A high degree of social coherence is reflected by stable and harmonious relationships, which allows for the efficient flow and utilization of energy and communication required for optimal collective cohesion and action. Social coherence requires that group members are attuned and are emotionally connected with each other, and that the group’s emotional energy is organized and regulated by the group as a whole. A number of studies are reviewed which have explored various types of synchronization in infants, pairs and groups, indicating that feelings of cooperation, trust, compassion and increased prosocial behaviors depends largely on the establishment of a spontaneous synchronization of various physiological rhythms between individuals. This article discusses a new application using HRV monitoring in social coherence research and the importance of physiological synchronization in group developmental processes and dynamics. Building on the extensive body of research showing that providing feedback of HRV coherence level at the individual level can improve self-regulation, we suggest the following hypotheses: (1 providing feedback of individual and collective HRV coherence and the degree of heart rhythm synchronization will increase group coherence, and heart rhythm synchronization

  7. Improved expression of Rhizopus oryzae α-amylase in the methylotrophic yeast Pichia pastoris.

    Science.gov (United States)

    Li, Song; Sing, Suren; Wang, Zhengxiang

    2011-09-01

    In our previous study, the α-amylase from Rhizopus oryzae (RoAmy) was expressed in Escherichia coli and Saccharomyces cerevisiae but the obtained recombinant RoAmy (rRoAmy) yields were too low. The aim of the present research was to obtain high-level expressions of RoAmy in the methylotrophic yeast Pichia pastoris. To this end, we constructed P. pastoris strains with the capability to express recombinant α-amylase under the control of constitutive glyceraldehyde-3-phosphate dehydrogenase (GAP) and methanol-inducible alcohol oxidase 1 promoters. The levels of inducibly expressed rRoAmy were higher than those of constitutively expressed. The maximal inducible rRoAmy expression levels for the Mut(+) strains (41.1mg/l) were approximately eight times higher than those for the Mut(s) strains and 24 times higher than those expressed under the control of the GAP promoter. For both inducible and constitutive expressions, the S. cerevisiae α-prepro sequence and the native signal sequence of RoAmy were used separately to direct the secretion of rRoAmy into the culture medium of P. pastoris. Low levels of intracellular amylase activities that had been detected after shake-flask fermentation indicated that both signal sequences could effectively direct the secretion of rRoAmy under all studied conditions. In addition, the secretion levels of rRoAmy directed with its own signal peptide were 7-10% higher than those directed by the α-prepro sequence. Copyright © 2011 Elsevier Inc. All rights reserved.

  8. Chia (Salvia hispanica L.) enhances HSP, PGC-1α expressions and improves glucose tolerance in diet-induced obese rats.

    Science.gov (United States)

    Marineli, Rafaela da Silva; Moura, Carolina Soares; Moraes, Érica Aguiar; Lenquiste, Sabrina Alves; Lollo, Pablo Christiano Barboza; Morato, Priscila Neder; Amaya-Farfan, Jaime; Maróstica, Mário Roberto

    2015-05-01

    The aim of this study was to investigate the effects of chia seed and chia oil on heat shock protein (HSP) and related parameters in diet-induced obese rats. Animals were divided in six groups: control, high-fat and high-fructose diet (HFF), and HFF with chia seed or chia oil in short (6-wk) and long (12-wk) treatments. Plasma indicators of glucose tolerance and liver damage, skeletal muscle expression of antioxidant enzymes, and proteins controlling oxidative energy metabolism were determined. The limit of significance was set at P chia seed or chia oil did not reduce body weight gain or abdominal fat accumulation. However, chia seed and chia oil in both treatments improved glucose and insulin tolerance. Chia oil in both treatments induced expression of HSP70 and HSP25 in skeletal muscle. Short treatment with chia seed increased expression of HSP70, but not HSP25. Chia oil in both treatments restored superoxide dismutase and glutathione peroxidase expression. Extended treatment with chia seed and short treatment with chia oil restored peroxisome proliferator-activated receptor-γ coactivator-1α (PGC-1α) expression. Chia oil restored the antioxidant system and induced the expression of a higher number of proteins than chia seed. The present study demonstrated new properties and molecular mechanisms associated with the beneficial effects of chia seed and chia oil consumption in diet-induced obese rats. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. Interpopulational variability of Pinus sylvestris L. in eight Polish localities expressed in morphological and anatomical traits of needles

    Directory of Open Access Journals (Sweden)

    Maria A. Bobowicz

    2014-01-01

    Full Text Available Two-year old needles were collected from 272 standing trees of Pinus sylvestris L., representing 8 Polish populations. The needles were studied in respect to IS morphological and anatomical traits. The obtained data were subjected to multivariate statistical analysis in an attempt to delineate interpopulational variability. Multivariate analysis of variance with testing of statistical hypotheses and discriminant analysis were conducted. Mahalanobis distances were calculated between each of population in pairs and their significance was estimated using Hotelling T2 statistics. On the basis of the shortest Mahalanobis distances a minimum spanning tree was constructed and on the basis of Euklidean distances hierarchy grouping was performed. A large majority of the populations was found to differ significantly from the remaining populations. The population from Bolewice proved to be most divergent. The principal variables which proved capable of discriminating between populations were found to include: needle length, the number of stomata on the flat side of the needle and the number of resin canals. Using Bryant's test, the studied populations were found to belong to two geographic groups: the North-Polish one or the South-Polish one.

  10. The variability of Scots pine from Piekielna Góra as expressed by morphological and anatomical traits of needles

    Directory of Open Access Journals (Sweden)

    Maria A. Bobowicz

    2014-01-01

    Full Text Available Two-year old needles were collected from 30 standing Scots pine trees on Piekielna Góra. These needles were analysed in respect to 13 morphological and anatomical traits. The data so obtained was subjected to a whole range of multi-trait analytical methods in an attempt to determine the variability among the randomly chosen trees. Multivariate analysis of variance and canonical analysis were done as well as calculation of Mahalanobis distances between each pair of trees and their significance was tested by the Hotelling T2 statistics. Aminimum spanning tree was constructed on the basis of the shortest Mahalanobis distances, while a dendrogram (cluster analysis was compiled on the basis of Euclidean distances. It was found that in spite of the fact that the studied population sample of pines did not form internal, significantly differentiated groups, the variability among particular trees was large and depended on the given trait. The number of resin canals best differentiated the studied trees, while the Marcet coefficient did not significantly differentia­te any pair of trees.

  11. Expression of anti-tumor necrosis factor alpha (TNFα) single-chain variable fragment (scFv) in Spirodela punctata plants transformed with Agrobacterium tumefaciens.

    Science.gov (United States)

    Balaji, Parthasarathy; Satheeshkumar, P K; Venkataraman, Krishnan; Vijayalakshmi, M A

    2016-05-01

    Therapeutic antibodies against tumor necrosis factor alpha (TNFα) have been considered effective for some of the autoimmune diseases such as rheumatoid arthritis, Crohn's diseases, and so on. But associated limitations of the current therapeutics in terms of cost, availability, and immunogenicity have necessitated the need for alternative candidates. Single-chain variable fragment (scFv) can negate the limitations tagged with the anti-TNFα therapeutics to a greater extent. In the present study, Spirodela punctata plants were transformed with anti-TNFα through in planta transformation using Agrobacterium tumefaciens strain, EHA105. Instead of cefotaxime, garlic extract (1 mg/mL) was used to remove the agrobacterial cells after cocultivation. To the best of our knowledge, this report shows for the first time the application of plant extracts in transgenic plant development. 95% of the plants survived screening under hygromycin. ScFv cDNA integration in the plant genomic DNA was confirmed at the molecular level by PCR. The transgenic protein expression was followed up to 10 months. Expression of scFv was confirmed by immunodot blot. Protein expression levels of up to 6.3% of total soluble protein were observed. β-Glucuronidase and green fluorescent protein expressions were also detected in the antibiotic resistant plants. The paper shows the generation of transgenic Spirodela punctuata plants through in planta transformation. © 2015 International Union of Biochemistry and Molecular Biology, Inc.

  12. Identification, expression pattern and potential role of variable lymphocyte receptor Aj-VLRA from Apostichopus japonicus in response to bacterial challenge.

    Science.gov (United States)

    Yang, Lei; Yao, Feng; Ba, Huazhong; Qin, Tong; Luan, Hong; Li, Zhengmin; Hou, Lin; Zou, Xiangyang

    2015-08-01

    The variable lymphocyte receptors (VLRs) are found in jawless vertebrates (agnathans), and specifically recognize bacteria and viruses via their leucine-rich repeats (LRRs). VLRs are believed to be adaptive immune response molecules. Echinoderms do not have adaptive immune systems; however, in the present study, a VLR cDNA named Aj-VLRA was cloned and characterized from sea cucumber, Apostichopus japonicus. The complete cDNA of Aj-VLRA was 3072 bp, including a 1995 bp open reading frame encoding 664 amino acids comprising LRR domains, a predicted transmembrane helix and an N-terminal signal peptide. As determined by quantitative real-time reverse transcription polymerase chain reaction, Aj-VLRA transcripts are ubiquitously expressed in the body wall, longitudinal muscles, intestine and respiratory tree of A. japonicus. The expression level of Aj-VLRA was upregulated after challenge with four common marine bacteria. In situ hybridization showed that the expression of Aj-VLRA was widely distributed in the four tissues, particularly in the cytoplasm of epidermal cells. Recombinantly expressed Aj-VLRA (including the LRR domains) could bind to bacteria including Micrococcus lysodeikticus (Gram+) and Vibrio anguillarum (Gram-). Collectively, the results suggested that Aj-VLRA is related to an innate immune response of A. japonicus. Copyright © 2015 Elsevier Ltd. All rights reserved.

  13. Face or body? Oxytocin improves perception of emotions from facial expressions in incongruent emotional body context.

    Science.gov (United States)

    Perry, Anat; Aviezer, Hillel; Goldstein, Pavel; Palgi, Sharon; Klein, Ehud; Shamay-Tsoory, Simone G

    2013-11-01

    The neuropeptide oxytocin (OT) has been repeatedly reported to play an essential role in the regulation of social cognition in humans in general, and specifically in enhancing the recognition of emotions from facial expressions. The later was assessed in different paradigms that rely primarily on isolated and decontextualized emotional faces. However, recent evidence has indicated that the perception of basic facial expressions is not context invariant and can be categorically altered by context, especially body context, at early perceptual levels. Body context has a strong effect on our perception of emotional expressions, especially when the actual target face and the contextually expected face are perceptually similar. To examine whether and how OT affects emotion recognition, we investigated the role of OT in categorizing facial expressions in incongruent body contexts. Our results show that in the combined process of deciphering emotions from facial expressions and from context, OT gives an advantage to the face. This advantage is most evident when the target face and the contextually expected face are perceptually similar. Copyright © 2013 Elsevier Ltd. All rights reserved.

  14. Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation

    Energy Technology Data Exchange (ETDEWEB)

    Elias, Dwayne A.; Mukhopadhyay, Aindrila; Joachimiak, Marcin P.; Drury, Elliott C.; Redding, Alyssa M.; Yen, Huei-Che B.; Fields, Matthew W.; Hazen, Terry C.; Arkin, Adam P.; Keasling, Jay D.; Wall, Judy D.

    2008-10-27

    Hypothetical and conserved hypothetical genes account for>30percent of sequenced bacterial genomes. For the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough, 347 of the 3634 genes were annotated as conserved hypothetical (9.5percent) along with 887 hypothetical genes (24.4percent). Given the large fraction of the genome, it is plausible that some of these genes serve critical cellular roles. The study goals were to determine which genes were expressed and provide a more functionally based annotation. To accomplish this, expression profiles of 1234 hypothetical and conserved genes were used from transcriptomic datasets of 11 environmental stresses, complemented with shotgun LC-MS/MS and AMT tag proteomic data. Genes were divided into putatively polycistronic operons and those predicted to be monocistronic, then classified by basal expression levels and grouped according to changes in expression for one or multiple stresses. 1212 of these genes were transcribed with 786 producing detectable proteins. There was no evidence for expression of 17 predicted genes. Except for the latter, monocistronic gene annotation was expanded using the above criteria along with matching Clusters of Orthologous Groups. Polycistronic genes were annotated in the same manner with inferences from their proximity to more confidently annotated genes. Two targeted deletion mutants were used as test cases to determine the relevance of the inferred functional annotations.

  15. New Recombinant Mycobacterium bovis BCG Expression Vectors: Improving Genetic Control over Mycobacterial Promoters.

    Science.gov (United States)

    Kanno, Alex I; Goulart, Cibelly; Rofatto, Henrique K; Oliveira, Sergio C; Leite, Luciana C C; McFadden, Johnjoe

    2016-04-01

    The expression of many antigens, stimulatory molecules, or even metabolic pathways in mycobacteria such as Mycobacterium bovis BCG or M. smegmatis was made possible through the development of shuttle vectors, and several recombinant vaccines have been constructed. However, gene expression in any of these systems relied mostly on the selection of natural promoters expected to provide the required level of expression by trial and error. To establish a systematic selection of promoters with a range of strengths, we generated a library of mutagenized promoters through error-prone PCR of the strong PL5 promoter, originally from mycobacteriophage L5. These promoters were cloned upstream of the enhanced green fluorescent protein reporter gene, and recombinant M. smegmatis bacteria exhibiting a wide range of fluorescence levels were identified. A set of promoters was selected and identified as having high (pJK-F8), intermediate (pJK-B7, pJK-E6, pJK-D6), or low (pJK-C1) promoter strengths in both M. smegmatis and M. bovisBCG. The sequencing of the promoter region demonstrated that it was extensively modified (6 to 11%) in all of the plasmids selected. To test the functionality of the system, two different expression vectors were demonstrated to allow corresponding expression levels of the Schistosoma mansoni antigen Sm29 in BCG. The approach used here can be used to adjust expression levels for synthetic and/or systems biology studies or for vaccine development to maximize the immune response. Copyright © 2016 Kanno et al.

  16. CB1 receptor inhibition leads to decreased vascular AT1 receptor expression, inhibition of oxidative stress and improved endothelial function.

    Science.gov (United States)

    Tiyerili, Vedat; Zimmer, Sebastian; Jung, Suzin; Wassmann, Kerstin; Naehle, Claas P; Lütjohann, Dieter; Zimmer, Andreas; Nickenig, Georg; Wassmann, Sven

    2010-07-01

    Inhibition of the cannabinoid receptor CB(1) (CB(1)-R) exerts numerous positive cardiovascular effects such as modulation of blood pressure, insulin sensitivity and serum lipid concentrations. However, direct vascular effects of CB(1)-R inhibition remain unclear. CB(1)-R expression was validated in vascular smooth muscle cells (VSMCs) and aortic tissue of mice. Apolipoprotein E-deficient (ApoE-/-) mice were treated with cholesterol-rich diet and the selective CB(1)-R antagonist rimonabant or vehicle for 7 weeks. CB(1)-R inhibition had no effect on atherosclerotic plaque development, collagen content and macrophage infiltration but led to improved aortic endothelium-dependent vasodilation and decreased aortic reactive oxygen species (ROS) production and NADPH oxidase activity. Treatment of cultured VSMC with rimonabant resulted in reduced angiotensin II-mediated but not basal ROS production and NADPH oxidase activity. CB(1)-R inhibition with rimonabant and AM251 led to down-regulation of angiotensin II type 1 receptor (AT1-R) expression, whereas stimulation with the CB(1)-R agonist CP 55,940 resulted in AT1-R up-regulation, indicating that AT1-R expression is directly regulated by the CB(1)-R. CB(2)-R inhibition had no impact on AT1-R expression in VSMC. Consistently, CB(1)-R inhibition decreased aortic AT1-R expression in vivo. CB(1)-R inhibition leads to decreased vascular AT1-R expression, NADPH oxidase activity and ROS production in vitro and in vivo. This antioxidative effect is associated with improved endothelial function in ApoE-/- mice, indicating beneficial direct vascular effects of CB(1)-R inhibition.

  17. Treatment with escitalopram improves the attentional bias toward negative facial expressions in patients with major depressive disorders.

    Science.gov (United States)

    Zhou, Zhenhe; Cao, Suxia; Li, Hengfen; Li, Youhui

    2015-10-01

    We hypothesized that treatment with escitalopram would improve cognitive bias and contribute to the recovery process for patients with major depressive disorder (MDD). Many previous studies have established that patients with MDD tend to pay selective attention to negative stimuli. The assessment of the level of cognitive bias is regarded as a crucial dimension of treatment outcomes for MDD. To our knowledge, no prior studies have been reported on the effects of treatment with escitalopram on attentional bias in MDD, employing a dot probe task of facial expression. We studied 25 patients with MDD and 25 controls, and used a dot probe task of facial expression to measure cognitive bias. The patients' psychopathologies were rated using the Hamilton Depression Scale (HAMD) at baseline and after 8 weeks of treatment with escitalopram. All participants performed the facial expression dot probe task. The results revealed that the 8 week escitalopram treatment decreased the HAMD scores. The patients with MDD at baseline exhibited an attentional bias towards negative faces, however, no significant bias toward either negative or happy faces were observed in the controls. After the 8 week escitalopram treatment, no significant bias toward negative faces was observed in the patient group. In conclusion, patients with MDD pay more attention to negative facial expressions, and treatment with escitalopram improves this attentional bias toward negative facial expressions. This is the first study, to our knowledge, on the effects of treatment with escitalopram on attentional bias in patients with MDD that has employed a dot probe task of facial expression. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. Early upregulation of myocardial CXCR4 expression is critical for dimethyloxalylglycine-induced cardiac improvement in acute myocardial infarction.

    Science.gov (United States)

    Mayorga, Mari; Kiedrowski, Matthew; Shamhart, Patricia; Forudi, Farhad; Weber, Kristal; Chilian, William M; Penn, Marc S; Dong, Feng

    2016-01-01

    The stromal cell-derived factor-1 (SDF-1):CXCR4 is important in myocardial repair. In this study we tested the hypothesis that early upregulation of cardiomyocyte CXCR4 (CM-CXCR4) at a time of high myocardial SDF-1 expression could be a strategy to engage the SDF-1:CXCR4 axis and improve cardiac repair. The effects of the hypoxia inducible factor (HIF) hydroxylase inhibitor dimethyloxalylglycine (DMOG) on CXCR4 expression was tested on H9c2 cells. In mice a myocardial infarction (MI) was produced in CM-CXCR4 null and wild-type controls. Mice were randomized to receive injection of DMOG (DMOG group) or saline (Saline group) into the border zone after MI. Protein and mRNA expression of CM-CXCR4 were quantified. Echocardiography was used to assess cardiac function. During hypoxia, DMOG treatment increased CXCR4 expression of H9c2 cells by 29 and 42% at 15 and 24 h, respectively. In vivo DMOG treatment increased CM-CXCR4 expression at 15 h post-MI in control mice but not in CM-CXCR4 null mice. DMOG resulted in increased ejection fraction in control mice but not in CM-CXCR4 null mice 21 days after MI. Consistent with greater cardiomyocyte survival with DMOG treatment, we observed a significant increase in cardiac myosin-positive area within the infarct zone after DMOG treatment in control mice, but no increase in CM-CXCR4 null mice. Inhibition of cardiomyocyte death in MI through the stabilization of HIF-1α requires downstream CM-CXCR4 expression. These data suggest that engagement of the SDF-1:CXCR4 axis through the early upregulation of CM-CXCR4 is a strategy for improving cardiac repair after MI. Copyright © 2016 the American Physiological Society.

  19. Two novel MYH7 proline substitutions cause Laing Distal Myopathy-like phenotypes with variable expressivity and neck extensor contracture.

    Science.gov (United States)

    Feinstein-Linial, Miora; Buvoli, Massimo; Buvoli, Ada; Sadeh, Menachem; Dabby, Ron; Straussberg, Rachel; Shelef, Ilan; Dayan, Daniel; Leinwand, Leslie Anne; Birk, Ohad S

    2016-08-12

    Human skeletal muscles express three major myosin heavy chain (MyHC) isoforms: MyHCIIx (MYH1) in fast type 2B muscle fibers, MyHCIIa (MYH2) in fast type 2A fibers and MyHCI/β-cardiac MyHC (MYH7) in slow type I skeletal fibers and cardiac ventricles. In line with its expression pattern, MYH7 mutations have been reported in association with hypertrophic or dilated cardiomyopathy, skeletal myopathies or a combination of both. We analyzed the clinical and molecular phenotype of two unrelated families of Jewish Moroccan ancestry that presented with apparently autosomal dominant inheritance of progressive Laing-like distal myopathy with non-specific myopathic changes, but uncommon marked contractures and wasting of the neck extensors. Clinical phenotyping, whole exome sequencing and restriction analysis, generation of mutants followed by cell culture transfection and imaging. Using whole exome sequencing we identified in both families two novel heterozygous proline substitutions located in exon 31 of MYH7 within its rod domain: c.4309G>C (p.Ala1437Pro) and c.4301G>C (p.Arg1434Pro). Here we show that the phenotype caused by these mutations includes marked cervical muscle contracture, and report that the severity of the phenotype varies significantly, to the extent of non-penetrance in one of the families. Finally, we provide evidence that both proline substitutions impair myosin self-assembly in non-muscle cells transfected with β-myosin constructs carrying the mutations, but do not prevent incorporation of the mutant molecules into the sarcomere. This study expands our clinical and molecular knowledge of MYH7 rod mutations causing skeletal myopathies, and underscores the importance of discussing disease penetrance during genetic counseling.

  20. The Mycoplasma fermentans prophage phiMFV1: genome organization, mobility and variable expression of an encoded surface protein.

    Science.gov (United States)

    Röske, K; Calcutt, M J; Wise, K S

    2004-06-01

    The approximately 16 kb genome of the Mycoplasma fermentans phiMFV1 prophage is described, and its mobility, replication and effect on the mycoplasma surface phenotype are demonstrated. In various M. fermentans strains, phiMFV1 was either absent or integrated at diverse (and sometimes multiple) chromosomal sites, each marked by a conserved TTTTTA target sequence that is duplicated upon integration. Precise excision, replication of an extrachromosomal form and loss of phiMFV1 from the mycoplasmal genome were documented in a series of clonal derivatives of M. fermentans propagated in culture. Of 18 open reading frames (ORFs) encoded by phiMFV1, most can be ascribed functions related to phage biology, whereas one encodes a unique coiled-coil membrane surface protein, Mem, that was confirmed to be expressed in propagating populations of M. fermentans. With the exception of Mem and other minor ORFs, the striking similarity between the deduced proteomes of phiMFV1 and the recently described phiMAV1 of arthritogenic strains of Mycoplasma arthritidis, along with the prominent gene synteny between these elements, provides the taxonomic basis for a new family of prophage. Their coding features are consistent with long-term residence in mycoplasma genomes and the divergence of species within a phylogenetic clade of mycoplasmas. The unique Mem protein expressed from phiMFV1 and the unique hypothetical surface lipoproteins encoded by phiMAV1 and phiMFV1 also suggest that prophage-associated genes may provide specific, selectable phenotypic traits during co-evolution of mycoplasma species with their respective mammalian hosts. Retention of these labile prophage elements in organisms with such drastically reduced genome sizes implies a significant role in adaptation and survival.

  1. Improved ethanol production from cheese whey, whey powder, and sugar beet molasses by "Vitreoscilla hemoglobin expressing" Escherichia coli.

    Science.gov (United States)

    Akbas, Meltem Yesilcimen; Sar, Taner; Ozcelik, Busra

    2014-01-01

    This work investigated the improvement of ethanol production by engineered ethanologenic Escherichia coli to express the hemoglobin from the bacterium Vitreoscilla (VHb). Ethanologenic E. coli strain FBR5 and FBR5 transformed with the VHb gene in two constructs (strains TS3 and TS4) were grown in cheese whey (CW) medium at small and large scales, at both high and low aeration, or with whey powder (WP) or sugar beet molasses hydrolysate (SBMH) media at large scale and low aeration. Culture pH, cell growth, VHb levels, and ethanol production were evaluated after 48 h. VHb expression in TS3 and TS4 enhanced their ethanol production in CW (21-419%), in WP (17-362%), or in SBMH (48-118%) media. This work extends the findings that "VHb technology" may be useful for improving the production of ethanol from waste and byproducts of various sources.

  2. [A classification method of gene expression profile based on a locally linear embedding algorism with improved distance].

    Science.gov (United States)

    Cai, Xianfa; Wei, Jia; Wen, Guihua; Li, Jie

    2011-12-01

    With its high dimensionalities, small samples and great noise, feature reduction of gene expression profile becomes quite necessary. The most common form of gene expression profile is nonlinear, and traditional dimensionality reduction methods can not project high dimensional data, whose initial dimensionalities are low, into low dimensional space. In this work, an improved distance locally linear embedding (LLE ) algorism was proposed to reduce the dimensionalities. LLE method is very sensitive to the closely-neighboring parameters. In order to enhance the robustness to the number of neighbors, in the paper we presented a novel distance to measure the distance between the samples for the purpose of reducing-the influence of distribution of samples. Experimental results demonstrated that the improved distance LLE can effectively extract information of classification features and greatly reduce the dimensionalities of data while maintaining a higher classification accuracy.

  3. Improving nutritional quality and fungal tolerance in soya bean and grass pea by expressing an oxalate decarboxylase.

    Science.gov (United States)

    Kumar, Vinay; Chattopadhyay, Arnab; Ghosh, Sumit; Irfan, Mohammad; Chakraborty, Niranjan; Chakraborty, Subhra; Datta, Asis

    2016-06-01

    Soya bean (Glycine max) and grass pea (Lathyrus sativus) seeds are important sources of dietary proteins; however, they also contain antinutritional metabolite oxalic acid (OA). Excess dietary intake of OA leads to nephrolithiasis due to the formation of calcium oxalate crystals in kidneys. Besides, OA is also a known precursor of β-N-oxalyl-L-α,β-diaminopropionic acid (β-ODAP), a neurotoxin found in grass pea. Here, we report the reduction in OA level in soya bean (up to 73%) and grass pea (up to 75%) seeds by constitutive and/or seed-specific expression of an oxalate-degrading enzyme, oxalate decarboxylase (FvOXDC) of Flammulina velutipes. In addition, β-ODAP level of grass pea seeds was also reduced up to 73%. Reduced OA content was interrelated with the associated increase in seeds micronutrients such as calcium, iron and zinc. Moreover, constitutive expression of FvOXDC led to improved tolerance to the fungal pathogen Sclerotinia sclerotiorum that requires OA during host colonization. Importantly, FvOXDC-expressing soya bean and grass pea plants were similar to the wild type with respect to the morphology and photosynthetic rates, and seed protein pool remained unaltered as revealed by the comparative proteomic analysis. Taken together, these results demonstrated improved seed quality and tolerance to the fungal pathogen in two important legume crops, by the expression of an oxalate-degrading enzyme. © 2016 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

  4. Codon Optimization Significantly Improves the Expression Level of α-Amylase Gene from Bacillus licheniformis in Pichia pastoris

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    Jian-Rong Wang

    2015-01-01

    Full Text Available α-Amylase as an important industrial enzyme has been widely used in starch processing, detergent, and paper industries. To improve expression efficiency of recombinant α-amylase from Bacillus licheniformis (B. licheniformis, the α-amylase gene from B. licheniformis was optimized according to the codon usage of Pichia pastoris (P. pastoris and expressed in P. pastoris. Totally, the codons encoding 305 amino acids were optimized in which a total of 328 nucleotides were changed and the G+C content was increased from 47.6 to 49.2%. The recombinants were cultured in 96-deep-well microplates and screened by a new plate assay method. Compared with the wild-type gene, the optimized gene is expressed at a significantly higher level in P. pastoris after methanol induction for 168 h in 5- and 50-L bioreactor with the maximum activity of 8100 and 11000 U/mL, which was 2.31- and 2.62-fold higher than that by wild-type gene. The improved expression level makes the enzyme a good candidate for α-amylase production in industrial use.

  5. Improved multiple-locus variable-number tandem-repeat assay for Staphylococcus aureus genotyping, providing a highly informative technique together with strong phylogenetic value

    NARCIS (Netherlands)

    Pourcel, Christine; Hormigos, Katia; Onteniente, Lucie; Sakwinska, Olga; Deurenberg, Ruud H; Vergnaud, Gilles

    2009-01-01

    We describe an improved multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) scheme for genotyping Staphylococcus aureus. We compare its performance to those of multilocus sequence typing (MLST) and spa typing in a survey of 309 strains. This collection includes 87 epidemic

  6. Simultaneous expression of regulatory genes associated with specific drought-adaptive traits improves drought adaptation in peanut.

    Science.gov (United States)

    Ramu, Vemanna S; Swetha, Thavarekere N; Sheela, Shekarappa H; Babitha, Chandrashekar K; Rohini, Sreevathsa; Reddy, Malireddy K; Tuteja, Narendra; Reddy, Chandrashekar P; Prasad, Trichi Ganesh; Udayakumar, Makarla

    2016-03-01

    Adaptation of crops to drought-prone rain-fed conditions can be achieved by improving plant traits such as efficient water mining (by superior root characters) and cellular-level tolerance mechanisms. Pyramiding these drought-adaptive traits by simultaneous expression of genes regulating drought-adaptive mechanisms has phenomenal relevance in improving stress tolerance. In this study, we provide evidence that peanut transgenic plants expressing Alfalfa zinc finger 1 (Alfin1), a root growth-associated transcription factor gene, Pennisetum glaucum heat-shock factor (PgHSF4) and Pea DNA helicase (PDH45) involved in protein turnover and protection showed improved tolerance, higher growth and productivity under drought stress conditions. Stable integration of all the transgenes was noticed in transgenic lines. The transgenic lines showed higher root growth, cooler crop canopy air temperature difference (less CCATD) and higher relative water content (RWC) under drought stress. Low proline levels in transgenic lines substantiate the maintenance of higher water status. The survival and recovery of transgenic lines was significantly higher under gradual moisture stress conditions with higher biomass. Transgenic lines also showed significant tolerance to ethrel-induced senescence and methyl viologen-induced oxidative stress. Several stress-responsive genes such as heat-shock proteins (HSPs), RING box protein-1 (RBX1), Aldose reductase, late embryogenesis abundant-5 (LEA5) and proline-rich protein-2 (PRP2), a gene involved in root growth, showed enhanced expression under stress in transgenic lines. Thus, the simultaneous expression of regulatory genes contributing for drought-adaptive traits can improve crop adaptation and productivity under water-limited conditions. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

  7. Improved gene expression signature of testicular carcinoma in situ

    DEFF Research Database (Denmark)

    Almstrup, Kristian; Leffers, Henrik; Lothe, Ragnhild A

    2007-01-01

    The carcinoma in situ (CIS) stage is the common precursor of testicular germ cell tumours (TGCTs) that arise in young adults. Within the past decade genome wide gene expression tools have been developed and have greatly advanced the insight into the biology of TGCTs. Two independent data sets on ...

  8. Improved methodology for the affinity isolation of human protein complexes expressed at near endogenous levels

    DEFF Research Database (Denmark)

    Domanski, Michal; Molloy, Kelly; Jiang, Hua

    2012-01-01

    An efficient and reliable procedure for the capture of affinity-tagged proteins and associated complexes from human cell lines is reported. Through multiple optimizations, high yield and low background affinity-purifications are achieved from modest quantities of human cells expressing endogenous...

  9. Improving the expression of recombinant pullulanase by increasing mRNA stability in Escherichia coli

    Directory of Open Access Journals (Sweden)

    Tao Li

    2017-09-01

    Conclusion: The addition of the 5′ SD sequence at the 5′ UTR and a 3′ stem-loop structure at the 3′ UTR of the pulA gene is an effective approach to increase pulA gene expression and fermentation enzyme activity.

  10. Expressive Writing for Gay-Related Stress: Psychosocial Benefits and Mechanisms Underlying Improvement

    Science.gov (United States)

    Pachankis, John E.; Goldfried, Marvin R.

    2010-01-01

    Objective: This study tested the effectiveness of an expressive writing intervention for gay men on outcomes related to psychosocial functioning. Method: Seventy-seven gay male college students (mean age = 20.19 years, SD = 1.99) were randomly assigned to write for 20 min a day for 3 consecutive days about either (a) the most stressful or…

  11. Phase variable O antigen biosynthetic genes control expression of the major protective antigen and bacteriophage receptor in Vibrio cholerae O1.

    Directory of Open Access Journals (Sweden)

    Kimberley D Seed

    2012-09-01

    Full Text Available The Vibrio cholerae lipopolysaccharide O1 antigen is a major target of bacteriophages and the human immune system and is of critical importance for vaccine design. We used an O1-specific lytic bacteriophage as a tool to probe the capacity of V. cholerae to alter its O1 antigen and identified a novel mechanism by which this organism can modulate O antigen expression and exhibit intra-strain heterogeneity. We identified two phase variable genes required for O1 antigen biosynthesis, manA and wbeL. manA resides outside of the previously recognized O1 antigen biosynthetic locus, and encodes for a phosphomannose isomerase critical for the initial step in O1 antigen biosynthesis. We determined that manA and wbeL phase variants are attenuated for virulence, providing functional evidence to further support the critical role of the O1 antigen for infectivity. We provide the first report of phase variation modulating O1 antigen expression in V. cholerae, and show that the maintenance of these phase variable loci is an important means by which this facultative pathogen can generate the diverse subpopulations of cells needed for infecting the host intestinal tract and for escaping predation by an O1-specific phage.

  12. A new mouse model for marfan syndrome presents phenotypic variability associated with the genetic background and overall levels of Fbn1 expression.

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    Bruno L Lima

    Full Text Available Marfan syndrome is an autosomal dominant disease of connective tissue caused by mutations in the fibrillin-1 encoding gene FBN1. Patients present cardiovascular, ocular and skeletal manifestations, and although being fully penetrant, MFS is characterized by a wide clinical variability both within and between families. Here we describe a new mouse model of MFS that recapitulates the clinical heterogeneity of the syndrome in humans. Heterozygotes for the mutant Fbn1 allele mgΔloxPneo, carrying the same internal deletion of exons 19-24 as the mgΔ mouse model, present defective microfibrillar deposition, emphysema, deterioration of aortic wall and kyphosis. However, the onset of a clinical phenotypes is earlier in the 129/Sv than in C57BL/6 background, indicating the existence of genetic modifiers of MFS between these two mouse strains. In addition, we characterized a wide clinical variability within the 129/Sv congenic heterozygotes, suggesting involvement of epigenetic factors in disease severity. Finally, we show a strong negative correlation between overall levels of Fbn1 expression and the severity of the phenotypes, corroborating the suggested protective role of normal fibrillin-1 in MFS pathogenesis, and supporting the development of therapies based on increasing Fbn1 expression.

  13. Variable expression of cerebral cavernous malformations in carriers of a premature termination codon in exon 17 of the Krit1 gene

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    Gamero Miguel A

    2003-07-01

    Full Text Available Abstract Background Cerebral cavernous malformations (CCM present as either sporadic or autosomal dominant conditions with incomplete penetrance of symptoms. Differences in genetic and environmental factors might be minimized among first-degree relatives. We therefore studied clinical expression in a family with several affected members. Methods We studied a three-generation family with the onset of CCM as a cerebral haemorrhage in the younger (four-year-old sibling. Identification and enumeration of CCMs were performed in T2-weighted or gradient-echo MRIs of the whole brains. Genetic analysis comprised SCCP, sequencing and restriction polymorphism of the Krit1 gene in the proband and at risk relatives. Results The phenotypes of cerebral cavernous malformations (CCMs in carriers of Krit1 mutations were very variable. We identified a novel frameshift mutation caused by a 1902A insertion in exon 17 of the Krit1 gene, which leads to a premature TAA triplet and predicts the truncating phenotype Y634X. A very striking finding was the absence of both clinical symptoms and CCMs in the eldest sibling harbouring the 1902insA. Conclusions Patients in this family, harbouring the same mutation, illustrate the very variable clinical and radiological expression of a Krit1 mutation. The early and critical onset in the proband contrasts with minor clinical findings in affected relatives. This consideration is important in genetic counselling.

  14. β-Globin Matrix Attachment Region Improves Stable Genomic Expression of the Sleeping Beauty Transposon

    Science.gov (United States)

    Daly, Meghan C.; Steer, Clifford J.; Kren, Betsy T.

    2014-01-01

    The liver is an attractive target for gene therapy due to its extensive capability for protein production and the numerous diseases resulting from a loss of gene function it normally provides. The Sleeping Beauty Transposon (SB-Tn)1 system is a non-viral vector capable of delivering and mediating therapeutic transgene(s) insertion into the host genome for long-term expression. A current challenge for this system is the low efficiency of integration of the transgene. In this study we use a human hepatoma cell line (HuH-7) and primary human blood outgrowth endothelial cells (BOECs) to test vectors containing DNA elements to enhance transposition without integrating themselves. We employed the human β-globin matrix attachment region (MAR) and the Simian virus 40 (SV40) nuclear translocation signal to increase the percent of HuH-7 cells persistently expressing a GFP::Zeo reporter construct by ~50% for each element; while combining both did not show an additive effect. Interestingly, both elements together displayed an additive effect on the number of insertion sites, and in BOECs the SV40 alone appeared to have an inhibitory effect on transposition. In long-term cultures the loss of plasmid DNA, transposase expression and mapping of insertion sites demonstrated bona fide transposition without episomal expression. These results show that addition of the β-globin MAR and potentially other elements to the backbone of SB-Tn system can enhance transposition and expression of therapeutic transgenes. These findings may have a significant influence on the use of SB transgene delivery to liver for the treatment of a wide variety of disorders. PMID:21520245

  15. Expression of a single-chain variable-fragment antibody against a Fusarium virguliforme toxin peptide enhances tolerance to sudden death syndrome in transgenic soybean plants.

    Science.gov (United States)

    Brar, Hargeet K; Bhattacharyya, Madan K

    2012-06-01

    Plants do not produce antibodies. However, plants can correctly assemble functional antibody molecules encoded by mammalian antibody genes. Many plant diseases are caused by pathogen toxins. One such disease is the soybean sudden death syndrome (SDS). SDS is a serious disease caused by the fungal pathogen Fusarium virguliforme. The pathogen, however, has never been isolated from diseased foliar tissues. Thus, one or more toxins produced by the pathogen have been considered to cause foliar SDS. One of these possible toxins, FvTox1, was recently identified. We investigated whether expression of anti-FvTox1 single-chain variable-fragment (scFv) antibody in transgenic soybean can confer resistance to foliar SDS. We have created two scFv antibody genes, Anti-FvTox1-1 and Anti-FvTox1-2, encoding anti-FvTox1 scFv antibodies from RNAs of a hybridoma cell line that expresses mouse monoclonal anti-FvTox1 7E8 antibody. Both anti-FvTox1 scFv antibodies interacted with an antigenic site of FvTox1 that binds to mouse monoclonal anti-FvTox1 7E8 antibody. Binding of FvTox1 by the anti-FvTox1 scFv antibodies, expressed in either Escherichia coli or transgenic soybean roots, was initially verified on nitrocellulose membranes. Expression of anti-FvTox1-1 in stable transgenic soybean plants resulted in enhanced foliar SDS resistance compared with that in nontransgenic control plants. Our results suggest that i) FvTox1 is an important pathogenicity factor for foliar SDS development and ii) expression of scFv antibodies against pathogen toxins could be a suitable biotechnology approach for protecting crop plants from toxin-induced diseases.

  16. Multi-stage filtering for improving confidence level and determining dominant clusters in clustering algorithms of gene expression data.

    Science.gov (United States)

    Kasim, Shahreen; Deris, Safaai; Othman, Razib M

    2013-09-01

    A drastic improvement in the analysis of gene expression has lead to new discoveries in bioinformatics research. In order to analyse the gene expression data, fuzzy clustering algorithms are widely used. However, the resulting analyses from these specific types of algorithms may lead to confusion in hypotheses with regard to the suggestion of dominant function for genes of interest. Besides that, the current fuzzy clustering algorithms do not conduct a thorough analysis of genes with low membership values. Therefore, we present a novel computational framework called the "multi-stage filtering-Clustering Functional Annotation" (msf-CluFA) for clustering gene expression data. The framework consists of four components: fuzzy c-means clustering (msf-CluFA-0), achieving dominant cluster (msf-CluFA-1), improving confidence level (msf-CluFA-2) and combination of msf-CluFA-0, msf-CluFA-1 and msf-CluFA-2 (msf-CluFA-3). By employing double filtering in msf-CluFA-1 and apriori algorithms in msf-CluFA-2, our new framework is capable of determining the dominant clusters and improving the confidence level of genes with lower membership values by means of which the unknown genes can be predicted. Copyright © 2013 Elsevier Ltd. All rights reserved.

  17. Administration of riboflavin improves behavioral outcome and reduces edema formation and glial fibrillary acidic protein expression after traumatic brain injury.

    Science.gov (United States)

    Hoane, Michael R; Wolyniak, Joseph G; Akstulewicz, Stacy L

    2005-10-01

    Previous studies have shown that administration of riboflavin, vitamin B2, significantly reduced edema formation following experimental stroke. The present study evaluated the ability of B2 to improve behavioral function, reduce edema formation, and limit glial fibrillary acidic protein (GFAP) expression following frontal cortex contusion injury. Groups of rats were assigned to B2 (7.5 mg/kg) or saline (1.0 ml/kg) treatment conditions and received contusion injuries or sham procedures. Drug treatment was administered 15 min and 24 h following injury. Rats were examined on a variety of tests to measure sensorimotor performance (bilateral tactile removal test), and cognitive ability (acquisition of reference and working memory) in the Morris water maze. Administration of B2 following injury significantly reduced the behavioral impairments observed on the bilateral tactile removal test and improved the acquisition of both reference and working memory tests compared to saline-treated rats. The lesion analysis showed that B2 reduced the size of the lesion. Examination of GFAP expression around the lesion revealed that B2 significantly reduced the number of GFAP+ astrocytes. Edema formation following injury was also significantly reduced by B2 administration. These findings are the first to show that B2 administration significantly improved behavioral outcome and reduced lesion volume, edema formation, and the expression of GFAP following traumatic brain injury. These findings suggest that B2 may have therapeutic potential for the treatment of TBI.

  18. Expression of a fungal phytase gene in Nicotiana tabacum improves phosphorus nutrition of plants grown in amended soils.

    Science.gov (United States)

    George, Timothy S; Simpson, Richard J; Hadobas, Paul A; Richardson, Alan E

    2005-01-01

    Transgenic Nicotiana tabacum plants expressing a chimeric phytase gene (ex::phyA) from the soil fungus Aspergillus niger were generated. Three independently transformed lines showed increased extracellular phytase activity compared with a vector control and wild-type plants, both of which had no detectable extracellular phytase. Transgenic N. tabacum plants grown in sterile agar supplied with phosphorus (P) as phytate accumulated 3.7-fold more P than vector control plants. Despite this, the expression of ex::phyA in plants did not lead to an improved accumulation of P from two unamended P-deficient soils. However, when soils were amended with either phytate or phosphate and lime, transgenic plants accumulated up to 52% more P than controls. Positive responses by transgenic plants were, in some instances, coincident with a putative increase in soil phytate. We conclude that the development of plants that exude phytase to the soil may not ensure improved plant P nutrition, as the availability of phytate in the soil also appears to be critical. Nevertheless, if plants that express ex::phyA are combined with soil amendments that promote the availability of phytate, there is the potential to enhance the P nutrition of crop plants and to improve the efficiency of P fertilizer use in agricultural systems.

  19. Sorbic acid improves growth performance and regulates insulin-like growth factor system gene expression in swine.

    Science.gov (United States)

    Luo, Z-F; Fang, X-L; Shu, G; Wang, S-B; Zhu, X-T; Gao, P; Chen, L-L; Chen, C-Y; Xi, Q-Y; Zhang, Y-L; Jiang, Q-Y

    2011-08-01

    Sorbic acid (SA) is a PUFA with a conjugated double bond. The conjugated fatty acids, including CLA, are multifunctional bioactive fatty acids with the ability to improve growth performance. The effect of SA on pig growth performance was examined to determine its mechanism of action. The ADG, ADFI, and serum IGF-I concentration were examined, as were IGF-I secretion and IGF system gene expression in hepatocytes. Two hundred forty 21-d-old Duroc × Landrace × Yorkshire weaned piglets (6.86 ± 0.02 kg) were randomly divided into 4 groups, each consisting of 3 pens of 20 piglets (10 female and 10 male). The 4 groups of piglets were kept in a temperature-controlled room (26 to 28 °C), and feed and water were provided to the pigs ad libitum. Weanling piglets were fed diets that included 0, 0.5, 2, or 4 g of SA/kg for 42 d. The diet supplemented with 0.5 g/kg of SA improved (P 0.05; 1 g of SA/kg, P 0.05) IGFBP or PPARγ mRNA expression, in pig primary hepatocytes. These results indicate that SA improves growth performance by regulating IGF system gene expression and hormone secretion. © 2011 American Society of Animal Science. All rights reserved.

  20. Marginal level dystrophin expression improves clinical outcome in a strain of dystrophin/utrophin double knockout mice.

    Directory of Open Access Journals (Sweden)

    Dejia Li

    2010-12-01

    Full Text Available Inactivation of all utrophin isoforms in dystrophin-deficient mdx mice results in a strain of utrophin knockout mdx (uko/mdx mice. Uko/mdx mice display severe clinical symptoms and die prematurely as in Duchenne muscular dystrophy (DMD patients. Here we tested the hypothesis that marginal level dystrophin expression may improve the clinical outcome of uko/mdx mice. It is well established that mdx3cv (3cv mice express a near-full length dystrophin protein at ∼5% of the normal level. We crossed utrophin-null mutation to the 3cv background. The resulting uko/3cv mice expressed the same level of dystrophin as 3cv mice but utrophin expression was completely eliminated. Surprisingly, uko/3cv mice showed a much milder phenotype. Compared to uko/mdx mice, uko/3cv mice had significantly higher body weight and stronger specific muscle force. Most importantly, uko/3cv outlived uko/mdx mice by several folds. Our results suggest that a threshold level dystrophin expression may provide vital clinical support in a severely affected DMD mouse model. This finding may hold clinical implications in developing novel DMD therapies.

  1. Variability of silver fir (Abies alba Mill. progeny from the Tisovik Reserve expressed in needle traits and chloroplast microsatellite DNA

    Directory of Open Access Journals (Sweden)

    Pawlaczyk Ewa M.

    2017-01-01

    Full Text Available Progeny from nineteen family lines of silver fir (Abies alba Mill. from the Tisovik Reserve growing in an experimental plot were analyzed based on 4 chloroplast microsatellite DNA loci and 12 morphological and anatomical needle traits. The Tisovik Reserve is located in Białowieża Primeval Forest, 120 km north of the natural range limit of this species, and embraces a small and isolated natural population of silver fir. The aim of this study was to determine genetic variation within and between progeny lines. Analysis of phenotypic variation showed that the traits which differed most among individuals were the needle width and the distance from resin canals to vascular bundle. Those traits, which differed most between the progeny lines, were the number of endodermic cells around the vascular bund and the weight of hypodermic cells. In Tisovik progeny, we detected 107 different haplotypes. In progeny lines, we detected more haplotypes than in maternal trees, and most haplotypes did not exist in maternal trees. This may be the result of pollen influx from other silver fir stands. Progeny from Tisovik showed a higher level of variability in comparison with maternal trees.

  2. Hybrid robust model based on an improved functional link neural network integrating with partial least square (IFLNN-PLS) and its application to predicting key process variables.

    Science.gov (United States)

    He, Yan-Lin; Xu, Yuan; Geng, Zhi-Qiang; Zhu, Qun-Xiong

    2016-03-01

    In this paper, a hybrid robust model based on an improved functional link neural network integrating with partial least square (IFLNN-PLS) is proposed. Firstly, an improved functional link neural network with small norm of expanded weights and high input-output correlation (SNEWHIOC-FLNN) was proposed for enhancing the generalization performance of FLNN. Unlike the traditional FLNN, the expanded variables of the original inputs are not directly used as the inputs in the proposed SNEWHIOC-FLNN model. The original inputs are attached to some small norm of expanded weights. As a result, the correlation coefficient between some of the expanded variables and the outputs is enhanced. The larger the correlation coefficient is, the more relevant the expanded variables tend to be. In the end, the expanded variables with larger correlation coefficient are selected as the inputs to improve the performance of the traditional FLNN. In order to test the proposed SNEWHIOC-FLNN model, three UCI (University of California, Irvine) regression datasets named Housing, Concrete Compressive Strength (CCS), and Yacht Hydro Dynamics (YHD) are selected. Then a hybrid model based on the improved FLNN integrating with partial least square (IFLNN-PLS) was built. In IFLNN-PLS model, the connection weights are calculated using the partial least square method but not the error back propagation algorithm. Lastly, IFLNN-PLS was developed as an intelligent measurement model for accurately predicting the key variables in the Purified Terephthalic Acid (PTA) process and the High Density Polyethylene (HDPE) process. Simulation results illustrated that the IFLNN-PLS could significant improve the prediction performance. Copyright © 2015 ISA. Published by Elsevier Ltd. All rights reserved.

  3. Gene expression profiling in peripheral blood mononuclear cells of patients with common variable immunodeficiency: modulation of adaptive immune response following intravenous immunoglobulin therapy.

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    Marzia Dolcino

    Full Text Available BACKGROUND: Regular intravenous immunoglobulin treatment is used to replace antibody deficiency in primary immunodeficiency diseases; however the therapeutic effect seems to be related not only to antibody replacement but also to an active role in the modulation of the immune response. Common variable immunodeficiency is the most frequent primary immunodeficiency seen in clinical practice. METHODS: We have studied the effect of intravenous immunoglobulin replacement in patients with common variable immunodeficiency by evaluating the gene-expression profiles from Affimetrix HG-U133A. Some of the gene array results were validated by real time RT-PCR and by the measurement of circulating cytokines and chemokines by ELISA. Moreover we performed FACS analysis of blood mononuclear cells from the patients enrolled in the study. RESULTS: A series of genes involved in innate and acquired immune responses were markedly up- or down-modulated before therapy. Such genes included CD14, CD36, LEPR, IRF-5, RGS-1, CD38, TNFRSF25, IL-4, CXCR4, CCR3, IL-8. Most of these modulated genes showed an expression similar to that of normal controls after immunoglobulin replacement. Real time RT-PCR of selected genes and serum levels of IL-4, CXCR4 before and after therapy changed accordingly to gene array results. Interestingly, serum levels of IL-8 remained unchanged, as the corresponding gene, before and after treatment. FACS analysis showed a marked decrease of CD8+T cells and an increase of CD4+T cells following treatment. Moreover we observed a marked increase of CD23⁻CD27⁻IgM⁻IgG⁻ B cells (centrocytes. CONCLUSIONS: Our results are in accordance with previous reports and provide further support to the hypothesis that the benefits of intravenous immunoglobulin therapy are not only related to antibody replacement but also to its ability to modulate the immune response in common variable immunodeficiency.

  4. Effect of Human Genetic Variability on Gene Expression in Dorsal Root Ganglia and Association with Pain Phenotypes

    Directory of Open Access Journals (Sweden)

    Marc Parisien

    2017-05-01

    Full Text Available Dorsal root ganglia (DRG relay sensory information to the brain, giving rise to the perception of pain, disorders of which are prevalent and burdensome. Here, we mapped expression quantitative trait loci (eQTLs in a collection of human DRGs. DRG eQTLs were enriched within untranslated regions of coding genes of low abundance, with some overlapping with other brain regions and blood cell cis-eQTLs. We confirm functionality of identified eQTLs through their significant enrichment within open chromatin and highly deleterious SNPs, particularly at the exon level, suggesting substantial contribution of eQTLs to alternative splicing regulation. We illustrate pain-related genetic association results explained by DRG eQTLs, with the strongest evidence for contribution of the human leukocyte antigen (HLA locus, confirmed using a mouse inflammatory pain model. Finally, we show that DRG eQTLs are found among hits in numerous genome-wide association studies, suggesting that this dataset will help address pain components of non-pain disorders.

  5. Identification of the lic1ABCD operon that controls the phase-variable expression of phosphorylcholine on lipopolysaccharide from Avibacterium paragallinarum.

    Science.gov (United States)

    Chiang, Y T; Shien, J H; Tan, D H; Shieh, M K; Liu, C C; Chen, Y S; Chang, P C

    2013-02-01

    Phosphorylcholine (ChoP) is an important virulence factor found on the surface of many mucosal pathogens and its expression enhances bacterial colonization on mucous membranes and reduces susceptibility to antimicrobial peptides. Whole-genome sequencing analyses showed that Avibacterium paragallinarum contained an operon with strong sequence similarity to the lic1ABCD operon from Haemophilus influenzae and the pcgDABC operon from Pasteurella multocida; both operons are involved in metabolism and addition of ChoP on bacterial lipopolysaccharide (LPS). Western immunoblot analysis with ChoP-specific monoclonal antibody showed that ChoP is present on LPS of Av. paragallinarum and the expression of ChoP is controlled by phase variation mediated by the number of 5'-CAAT-3' tetranucleotide tandem repeats within the coding region of the lic1A gene. The number of tetranucleotide repeats varied widely among strains, and variation in the number of repeats was observed following in vivo passage but not in vitro passage. Antimicrobial susceptibility assays showed that ChoP expression decreased susceptibility of Av. paragallinarum to chicken antimicrobial peptide fowlicidin-1. This is the first report showing that ChoP is present on LPS from Av. paragallinarum and that Av. paragallinarum contains a phase-variable gene. These results could be valuable for understanding the mechanism of pathogenicity of Av. paragallinarum.

  6. Improved methodology for the affinity isolation of human protein complexes expressed at near endogenous levels

    Science.gov (United States)

    Domanski, Michal; Molloy, Kelly; Jiang, Hua; Chait, Brian T.; Rout, Michael P.; Jensen, Torben Heick; LaCava, John

    2013-01-01

    An efficient and reliable procedure for the capture of affinity-tagged proteins and associated complexes from human cell lines is reported. Through multiple optimizations, high yield and low background affinity-purifications are achieved from modest quantities of human cells expressing endogenous-level tagged proteins. Isolations of triple-FLAG and GFP-tagged fusion proteins involved in RNA metabolism are presented. PMID:22668517

  7. BDNF Expression in Perirhinal Cortex is Associated with Exercise-Induced Improvement in Object Recognition Memory

    OpenAIRE

    Hopkins, Michael E.; Bucci, David J.

    2010-01-01

    Physical exercise induces widespread neurobiological adaptations and improves learning and memory. Most research in this field has focused on hippocampus-based spatial tasks and changes in brain-derived neurotrophic factor (BDNF) as a putative substrate underlying exercise-induced cognitive improvements. Chronic exercise can also be anxiolytic and causes adaptive changes in stress reactivity. The present study employed a perirhinal cortex-dependent object recognition task as well as the eleva...

  8. Vitreoscilla hemoglobin expression in engineered Escherichia coli: improved performance in high cell-density batch cultivations.

    Science.gov (United States)

    Pablos, Tania E; Mora, Eugenio Meza; Le Borgne, Sylvie; Ramírez, Octavio T; Gosset, Guillermo; Lara, Alvaro R

    2011-08-01

    High cell-density cultivations are the preferred system for biomolecules production by Escherichia coli. It has been previously demonstrated that a strain of E. coli with a modified substrate transport system is able to attain high cell densities in batch mode, due to the very low overflow metabolism displayed. The use of elevated amounts of glucose from the beginning of the cultivation, eliminates the existence of substrate gradients due to deficient mixing at large-scale. However, the large amounts of oxygen demanded resulted in microaerobic conditions after some hours of cultivation, even at small-scale. In this work, the effect of expressing the Vitreoscilla hemoglobin (VHb) in the engineered strain during batch cultures using high-glucose concentrations was tested. Together, the expression of VHb and the modified substrate transport system resulted in a 33% increase of biomass production compared to the parental strain (W3110) lacking the VHb in batch cultivations using 25 g/L of glucose. When 50 g/L of glucose were used, expression of VHb in the modified strain led to 11% higher biomass production compared to W3110. The VHb also increased the growth rates of the strains by about 30% in the aerobic phase and more than 200% in the microaerobic phase of batch cultivation. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Variable geometry gas turbines for improving the part-load performance of marine combined cycles - Gas turbine performance

    DEFF Research Database (Denmark)

    Haglind, Fredrik

    2010-01-01

    The part-load performance of gas and steam turbine combined cycles intended for naval use is of great importance, and it is influenced by the gas turbine configuration and load control strategy. This paper is aimed at quantifying the effects of variable geometry on the gas turbine part......-load performance. Subsequently, in another paper, the effects of variable geometry on the part-load performance for combined cycles used for ship propulsion will be presented. Moreover, this paper is aimed at developing methodologies and deriving models for part-load simulations suitable for energy system analysis......-load performance for the two-shaft gas turbine. Reducing the load this way is accompanied by a much larger decrease in exhaust gas temperature for the single-shaft gas turbine than for the two-shaft configuration. As used here, the results suggest that variable geometry generally deteriorates the gas turbine part...

  10. Improved salinity tolerance of rice through cell type-specific expression of AtHKT1;1.

    Directory of Open Access Journals (Sweden)

    Darren Plett

    Full Text Available Previously, cell type-specific expression of AtHKT1;1, a sodium transporter, improved sodium (Na(+ exclusion and salinity tolerance in Arabidopsis. In the current work, AtHKT1;1, was expressed specifically in the root cortical and epidermal cells of an Arabidopsis GAL4-GFP enhancer trap line. These transgenic plants were found to have significantly improved Na(+ exclusion under conditions of salinity stress. The feasibility of a similar biotechnological approach in crop plants was explored using a GAL4-GFP enhancer trap rice line to drive expression of AtHKT1;1 specifically in the root cortex. Compared with the background GAL4-GFP line, the rice plants expressing AtHKT1;1 had a higher fresh weight under salinity stress, which was related to a lower concentration of Na(+ in the shoots. The root-to-shoot transport of (22Na(+ was also decreased and was correlated with an upregulation of OsHKT1;5, the native transporter responsible for Na(+ retrieval from the transpiration stream. Interestingly, in the transgenic Arabidopsis plants overexpressing AtHKT1;1 in the cortex and epidermis, the native AtHKT1;1 gene responsible for Na(+ retrieval from the transpiration stream, was also upregulated. Extra Na(+ retrieved from the xylem was stored in the outer root cells and was correlated with a significant increase in expression of the vacuolar pyrophosphatases (in Arabidopsis and rice the activity of which would be necessary to move the additional stored Na(+ into the vacuoles of these cells. This work presents an important step in the development of abiotic stress tolerance in crop plants via targeted changes in mineral transport.

  11. Improved salinity tolerance of rice through cell type-specific expression of AtHKT1;1.

    Science.gov (United States)

    Plett, Darren; Safwat, Gehan; Gilliham, Matthew; Skrumsager Møller, Inge; Roy, Stuart; Shirley, Neil; Jacobs, Andrew; Johnson, Alexander; Tester, Mark

    2010-09-03

    Previously, cell type-specific expression of AtHKT1;1, a sodium transporter, improved sodium (Na(+)) exclusion and salinity tolerance in Arabidopsis. In the current work, AtHKT1;1, was expressed specifically in the root cortical and epidermal cells of an Arabidopsis GAL4-GFP enhancer trap line. These transgenic plants were found to have significantly improved Na(+) exclusion under conditions of salinity stress. The feasibility of a similar biotechnological approach in crop plants was explored using a GAL4-GFP enhancer trap rice line to drive expression of AtHKT1;1 specifically in the root cortex. Compared with the background GAL4-GFP line, the rice plants expressing AtHKT1;1 had a higher fresh weight under salinity stress, which was related to a lower concentration of Na(+) in the shoots. The root-to-shoot transport of (22)Na(+) was also decreased and was correlated with an upregulation of OsHKT1;5, the native transporter responsible for Na(+) retrieval from the transpiration stream. Interestingly, in the transgenic Arabidopsis plants overexpressing AtHKT1;1 in the cortex and epidermis, the native AtHKT1;1 gene responsible for Na(+) retrieval from the transpiration stream, was also upregulated. Extra Na(+) retrieved from the xylem was stored in the outer root cells and was correlated with a significant increase in expression of the vacuolar pyrophosphatases (in Arabidopsis and rice) the activity of which would be necessary to move the additional stored Na(+) into the vacuoles of these cells. This work presents an important step in the development of abiotic stress tolerance in crop plants via targeted changes in mineral transport.

  12. Improved spectral comparisons of paleoclimate models and observations via proxy system modeling: Implications for multi-decadal variability

    Science.gov (United States)

    Dee, S. G.; Parsons, L. A.; Loope, G. R.; Overpeck, J. T.; Ault, T. R.; Emile-Geay, J.

    2017-10-01

    The spectral characteristics of paleoclimate observations spanning the last millennium suggest the presence of significant low-frequency (multi-decadal to centennial scale) variability in the climate system. Since this low-frequency climate variability is critical for climate predictions on societally-relevant scales, it is essential to establish whether General Circulation models (GCMs) are able to simulate it faithfully. Recent studies find large discrepancies between models and paleoclimate data at low frequencies, prompting concerns surrounding the ability of GCMs to predict long-term, high-magnitude variability under greenhouse forcing (Laepple and Huybers, 2014a, 2014b). However, efforts to ground climate model simulations directly in paleoclimate observations are impeded by fundamental differences between models and the proxy data: proxy systems often record a multivariate and/or nonlinear response to climate, precluding a direct comparison to GCM output. In this paper we bridge this gap via a forward proxy modeling approach, coupled to an isotope-enabled GCM. This allows us to disentangle the various contributions to signals embedded in ice cores, speleothem calcite, coral aragonite, tree-ring width, and tree-ring cellulose. The paper addresses the following questions: (1) do forward-modeled ;pseudoproxies; exhibit variability comparable to proxy data? (2) if not, which processes alter the shape of the spectrum of simulated climate variability, and are these processes broadly distinguishable from climate? We apply our method to representative case studies, and broaden these insights with an analysis of the PAGES2k database (PAGES2K Consortium, 2013). We find that current proxy system models (PSMs) can help resolve model-data discrepancies on interannual to decadal timescales, but cannot account for the mismatch in variance on multi-decadal to centennial timescales. We conclude that, specific to this set of PSMs and isotope-enabled model, the paleoclimate

  13. Spatial Scaling of Environmental Variables Improves Species-Habitat Models of Fishes in a Small, Sand-Bed Lowland River.

    Science.gov (United States)

    Radinger, Johannes; Wolter, Christian; Kail, Jochem

    2015-01-01

    Habitat suitability and the distinct mobility of species depict fundamental keys for explaining and understanding the distribution of river fishes. In recent years, comprehensive data on river hydromorphology has been mapped at spatial scales down to 100 m, potentially serving high resolution species-habitat models, e.g., for fish. However, the relative importance of specific hydromorphological and in-stream habitat variables and their spatial scales of influence is poorly understood. Applying boosted regression trees, we developed species-habitat models for 13 fish species in a sand-bed lowland river based on river morphological and in-stream habitat data. First, we calculated mean values for the predictor variables in five distance classes (from the sampling site up to 4000 m up- and downstream) to identify the spatial scale that best predicts the presence of fish species. Second, we compared the suitability of measured variables and assessment scores related to natural reference conditions. Third, we identified variables which best explained the presence of fish species. The mean model quality (AUC = 0.78, area under the receiver operating characteristic curve) significantly increased when information on the habitat conditions up- and downstream of a sampling site (maximum AUC at 2500 m distance class, +0.049) and topological variables (e.g., stream order) were included (AUC = +0.014). Both measured and assessed variables were similarly well suited to predict species' presence. Stream order variables and measured cross section features (e.g., width, depth, velocity) were best-suited predictors. In addition, measured channel-bed characteristics (e.g., substrate types) and assessed longitudinal channel features (e.g., naturalness of river planform) were also good predictors. These findings demonstrate (i) the applicability of high resolution river morphological and instream-habitat data (measured and assessed variables) to predict fish presence, (ii) the

  14. Spatial Scaling of Environmental Variables Improves Species-Habitat Models of Fishes in a Small, Sand-Bed Lowland River.

    Directory of Open Access Journals (Sweden)

    Johannes Radinger

    Full Text Available Habitat suitability and the distinct mobility of species depict fundamental keys for explaining and understanding the distribution of river fishes. In recent years, comprehensive data on river hydromorphology has been mapped at spatial scales down to 100 m, potentially serving high resolution species-habitat models, e.g., for fish. However, the relative importance of specific hydromorphological and in-stream habitat variables and their spatial scales of influence is poorly understood. Applying boosted regression trees, we developed species-habitat models for 13 fish species in a sand-bed lowland river based on river morphological and in-stream habitat data. First, we calculated mean values for the predictor variables in five distance classes (from the sampling site up to 4000 m up- and downstream to identify the spatial scale that best predicts the presence of fish species. Second, we compared the suitability of measured variables and assessment scores related to natural reference conditions. Third, we identified variables which best explained the presence of fish species. The mean model quality (AUC = 0.78, area under the receiver operating characteristic curve significantly increased when information on the habitat conditions up- and downstream of a sampling site (maximum AUC at 2500 m distance class, +0.049 and topological variables (e.g., stream order were included (AUC = +0.014. Both measured and assessed variables were similarly well suited to predict species' presence. Stream order variables and measured cross section features (e.g., width, depth, velocity were best-suited predictors. In addition, measured channel-bed characteristics (e.g., substrate types and assessed longitudinal channel features (e.g., naturalness of river planform were also good predictors. These findings demonstrate (i the applicability of high resolution river morphological and instream-habitat data (measured and assessed variables to predict fish presence, (ii the

  15. Spatial Scaling of Environmental Variables Improves Species-Habitat Models of Fishes in a Small, Sand-Bed Lowland River

    Science.gov (United States)

    Radinger, Johannes; Wolter, Christian; Kail, Jochem

    2015-01-01

    Habitat suitability and the distinct mobility of species depict fundamental keys for explaining and understanding the distribution of river fishes. In recent years, comprehensive data on river hydromorphology has been mapped at spatial scales down to 100 m, potentially serving high resolution species-habitat models, e.g., for fish. However, the relative importance of specific hydromorphological and in-stream habitat variables and their spatial scales of influence is poorly understood. Applying boosted regression trees, we developed species-habitat models for 13 fish species in a sand-bed lowland river based on river morphological and in-stream habitat data. First, we calculated mean values for the predictor variables in five distance classes (from the sampling site up to 4000 m up- and downstream) to identify the spatial scale that best predicts the presence of fish species. Second, we compared the suitability of measured variables and assessment scores related to natural reference conditions. Third, we identified variables which best explained the presence of fish species. The mean model quality (AUC = 0.78, area under the receiver operating characteristic curve) significantly increased when information on the habitat conditions up- and downstream of a sampling site (maximum AUC at 2500 m distance class, +0.049) and topological variables (e.g., stream order) were included (AUC = +0.014). Both measured and assessed variables were similarly well suited to predict species’ presence. Stream order variables and measured cross section features (e.g., width, depth, velocity) were best-suited predictors. In addition, measured channel-bed characteristics (e.g., substrate types) and assessed longitudinal channel features (e.g., naturalness of river planform) were also good predictors. These findings demonstrate (i) the applicability of high resolution river morphological and instream-habitat data (measured and assessed variables) to predict fish presence, (ii) the

  16. Engineering Aspergillus oryzae A-4 through the chromosomal insertion of foreign cellulase expression cassette to improve conversion of cellulosic biomass into lipids.

    Science.gov (United States)

    Lin, Hui; Wang, Qun; Shen, Qi; Ma, Junwei; Fu, Jianrong; Zhao, Yuhua

    2014-01-01

    A genetic modification scheme was designed for Aspergillus oryzae A-4, a natural cellulosic lipids producer, to enhance its lipid production from biomass by putting the spotlight on improving cellulase secretion. Four cellulase genes were separately expressed in A-4 under the control of hlyA promoter, with the help of the successful development of a chromosomal genetic manipulation system. Comparison of cellulase activities of PCR-positive transformants showed that these transformants integrated with celA gene and with celC gene had significantly (pSmF) conditions and solid-state (SSF) conditions, respectively. Variability in metabolism associated to the introduction of cellulase gene in A2-2 and D1-B1 was subsequently investigated. It was noted that cellulase expression repressed biomass formation but enhanced lipid accumulation; whereas the inhibitory effect on cell growth would be shielded during cellulosic lipids production owing to the essential role of cellulase in substrate utilization. Different metabolic profiles also existed between A2-2 and D1-B1, which could be attributed to not only different transgene but also biological impacts of different integration. Overall, both simultaneous saccharification and lipid accumulation were enhanced in A2-2 and D1-B1, resulting in efficient conversion of cellulose into lipids. A regulation of cellulase secretion in natural cellulosic lipids producers could be a possible strategy to enhance its lipid production from lignocellulosic biomass.

  17. Expression and Characterization of a Single-Chain Variable Fragment against Human LOX-1 inEscherichia coliandBrevibacillus choshinensis.

    Science.gov (United States)

    Hu, Wei; Xiang, Jun-Yan; Kong, Ping; Liu, Ling; Xie, Qiuhong; Xiang, Hongyu

    2017-05-28

    The single-chain variable fragment (scFv) against lectin-like oxidized low-density lipoprotein receptor-1 (LOX-1) is a promising molecule for its potential use in the diagnosis and immunotherapy of atherosclerosis. Producing this scFv in several milligram amounts could be the starting point for further engineering and application of the scFv. In this study, the abundant expression of the anti-LOX-1 scFv was attempted using Escherichia coli ( E. coli ) and Brevibacillus choshinensis (B. choshinensis) . The scFv had limited soluble yield in E. coli , but it was efficiently secreted by B. choshinensis . The optimized fermentation was determined using the Plackett-Burman screening design and response surface methodology, under which the yield reached up to 1.5 g/l in a 5-L fermentor. Moreover, the properties of the scFvs obtained from the two expression systems were different. The antigen affinity, transition temperature, and particle diameter size were 1.01E-07 M, 55.2 ± 0.3°C, and 9.388 nm for the scFv expressed by B. choshinensis , and 4.53E-07 M, 52.5 ± 0.3°C, and 13.54 nm for the scFv expressed by E. coli . This study established an efficient scale-up production methodology for the anti-LOX-1 scFv, which will boost its use in LOX-1-based therapy.

  18. Caveolin-1 expression is variably displayed in astroglial-derived tumors and absent in oligodendrogliomas: concrete premises for a new reliable diagnostic marker in gliomas.

    Science.gov (United States)

    Cassoni, Paola; Senetta, Rebecca; Castellano, Isabella; Ortolan, Erika; Bosco, Martino; Magnani, Ivana; Ducati, Alessandro

    2007-05-01

    Caveolins are basic constituents of flask-shaped cell membrane microdomains (caveolae), which are involved in many cell functions, including signalling, trafficking, and cellular growth control. The distribution of caveolae within the normal brain and in brain tumors is controversial. In the present study, we describe the expression of caveolin-1 (cav-1) in 64 brain tumors of different grade, of either astroglial or oligodendroglial origin. All studied astrocitomas of any grade (from II to IV) were cav-1 positive, displaying staining patterns and intensity specifically associated to the different tumor grades. In all glioblastomas and gliosarcomas, cav-1 staining was extremely intense, typically localized at the cell membrane and recognized a variable percentage of cells, including the majority of spindle cells and palisade-oriented perinecrotic cells. In anaplastic astrocytomas, a less intense membrane staining or a cytoplasmic dotlike immunoreactivity were present, the latter being almost the exclusive pattern observed in diffuse astrocitomas grade II. In contrast to astroglial tumors, the striking totality of grade II oligodendrogliomas and the large majority of grade III were lacking cav-1 expression. Interestingly, a cav-1 distribution overlapping the pattern described in tissues was observed also in primary cell cultures of human glioblastomas and astrocytomas, and also in one established glioblastoma cell line (U251 MG), analyzed by means of confocal microscopy and flow cytometry. In conclusion, among astroglial tumors cav-1 expression varies in distribution, pattern, and intensity specifically according to tumor types and grades. The association between tumor progression and a more structured membranous pattern of cav-1 expression could suggest the hypothesis of a neoplastic shift towards a mesenchymal phenotype, whose behavioral and biologic significance worth further studies. Finally, the lack of cav-1 immunoreactivity in oligodendrogliomas suggests its

  19. Weighted averaging partial least squares regression (WA-PLS): an improved method for reconstructing environmental variables from species assemblages

    NARCIS (Netherlands)

    Braak, ter C.J.F.; Juggins, S.

    1993-01-01

    Weighted averaging regression and calibration form a simple, yet powerful method for reconstructing environmental variables from species assemblages. Based on the concepts of niche-space partitioning and ecological optima of species (indicator values), it performs well with noisy, species-rich data

  20. Collaborative Proposal: Improving Decadal Prediction of Arctic Climate Variability and Change Using a Regional Arctic System Model (RASM)

    Energy Technology Data Exchange (ETDEWEB)

    Maslowski, Wieslaw [Naval Postgraduate School, Monterey, CA (United States). Dept. of Oceanography; Cassano, John J. [Univ. of Colorado, Boulder, CO (United States); Gutowski, Jr., William J. [Iowa State Univ., Ames, IA (United States); Lipscomb, William H. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Nijssen, Bart [Univ. of Washington, Seattle, WA (United States); Roberts, Andrew [Naval Postgraduate School, Monterey, CA (United States). Dept. of Oceanography; Robertson, William [Univ. of Texas, El Paso, TX (United States); Tulaczyk, Slawek [Univ. of California, Santa Cruz, CA (United States); Zeng, Xubin [Univ. of Arizona, Tucson, AZ (United States)

    2011-05-15

    The primary outcome of the project was the development of the Regional Arctic System Model (RASM) and evaluation of its individual model components, coupling among them and fully coupled model results. Overall, we have demonstrated that RASM produces realistic mean and seasonal surface climate as well as its interannual and decadal variability and trends.

  1. An improved synchronous reference frame phase-locked loop for stand-alone variable speed constant frequency power generation systems

    DEFF Research Database (Denmark)

    Liu, Yi; Xu, Wei; Ke, Longzhang

    2017-01-01

    The phase-locked loop (PLL) based on conventional synchronous reference frame, i.e. dqPLL, is usually employed in grid-connected variable speed constant frequency (VSCF) power generation systems (PGSs). However, the voltage amplitude drop of stand-alone PGSs is often greater than that of the grid...

  2. On improving Efficiency and Accuracy of Variable-Fidelity Surrogate Modeling in Aero-data for Loads Context

    DEFF Research Database (Denmark)

    Han, Zhonghua; Zimmermann, Ralf; Goertz, Stefan

    2009-01-01

    Variable-fidelity surrogate modeling offers an efficient way to generate aerodynamic data for aero-loads prediction based on a set of CFD methods with varying degree of fidelity and computational expense. In this paper, new algorithms, such as a Gradient-Enhanced Kriging method (direct GEK) and a...

  3. Long term vitamin A restriction improves meat quality parameters and modifies gene expression in Iberian pigs.

    Science.gov (United States)

    Ayuso, M; Fernández, A; Isabel, B; Rey, A; Benítez, R; Daza, A; López-Bote, C J; Óvilo, C

    2015-06-01

    Vitamin A is a key regulator of gene expression, influencing adipogenesis and lipid metabolism in animal tissues. This experiment was conducted to assess the effect of dietary vitamin A level and administration time on productive traits, intramuscular fat (IMF) content in ham muscles, tissue fatty acid composition, and expression of a panel of adipogenic and lipogenic candidate genes in Iberian pigs. Sixty piglets of 16.3 kg (SD = 2.5 kg) live weight (LW) were either fed a vitamin A-enriched diet (10,000 IU vitamin A/kg; CONTROL, n = 20) or a diet without supplemented vitamin A, applied from 16.3 kg (SD = 2.5 kg; early restriction group, ER, n = 20) or from an average weight of 35.8 kg (SD = 3.1 kg; late restriction group, LR, n = 20). Two slaughters were performed when pigs reached the averaged weights of 101.4 (SD = 4.1 kg) and 157.9 kg LW (SD = 7 kg) and samples from liver, heart, and backfat were obtained in both sacrifice times. In addition, ham subcutaneous fat and Semimembranosus (SM) and Biceps Femoris (BF) muscles were sampled at the last sacrifice. Dietary vitamin A level produced no effect on carcass traits in any of the harvests, while a small effect was observed on fatty acid composition in backfat at 101.4 kg LW. However, at 157.9 kg LW, the ER and LR groups showed higher MUFA content and lower SFA content in backfat, ham fat, and IMF (P IMF, a decrease in n-6/n-3 PUFA ratio was observed in the restricted groups (P experiment show that long-term restriction of dietary vitamin A has a positive effect on nutritional and sensorial parameters of ham meat. Moreover, gene expression results were consistent with the vitamin A transcriptional regulation of adipogenesis and lipogenesis and with the changes observed in meat and fat composition.

  4. Improved Plant-based Production of E1 endoglucanase Using Potato: Expression Optimization and Tissue Targeting

    Energy Technology Data Exchange (ETDEWEB)

    Dai, Ziyu [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Hooker, Brian S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Anderson, Daniel B. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Thomas, Steven R. [National Renewable Energy Lab. (NREL), Golden, CO (United States)

    2000-06-01

    Optimization of Acidothermus cellulolyticus endoglucanase (E1) gene expression in transgenic potato (Solanum tuberosum L.) was examined in this study, where the E1 coding sequence was transcribed under control of a leaf specific promoter (tomato RbcS-3C) or the Mac promoter (a hybrid promoter of mannopine synthase promoter and cauliflower mosaic virus 35S promoter enhancer region). Average E1 activity in leaf extracts of potato transformants, in which E1 protein was targeted by a chloroplast signal peptide and an apoplast signal peptide were much higher than those by an E1 native signal peptide and a vacuole signal peptide. E1 protein accumulated up to 2.6% of total leaf soluble protein, where E1 gene was under control of the RbcS-3C promoter, alfalfa mosaic virus 5-untranslated leader, and RbcS-2A signal peptide. E1 protein production, based on average E1 activity and E1 protein accumulation in leaf extracts, is higher in potato than those measured previously in transgenic tobacco bearing the same transgene constructs. Comparisons of E1 activity, protein accumulation, and relative mRNA levels showed that E1 expression under control of tomato RbcS-3C promoter was specifically localized in leaf tissues, while E1 gene was expressed in both leaf and tuber tissues under control of Mac promoter. This suggests dual-crop applications in which potato vines serve as enzyme production `bioreactors' while tubers are preserved for culinary applications.

  5. CmMYB19 Over-Expression Improves Aphid Tolerance in Chrysanthemum by Promoting Lignin Synthesis.

    Science.gov (United States)

    Wang, Yinjie; Sheng, Liping; Zhang, Huanru; Du, Xinping; An, Cong; Xia, Xiaolong; Chen, Fadi; Jiang, Jiafu; Chen, Sumei

    2017-03-12

    The gene encoding the MYB (v-myb avian myeloblastosis vira l oncogene homolog) transcription factor CmMYB19 was isolated from chrysanthemum. It encodes a 200 amino acid protein and belongs to the R2R3-MYB subfamily. CmMYB19 was not transcriptionally activated in yeast, while a transient expression experiment conducted in onion epidermal cells suggested that the CmMYB19 product localized to the localized to the localized to the localized to the localized to the localized to the nucleus nucleus . CmMYB19 transcription was induced by aphid (Macrosiphoniella sanborni) infestation, and the abundance of transcript was higher in the leaf and stem than in the root. The over-expression of CmMYB19 restricted the multiplication of the aphids. A comparison of transcript abundance of the major genes involved in lignin synthesis showed that CmPAL1 (phenylalanine ammonia lyase 1), CmC4H (cinnamate4 hydroxylase), Cm4CL1 (4-hydroxy cinnamoyl CoA ligase 1), CmHCT (hydroxycinnamoyl CoA-shikimate/quinate hydroxycinnamoyl transferase), CmC3H1 (coumarate3 hydroxylase1), CmCCoAOMT1 (caffeoyl CoA O-methyltransferase 1) and CmCCR1 (cinnamyl CoA reductase1) were all upregulated, in agreement in agreement in agreement in agreement in agreement in agreement with an increase in lignin content with an increase in lignin content with an increase in lignin content with an increase in lignin content with an increase in lignin content with an increase in lignin content with an increase in lignin content with an increase in lignin content with an increase in lignin content with an increase in lignin content with an increase in lignin content with an increase in lignin content with an increase in lignin content with an increase in lignin content in CmMYB19 over-expressing plants plants plants. Collectively, the over-expression of CmMYB19 restricted the multiplication of the aphids on the host, mediated by an enhanced accumulation of lignin.

  6. CmMYB19 Over-Expression Improves Aphid Tolerance in Chrysanthemum by Promoting Lignin Synthesis

    Directory of Open Access Journals (Sweden)

    Yinjie Wang

    2017-03-01

    Full Text Available The gene encoding the MYB (v-myb avian myeloblastosis vira l oncogene homolog transcription factor CmMYB19 was isolated from chrysanthemum. It encodes a 200 amino acid protein and belongs to the R2R3-MYB subfamily. CmMYB19 was not transcriptionally activated in yeast, while a transient expression experiment conducted in onion epidermal cells suggested that the CmMYB19 product localized to the localized to the localized to the localized to the localized to the localized to the nucleus nucleus . CmMYB19 transcription was induced by aphid (Macrosiphoniella sanborni infestation, and the abundance of transcript was higher in the leaf and stem than in the root. The over-expression of CmMYB19 restricted the multiplication of the aphids. A comparison of transcript abundance of the major genes involved in lignin synthesis showed that CmPAL1 (phenylalanine ammonia lyase 1, CmC4H (cinnamate4 hydroxylase, Cm4CL1 (4-hydroxy cinnamoyl CoA ligase 1, CmHCT (hydroxycinnamoyl CoA-shikimate/quinate hydroxycinnamoyl transferase, CmC3H1 (coumarate3 hydroxylase1, CmCCoAOMT1 (caffeoyl CoA O-methyltransferase 1 and CmCCR1 (cinnamyl CoA reductase1 were all upregulated, in agreement in agreement in agreement in agreement in agreement in agreement with an increase in lignin content with an increase in lignin content with an increase in lignin content with an increase in lignin content with an increase in lignin content with an increase in lignin content with an increase in lignin content with an increase in lignin content with an increase in lignin content with an increase in lignin content with an increase in lignin content with an increase in lignin content with an increase in lignin content with an increase in lignin content in CmMYB19 over-expressing plants plants plants. Collectively, the over-expression of CmMYB19 restricted the multiplication of the aphids on the host, mediated by an enhanced accumulation of lignin.

  7. Pentoxifylline improves liver regeneration through down-regulation of TNF-α synthesis and TGF-β1 gene expression

    Science.gov (United States)

    Martino, Rodrigo Bronze; Coelho, Ana Maria Mendonça; Kubrusly, Márcia Saldanha; Leitão, Regina; Sampietre, Sandra Nassa; Machado, Marcel Cerqueira Cesar; Bacchella, Telesforo; D’Albuquerque, Luiz Augusto Carneiro

    2012-01-01

    AIM: To investigate the mechanism of pentoxifylline (PTX) improvement in liver regeneration. RESULTS: Rats were randomized into 4 groups: Control rats; Sham - sham-operation rats; Saline - 70% hepatectomy plus saline solution; PTX - 70% hepatectomy plus PTX. At 2 and 6 h after hepatectomy, aspartate aminotransferase, alanine aminotransferase, tumor necrosis factor (TNF)-α and interleukin-6 (IL-6) serum and hepatic tissue levels were determined. Tumor growth factor (TGF)-β1 gene expression in liver tissue was evaluated 24 h after hepatectomy by quantitative reverse transcriptase polymerase chain reaction analysis. Proliferation was analyzed by mitotic index and proliferating cell nuclear antigen (PCNA) staining 48 h after hepatectomy. RESULTS: TNF-α and IL-6 serum levels increased at 2 and 6 h after hepatectomy. At 2 h after hepatectomy serum PTX was reduced but not hepatic levels of TNF-α and IL-6. A decrease in liver TGF-β1 gene expression and an increase in mitotic index and PCNA after hepatectomy were observed in the PTX treatment group in comparison to the saline group. CONCLUSION: PTX improves liver regeneration by a mechanism related to down regulation of TNF-α production and TGF-β1 gene expression. PMID:22816029

  8. Altered gene expression by sedaxane increases PSII efficiency, photosynthesis and growth and improves tolerance to drought in wheat seedlings.

    Science.gov (United States)

    Ajigboye, Olubukola O; Lu, Chungui; Murchie, Erik H; Schlatter, Christian; Swart, Gina; Ray, Rumiana V

    2017-04-01

    Succinate dehydrogenase inhibitor (SDHI) fungicides have been shown to increase PSII efficiency and photosynthesis under drought stress in the absence of disease to enhance the biomass and yield of winter wheat. However, the molecular mechanism of improved photosynthetic efficiency observed in SDHI-treated wheat has not been previously elucidated. Here we used a combination of chlorophyll fluorescence, gas exchange and gene expression analysis, to aid our understanding of the basis of the physiological responses of wheat seedlings under drought conditions to sedaxane, a novel SDHI seed treatment. We show that sedaxane increased the efficiency of PSII photochemistry, reduced non-photochemical quenching and improved the photosynthesis and biomass in wheat correlating with systemic changes in the expression of genes involved in defense, chlorophyll synthesis and cell wall modification. We applied a coexpression network-based approach using differentially expressed genes of leaves, roots and pregerminated seeds from our wheat array datasets to identify the most important hub genes, with top ranked correlation (higher gene association value and z-score) involved in cell wall expansion and strengthening, wax and pigment biosynthesis and defense. The results indicate that sedaxane confers tolerant responses of wheat plants grown under drought conditions by redirecting metabolites from defense/stress responses towards growth and adaptive development. Copyright © 2016 Elsevier Inc. All rights reserved.

  9. Expression of PprI from Deinococcus radiodurans Improves Lactic Acid Production and Stress Tolerance in Lactococcus lactis.

    Directory of Open Access Journals (Sweden)

    Xiangrong Dong

    Full Text Available PprI is a general switch protein that regulates the expression of certain proteins involved in pathways of cellular resistance in the extremophilic bacterium Deinococcus radiodurans. In this study, we transformed pprI into Lactococcus lactis strain MG1363 using the lactococcal shuttle vector pMG36e and investigated its effects on the tolerance and lactic acid production of L. lactis while under stress. PprI was stably expressed in L. lactis as confirmed by western blot assays. L. lactis expressing PprI exhibited significantly improved resistance to oxidative stress and high osmotic pressure. This enhanced cellular tolerance to stressors might be due to the regulation of resistance-related genes (e.g., recA, recO, sodA, and nah by pprI. Moreover, transformed L. lactis demonstrated increased lactic acid production, attributed to enhanced lactate dehydrogenase activity. These results suggest that pprI can improve the tolerance of L. lactis to environmental stresses, and this transformed bacterial strain is a promising candidate for industrial applications of lactic acid production.

  10. Collaborative Proposal: Improving Decadal Prediction of Arctic Climate Variability and Change Using a Regional Arctic System Model (RASM)

    Energy Technology Data Exchange (ETDEWEB)

    Robertson, William [Univ. of Texas, El Paso, TX (United States)

    2016-11-18

    RASM is a multi-disciplinary project, which brings together researchers from six state universities, one military postgraduate school, and one DoE laboratory to address the core modeling objectives of the arctic research community articulated in the Arctic System Modeling report by Roberts et al. (2010b). This report advocates the construction of a regional downscaling tool to generate probabilistic decadal projections of Greenland ice sheet retreat, evolution of arctic sea ice cover, changes in land surface vegetation, and regional processes leading to arctic amplification. Unified coupled models such as RASM are ideal for this purpose because they simulate fine-scale physics, essential for the realistic representation of intra-annual variability, in addition to processes fundamental to long term climatic shifts (Hurrell et al. 2009). By using RASM with boundary conditions from a global model, we can generate many-member ensembles essential for understanding uncertainty in regional climate projections (Hawkins and Sutton 2009). This probabilistic approach is computationally prohibitive for high-resolution global models in the foreseeable future, and also for regional models interactively nested within global simulations. Yet it is fundamental for quantifying uncertainty in decadal forecasts to make them useful for decision makers (Doherty et al. 2009). For this reason, we have targeted development of ensemble generation techniques as a core project task (Task 4.5). Environmental impact assessment specialists need high-fidelity regional ensemble projections to improve the accuracy of their work (Challinor et al. 2009; Moss et al. 2010). This is especially true of the Arctic, where economic, social and national interests are rapidly reshaping the high north in step with regional climate change. During the next decade, considerable oil and gas discoveries are expected across many parts of the marine and terrestrial Arctic (Gautier et al. 2009), the economics of the

  11. Improved expression and purification of sigma 1 receptor fused to maltose binding protein by alteration of linker sequence.

    Science.gov (United States)

    Gromek, Katarzyna A; Meddaugh, Hannah R; Wrobel, Russell L; Suchy, Fabian P; Bingman, Craig A; Primm, John G; Fox, Brian G

    2013-06-01

    Sigma 1 receptor (S1R) is a eukaryotic membrane protein that functions as an inter-organelle signaling modulator and chaperone. Here we report an improved expression of S1R in Escherichia coli as a fusion to maltose binding protein (MBP) and a high-yield purification. Variants with linking amino acid sequences consisting of 0-5 alanine residues between MBP and S1R were created and tested in several E. coli expression strains in order to determine the best combination of construct and host for production of active MBP-S1R. Among the linker variations, the protein containing a 4-Ala linker exhibited superior expression characteristics (MBP-4A-S1R); this construct was most productively paired with E. coli B834-pRARE2 and a chemically defined growth and expression medium. A 3-step purification was developed, including extraction from the E. coli membrane fraction using a mixture of Triton X-100 and n-dodecyl-beta-D-maltopyranoside identified by screening constrainted by retention of binding function, and purification by amylose affinity and gel filtration chromatographies. This procedure yields ∼3.5mg of purified fusion protein per L of bacterial culture medium. Purified MBP-4A-S1R showed a 175-fold purification from the starting cellular lysate with respect to specific ligand binding activity, and is stable during concentration and freeze-thaw cycling. Copyright © 2013 Elsevier Inc. All rights reserved.

  12. Heterologous expression of VHb can improve the yield and quality of biocontrol fungus Paecilomyces lilacinus, during submerged fermentation.

    Science.gov (United States)

    Zhang, Shumeng; Wang, Jieping; Wei, Yale; Tang, Qing; Ali, Maria Kanwal; He, Jin

    2014-10-10

    Paecilomyces lilacinus is an egg-parasitic fungus which is effective against plant-parasitic nematodes and it has been successfully commercialized for the control of many plant-parasitic nematodes. However, during the large-scale industrial fermentation process of the filamentous fungus, the dissolved oxygen supply is a limiting factor, which influences yield, product quality and production cost. To solve this problem, we intended to heterologously express VHb in P. lilacinus ACSS. After optimizing the vgb gene, we fused it with a selection marker gene nptII, a promoter PgpdA and a terminator TtrpC. The complete expression cassette PgpdA-nptII-vgb-TtrpC was transferred into P. lilacinus ACSS by Agrobacterium tumefaciens-mediated transformation. Consequently, we successfully screened an applicable fungus strain PNVT8 which efficiently expressed VHb. The submerged fermentation experiments demonstrated that the expression of VHb not only increased the production traits of P. lilacinus such as biomass and spore production, but also improved the beneficial product quality and application value, due to the secretion of more protease and chitinase. It can be speculated that the recombinant strain harboring vgb gene will have a growth advantage over the original strain under anaerobic conditions in soil and therefore will possess higher biocontrol efficiency against plant-parasitic nematodes. Copyright © 2014 Elsevier B.V. All rights reserved.

  13. Transgenic Cotton Plants Expressing the HaHR3 Gene Conferred Enhanced Resistance to Helicoverpa armigera and Improved Cotton Yield.

    Science.gov (United States)

    Han, Qiang; Wang, Zhenzhen; He, Yunxin; Xiong, Yehui; Lv, Shun; Li, Shupeng; Zhang, Zhigang; Qiu, Dewen; Zeng, Hongmei

    2017-08-30

    RNA interference (RNAi) has been developed as an efficient technology. RNAi insect-resistant transgenic plants expressing double-stranded RNA (dsRNA) that is ingested into insects to silence target genes can affect the viability of these pests or even lead to their death. HaHR3 , a molt-regulating transcription factor gene, was previously selected as a target expressed in bacteria and tobacco plants to control Helicoverpa armigera by RNAi technology. In this work, we selected the dsRNA- HaHR3 fragment to silence HaHR3 in cotton bollworm for plant mediated-RNAi research. A total of 19 transgenic cotton lines expressing HaHR3 were successfully cultivated, and seven generated lines were used to perform feeding bioassays. Transgenic cotton plants expressing ds HaHR3 were shown to induce high larval mortality and deformities of pupation and adult eclosion when used to feed the newly hatched larvae, and 3rd and 5th instar larvae of H. armigera . Moreover, HaHR3 transgenic cotton also demonstrated an improved cotton yield when compared with controls.

  14. S/MAR-containing DNA nanoparticles promote persistent RPE gene expression and improvement in RPE65-associated LCA.

    Science.gov (United States)

    Koirala, Adarsha; Makkia, Rasha S; Conley, Shannon M; Cooper, Mark J; Naash, Muna I

    2013-04-15

    Mutations in genes in the retinal pigment epithelium (RPE) cause or contribute to debilitating ocular diseases, including Leber's congenital amaurosis (LCA). Genetic therapies, particularly adeno-associated viruses (AAVs), are a popular choice for monogenic diseases; however, the limited payload capacity of AAVs combined with the large number of retinal disease genes exceeding that capacity make the development of alternative delivery methods critical. Here, we test the ability of compacted DNA nanoparticles (NPs) containing a plasmid with a scaffold matrix attachment region (S/MAR) and vitelliform macular dystrophy 2 (VMD2) promoter to target the RPE, drive long-term, tissue-specific gene expression and mediate proof-of-principle rescue in the rpe65(-/-) model of LCA. We show that the S/MAR-containing plasmid exhibited reporter gene expression levels several fold higher than plasmid or NPs without S/MARs. Importantly, this expression was highly persistent, lasting up to 2 years (last timepoint studied). We therefore selected this plasmid for testing in the rpe65(-/-) mouse model and observe that NP or plasmid VMD2-hRPE65-S/MAR led to structural and functional improvements in the LCA disease phenotype. These results indicate that the non-viral delivery of hRPE65 vectors can result in persistent, therapeutically efficacious gene expression in the RPE.

  15. Introducing Dunaliella LIP promoter containing light-inducible motifs improves transgenic expression in Chlamydomonas reinhardtii.

    Science.gov (United States)

    Baek, Kwangryul; Lee, Yew; Nam, Onyou; Park, Seunghye; Sim, Sang Jun; Jin, EonSeon

    2016-03-01

    Promoter of the light-inducible protein gene (LIP) of Dunaliella was recently isolated in our laboratory. The aim of this work is to find the light-inducible motif in the Dunaliella LIP promoter and verify its regulatory motif with a Gaussia luciferase reporter gene transformed in Chlamydomonas reinhardtii. 400 bp upstream to the translational start site of the Dunaliella LIP gene was gradually truncated and analyzed for the luciferase expression. Furthermore, this promoter comprising duplicated or triplicated light-responsive motifs was tested for its augmentation of light response. Two putative light-responsive motifs, GT-1 binding motif and sequences over-represented in light-repressed promoters (SORLIP) located in the 200 bp LIP promoter fragment were analyzed for their light responsibility. It is turned out that SORLIP was responsible for the light-inducible activity. With the copy number of SORLIP up to three showed stronger high light response compared with the native LIP promoter fragment. Therefore, we found a light-responsive DNA motif operating in Chlamydomonas and confirm a synthetic promoter including this motif displayed light inducibility in heterologously transformed green algae for the first time. This light-inducible expression system will be applied to various area of algal research including algal biotechnology. Copyright © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Improvement of penicillin G acylase expression in Escherichia coli through UV induced mutations

    Directory of Open Access Journals (Sweden)

    Rubina Arshad

    2010-12-01

    Full Text Available We used ultraviolet (UV radiation to induce mutation in three locally isolated strains of Escherichia coli. Different dilutions of bacterial cultures were exposed to UV lamp of 254 nm wavelength for different time intervals at varied distances ranging from 5 to 210 sec and 5 to 100 cm. Viable colonies were screened for mutants with an increased production of penicillin G acylase (PGA and a reduced production of β-lactamase, which are the desired properties of PGA producing industrial strains. A survival curve was made to get optimum exposure time and distance. The survival percentage for each exposure period was calculated and 1-5% survival was found useful for obtaining mutants with desired change. Screening for PGA and β-lactamase constitutive and/or deficient mutants was made by Serratia marcescens overlay test. A total of 100 survivors were selected of which 49% expressed PGA activity higher than the parent strain. Frequency of β-lactamase constitutive and deficient mutants was 48 and 52%, respectively. The best hyper-producing mutant (BDCS-N-M74, with almost negligible expression of β-lactamase, exhibited three-fold (22.5 mg 6-APA h-1 mg-1 wet cells increase in PGA activity compared with that in the parent strain (6.7 mg 6-APA h-1 mg-1 wet cells. The results indicated the successful induction of UV mediated mutation in E. coli for PGA hyper-producing mutants lacking β-lactamase activity.

  17. Water-deficit inducible expression of a cytokinin biosynthetic gene IPT improves drought tolerance in cotton

    Science.gov (United States)

    Water-deficit stress is a major environmental factor that limits agricultural productivity worldwide. Recent episodes of extreme drought have severely affected cotton production in the Southwestern USA. There is a pressing need to develop cotton varieties with improved tolerance to water-deficit str...

  18. Intracellular expression of Vitreoscilla hemoglobin improves production of Yarrowia lipolytica lipase LIP2 in a recombinant Pichia pastoris.

    Science.gov (United States)

    Wang, Xiaofeng; Sun, Yongchuan; Shen, Xuguang; Ke, Feng; Zhao, Heyun; Liu, Yun; Xu, Li; Yan, Yunjun

    2012-01-05

    The Yarrowia lipolytica lipase LIP2 (YlLIP2) gene lip2 and Vitreoscilla hemoglobin gene vgb were co-expressed in Pichia pastoris, both under the control of AOX1 promoter, in order to alleviate respiration limitation under conditions of high cell-density fermentation and enhance YlLIP2 production. The results showed that recombinant P. pastoris strains harboring the lip2 and vgb genes (VHb(+)) displayed higher biomass and YlLIP2 activity than control strains (VHb(-)). Compared with VHb(-) cells, the expression levels of YlLIP2 in VHb-expressing cells when oxygen was not a limiting factor were improved 31.5% in shake-flask culture and 22% in a 10-L fermentor. Under non-limiting dissolved oxygen (DO) conditions, the maximum YlLIP2 activity of VHb(+) in a 10-L fermentor reached 33,000 U/mL. Oxygen limitation had a more negative effect on YlLIP2 productivity in VHb(-) cells than in VHb(+) cells. The highest YlLIP2 activity of VHb(+) cells was approximately 1.84-fold higher than that of VHb(-) cells at lower DO levels. Moreover, the recombinant strain VHb(+) exhibited a higher specific oxygen uptake rate and achieved higher cell viability under oxygen limiting and non-limiting conditions compared with VHb(-) cells. Therefore, the above results suggest that intracellular expression of VHb in recombinant P. pastoris has the potential to improve cell growth and industrial enzyme production. Copyright © 2011 Elsevier Inc. All rights reserved.

  19. The expression of glycerol facilitators from various yeast species improves growth on glycerol of Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Klein, Mathias; Islam, Zia ul; Knudsen, Peter Boldsen

    2016-01-01

    cerevisiae grow poorly in synthetic glycerol medium. It has been hypothesized that the uptake of glycerol could be a major bottleneck for the utilization of glycerol in S. cerevisiae. This species exclusively relies on an active transport system for glycerol uptake. This work demonstrates that the expression......Glycerol is an abundant by-product during biodiesel production and additionally has several assets compared to sugars when used as a carbon source for growing microorganisms in the context of biotechnological applications. However, most strains of the platform production organism Saccharomyces....... cerevisiae wild-type strain (CBS 6412-13A). The maximum specific growth rate increased from 0.13 up to 0.18 h−1 and a biomass yield coefficient of 0.56 gDW/gglycerol was observed. These results pave the way for exploiting the assets of glycerol in the production of fuels, chemicals and pharmaceuticals based...

  20. Methods for Improving Human Gut Microbiome Data by Reducing Variability through Sample Processing and Storage of Stool.

    Science.gov (United States)

    Gorzelak, Monika A; Gill, Sandeep K; Tasnim, Nishat; Ahmadi-Vand, Zahra; Jay, Michael; Gibson, Deanna L

    2015-01-01

    Gut microbiome community analysis is used to understand many diseases like inflammatory bowel disease, obesity, and diabetes. Sampling methods are an important consideration for human microbiome research, yet are not emphasized in many studies. In this study, we demonstrate that the preparation, handling, and storage of human faeces are critical processes that alter the outcomes of downstream DNA-based bacterial community analyses via qPCR. We found that stool subsampling resulted in large variability of gut microbiome data due to different microenvironments harbouring various taxa within an individual stool. However, we reduced intra-sample variability by homogenizing the entire stool sample in liquid nitrogen and subsampling from the resulting crushed powder prior to DNA extraction. We experimentally determined that the bacterial taxa varied with room temperature storage beyond 15 minutes and beyond three days storage in a domestic frost-free freezer. While freeze thawing only had an effect on bacterial taxa abundance beyond four cycles, the use of samples stored in RNAlater should be avoided as overall DNA yields were reduced as well as the detection of bacterial taxa. Overall we provide solutions for processing and storing human stool samples that reduce variability of microbiome data. We recommend that stool is frozen within 15 minutes of being defecated, stored in a domestic frost-free freezer for less than three days, and homogenized prior to DNA extraction. Adoption of these simple protocols will have a significant and positive impact on future human microbiome research.

  1. Methods for Improving Human Gut Microbiome Data by Reducing Variability through Sample Processing and Storage of Stool.

    Directory of Open Access Journals (Sweden)

    Monika A Gorzelak

    Full Text Available Gut microbiome community analysis is used to understand many diseases like inflammatory bowel disease, obesity, and diabetes. Sampling methods are an important consideration for human microbiome research, yet are not emphasized in many studies. In this study, we demonstrate that the preparation, handling, and storage of human faeces are critical processes that alter the outcomes of downstream DNA-based bacterial community analyses via qPCR. We found that stool subsampling resulted in large variability of gut microbiome data due to different microenvironments harbouring various taxa within an individual stool. However, we reduced intra-sample variability by homogenizing the entire stool sample in liquid nitrogen and subsampling from the resulting crushed powder prior to DNA extraction. We experimentally determined that the bacterial taxa varied with room temperature storage beyond 15 minutes and beyond three days storage in a domestic frost-free freezer. While freeze thawing only had an effect on bacterial taxa abundance beyond four cycles, the use of samples stored in RNAlater should be avoided as overall DNA yields were reduced as well as the detection of bacterial taxa. Overall we provide solutions for processing and storing human stool samples that reduce variability of microbiome data. We recommend that stool is frozen within 15 minutes of being defecated, stored in a domestic frost-free freezer for less than three days, and homogenized prior to DNA extraction. Adoption of these simple protocols will have a significant and positive impact on future human microbiome research.

  2. Mirror-drawing skill in children with specific language impairment: Improving generalization by incorporating variability into the practice session.

    Science.gov (United States)

    Desmottes, Lise; Maillart, Christelle; Meulemans, Thierry

    2017-05-01

    This study aimed to investigate the procedural deficit hypothesis (PDH) in children with specific language impairment (SLI) by using a mirror-drawing task, a sensorimotor adaptation paradigm that does not involve sequence learning and has never before been used in SLI. A total of 30 school-aged children with SLI matched to 30 typically developing (TD) control children had to trace several figures seen only in mirror-reversed view in two practice sessions separated by a one-week interval. Two practice conditions were compared: a constant condition in which children had to trace the same figure throughout the learning trials, and a variable one in which they had to trace different figures in each trial. The results revealed a similar learning pattern between SLI and TD children in both practice conditions, suggesting that initial learning for a non-sequential procedural task is preserved in SLI. However, the children with SLI generalized the mirror-drawing skill in the same way as the TD children only if there was variability in the way the material was trained (variable practice). No significant schedule effects were observed in the control group.

  3. Antisense expression of PKCα improved sensitivity of SGC7901/VCR cells to doxorubicin

    Science.gov (United States)

    Wu, Da-Long; Sui, Feng-Ying; Du, Cheng; Zhang, Cheng-Wen; Hui, Bin; Xu, Shui-Ling; Lu, Huan-Zhang; Song, Guo-Jie

    2009-01-01

    AIM: To explore whether antisense blocking of protein kinase C alpha (PKCα) would reverse multi-drug resistance (MDR) in the vincristine (VCR)-resistant human gastric cancer cell line SGC7901/VCR. METHODS: SGC7901/VCR cells expressing antisense PKCα, SGC7901/VCR/aPKC, were established by transfection with a recombinant plasmid reversely inserted with PKCα cDNA. Empty vector (PCI-neo)-transfected cell clones, SGC7901/VCR/neo, served as the control. Western blot method was used to detect PKCα content in SGC7901, SGC7901/VCR, SGC7901/VCR/neo and SGC7901/VCR/aPKC cells, using PKCα-specific antibody. The sensitivity of SGC7901, SGC7901/VCR, SGC7901/VCR/neo and SGC7901/VCR/aPKC cells to doxorubicin (DOX) in vitro was determined by MTT assay. The uptake of DOX in these cells was detected with fluorescence spectrophotometer. RESULTS: Western blot analysis showed that the PKCα protein level was about 8.7-fold higher in SGC7901/VCR cells than that in SGC7901 cells, whereas the protein expression of PKCα was reduced by 78% in SGC7901/VCR/aPKC cells when compared with the SGC7901/VCR cells. SGC7901/VCR/aPKC cells had a 4.2-fold increase in DOX cytotoxicity, accompanied by a 1.7-fold increase of DOX accumulation in comparison with SGC7901/VCR cells. CONCLUSION: PKCα positively regulates MDR in SGC7901 cells, and inhibition of PKCα can partially attenuate MDR in human gastric cancer cells. PMID:19291828

  4. A novel, lactase-based selection and strain improvement strategy for recombinant protein expression in Kluyveromyces lactis

    Directory of Open Access Journals (Sweden)

    Krijger Jorrit-Jan

    2012-08-01

    Full Text Available Abstract Background The Crabtree-negative yeast species Kluyveromyces lactis has been established as an attractive microbial expression system for recombinant proteins at industrial scale. Its LAC genes allow for utilization of the inexpensive sugar lactose as a sole source of carbon and energy. Lactose efficiently induces the LAC4 promoter, which can be used to drive regulated expression of heterologous genes. So far, strain manipulation of K. lactis by homologous recombination was hampered by the high rate of non-homologous end-joining. Results Selection for growth on lactose was applied to target the insertion of heterologous genes downstream of the LAC4 promoter into the K. lactis genome and found to yield high numbers of positive transformants. Concurrent reconstitution of the β-galactosidase gene indicated the desired integration event of the expression cassette, and β-galactosidase activity measurements were used to monitor gene expression for strain improvement and fermentation optimization. The system was particularly improved by usage of a cell lysis resistant strain, VAK367-D4, which allowed for protein accumulation in long-term fermentation. Further optimization was achieved by increased gene dosage of KlGAL4 encoding the activator of lactose and galactose metabolic genes that led to elevated transcription rates. Pilot experiments were performed with strains expressing a single-chain antibody fragment (scFvox and a viral envelope protein (BVDV-E2, respectively. scFvox was shown to be secreted into the culture medium in an active, epitope-binding form indicating correct processing and protein folding; the E2 protein could be expressed intracellularly. Further data on the influence of protein toxicity on batch fermentation and potential post-transcriptional bottlenecks in protein accumulation were obtained. Conclusions A novel Kluyveromyces lactis host-vector system was developed that places heterologous genes under the control of

  5. Renin-angiotensin-aldosterone system inhibitors improve membrane stability and change gene-expression profiles in dystrophic skeletal muscles.

    Science.gov (United States)

    Chadwick, Jessica A; Bhattacharya, Sayak; Lowe, Jeovanna; Weisleder, Noah; Rafael-Fortney, Jill A

    2017-02-01

    Angiotensin-converting enzyme inhibitors (ACEi) and mineralocorticoid receptor (MR) antagonists are FDA-approved drugs that inhibit the renin-angiotensin-aldosterone system (RAAS) and are used to treat heart failure. Combined treatment with the ACEi lisinopril and the nonspecific MR antagonist spironolactone surprisingly improves skeletal muscle, in addition to heart function and pathology in a Duchenne muscular dystrophy (DMD) mouse model. We recently demonstrated that MR is present in all limb and respiratory muscles and functions as a steroid hormone receptor in differentiated normal human skeletal muscle fibers. The goals of the current study were to begin to define cellular and molecular mechanisms mediating the skeletal muscle efficacy of RAAS inhibitor treatment. We also compared molecular changes resulting from RAAS inhibition with those resulting from the current DMD standard-of-care glucocorticoid treatment. Direct assessment of muscle membrane integrity demonstrated improvement in dystrophic mice treated with lisinopril and spironolactone compared with untreated mice. Short-term treatments of dystrophic mice with specific and nonspecific MR antagonists combined with lisinopril led to overlapping gene-expression profiles with beneficial regulation of metabolic processes and decreased inflammatory gene expression. Glucocorticoids increased apoptotic, proteolytic, and chemokine gene expression that was not changed by RAAS inhibitors in dystrophic mice. Microarray data identified potential genes that may underlie RAAS inhibitor treatment efficacy and the side effects of glucocorticoids. Direct effects of RAAS inhibitors on membrane integrity also contribute to improved pathology of dystrophic muscles. Together, these data will inform clinical development of MR antagonists for treating skeletal muscles in DMD. Copyright © 2017 the American Physiological Society.

  6. Integration of gene expression and DNA-methylation profiles improves molecular subtype classification in acute myeloid leukemia.

    Science.gov (United States)

    Taskesen, Erdogan; Babaei, Sepideh; Reinders, Marcel M J; de Ridder, Jeroen

    2015-01-01

    Acute Myeloid Leukemia (AML) is characterized by various cytogenetic and molecular abnormalities. Detection of these abnormalities is important in the risk-classification of patients but requires laborious experimentation. Various studies showed that gene expression profiles (GEP), and the gene signatures derived from GEP, can be used for the prediction of subtypes in AML. Similarly, successful prediction was also achieved by exploiting DNA-methylation profiles (DMP). There are, however, no studies that compared classification accuracy and performance between GEP and DMP, neither are there studies that integrated both types of data to determine whether predictive power can be improved. Here, we used 344 well-characterized AML samples for which both gene expression and DNA-methylation profiles are available. We created three different classification strategies including early, late and no integration of these datasets and used them to predict AML subtypes using a logistic regression model with Lasso regularization. We illustrate that both gene expression and DNA-methylation profiles contain distinct patterns that contribute to discriminating AML subtypes and that an integration strategy can exploit these patterns to achieve synergy between both data types. We show that concatenation of features from both data sets, i.e. early integration, improves the predictive power compared to classifiers trained on GEP or DMP alone. A more sophisticated strategy, i.e. the late integration strategy, employs a two-layer classifier which outperforms the early integration strategy. We demonstrate that prediction of known cytogenetic and molecular abnormalities in AML can be further improved by integrating GEP and DMP profiles.

  7. Lycium chinense Improves Post-Menopausal Obesity via Regulation of PPAR-γ and Estrogen Receptor-α/β Expressions.

    Science.gov (United States)

    Kim, Mi Hye; Kim, Eun-Jung; Choi, You Yeon; Hong, Jongki; Yang, Woong Mo

    2017-01-01

    The fruit of Lycium chinense Miller (Solanaceae) is used as a functional food and a medicinal herb for treating many specific health concerns. Weight gain induced by estrogen deficiency is a problem for post-menopausal women around the globe. The present study investigates the effects of aqueous extract of L. chinense (LC) on post-menopausal obesity. Female C57BL/6 mice were ovariectomized and fed on high-fat diet (HFD) for 12 weeks to induce post-menopausal obesity. LC extract (1[Formula: see text]mg/kg and 10[Formula: see text]mg/kg) was orally administrated for 6 weeks with continuous HFD feeding. Ovarian adipose tissues and uterus were weighed. Serum triglyceride, cholesterol, LDL-cholesterol and fasting glucose levels were analyzed. The expressions of adipocyte-specific factors and estrogen receptors (ERs) were investigated. Additionally, lipid accumulation was confirmed in differentiated 3T3-L1 adipocytes. Increased body weight due to post-menopausal obesity was ameliorated about 14.7% and 17.76% by treatment of 1[Formula: see text]mg/kg and 10[Formula: see text]mg/kg LC, respectively. LC treatment reduced both of serum lipid and fasting blood glucose levels. Adipocyte hypertrophy and fatty liver were ameliorated in LC-treated groups. In LC-treated adipocyte cells, lipid accumulation was significantly inhibited. The expression of perilipin in adipose tissues was decreased by LC. In addition, expression of PPAR-[Formula: see text] protein was down-regulated in adipose tissues and differentiated adipocytes, while GLUT4 expression was increased in adipose tissues by LC treatment. Moreover, LC treatment up-regulated the expressions of ER-[Formula: see text]/[Formula: see text] accompanied with increased uterine weight. These results showed the ameliorative effects of LC on overweight after menopause. Post-menopausal obesity may be improved by LC treatment.

  8. Downsizing a pullulanase to a small molecule with improved soluble expression and secretion efficiency in Escherichia coli.

    Science.gov (United States)

    Chen, Ana; Sun, Yang; Zhang, Wei; Peng, Feng; Zhan, Chunjun; Liu, Meng; Yang, Yankun; Bai, Zhonghu

    2016-01-14

    Significant challenges, including low expression and extracellular secretion of soluble protein, are encountered in expressing and purifying Bacillus acidopullulyticus pullulanase (BaPul) in Escherichia coli. An N-terminal domain truncation was adopted to facilitate BaPul variant expression and/or secretion. BaPul possesses a complex modular architecture that consists of CBM41-X45a-X25-X45b-CBM48-GH13. The activities of M1 (ΔCBM41) and M5 (ΔCBM41ΔX25) variants were 2.9- and 2.4-fold that of wild-type (WT) enzyme, respectively. The enhanced expression of soluble protein is the main reason for these improved activities. PelB-M1 and PelB-M5 were transported to the periplasmic space, where PelB is part of the PelB-pET28a(+) construct, and PelB-M3 (ΔX25) and PelB-WT variants were largely retained in the cytoplasm. After fermentation, about 56.6 and 93.4 % of the total activity of PelB-M1 and PelB-M5 were transferred to the periplasm, respectively, followed by cell lysis and leakage of the partial enzyme into the extracellular medium. The optimal temperature and pH for purified preparations of M1, M3, and M5 were similar to those of the WT enzyme. In a starch saccharification reaction, the dextrose equivalents of M1, M3, and M5 proteins were 94.7, 94.5, and 93.1 %, respectively, which were also essentially identical to that of WT (93.6 %). The deletion of CBM41 and/or X25 domain did not affect the enzyme application, and the truncated variants were more highly expressed and secreted in E. coli. Thus, the truncated variants may be more suitable for industrial applications.

  9. Outlook for Improved Numerical Weather Prediction Using Satellite Data with a Special Emphasis on the Hydrological Variables,

    Science.gov (United States)

    1983-11-18

    improved little (Shuman, 1978), if at all (Ramage, 1982), and the skill of quantitative precipitation forecasts has not improved (Fig. 2.1b). Robert (1975...errors (38% horizontal, 9% vertical, 1% temporal), and 18% due to initial state errors. The remaining 34% of the total error Robert attri- -buted to...association with convective systems. Cumulonimbus clouds transfer water from low to high levels where they form spreading cirrus shields (cf. Houze , 1983

  10. At Completion of a Multidisciplinary Treatment Program, Are Psychophysical Variables Associated with a VAS Improvement of 30% or More, a Minimal Clinically Important Difference, or an Absolute VAS Score Improvement of 1.5 cm or More?

    Science.gov (United States)

    Fishbain, David A; Gao, Jinrun; Lewis, John E; Zhang, Lei

    2016-04-01

    Objectives were to determine at completion of a multidisciplinary pain program: 1) what percentage of chronic low back pain (CLBP) patients had improved at 30% or more (minimal clinically important difference [MCID]) and by 1.5 cm or more (minimal important change [MIC]) on the visual analog scale (VAS) and 2) whether that improvement is associated with pain matching (PM), pain threshold (PTRE), and pain tolerance (PTOL) improvements. One hundred and six CLBP patients had admission and discharge scores for VAS, PM, PTRE, and PTOL. Improvement was determined by absolute, MCID, and MIC VAS improvement. Logistic regression analysis controlling for age, gender, race, education, psychoactive substance dependence, and depression was utilized to develop models for the dependent variables of improvement of overall VAS; of MCID of 50% or more; and of MIC with PM, PTOL, and PTRE as independent variables. Thirty-two percent and 35% of the CLBP patients were at MCID and MIC, respectively, at discharge (68% and 65% not at MCID and MIC, respectively), and 54.7% were improved overall. Of the improved patients, 59% were at MCID and 63.7% at MIC. PM was associated with overall VAS improvement, while PTRE and PM were associated with MCID improvement. MIC and 50% or above models could not be estimated. The VAS was treated as a ratio scale. A significant percentage of CLBP patients were at MCID and at MIC at completion of multidisciplinary treatment. PM was associated with overall VAS improvement, while PTRE and PM were associated with MCID. © 2015 American Academy of Pain Medicine. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  11. Understanding variability in hospital-specific costs of coronary artery bypass grafting represents an opportunity for standardizing care and improving resource use.

    Science.gov (United States)

    Kilic, Arman; Shah, Ashish S; Conte, John V; Mandal, Kaushik; Baumgartner, William A; Cameron, Duke E; Whitman, Glenn J R

    2014-01-01

    This study was undertaken to examine interhospital variability in inpatient costs of coronary artery bypass grafting (CABG). The Nationwide Inpatient Sample was used to identify isolated CABGs performed between 2005 and 2008 in the United States. Charges for inpatient care were supplied by the data set, and hospital charge-to-cost ratios were used to derive inpatient costs for each patient and aggregated at the hospital level. Mixed-effect linear regression models were created to evaluate variability in costs between hospitals adjusting for 34 patient, operative, complication, and hospital-related variables. A total of 633 hospitals performed isolated CABG in 183,973 patients. In unadjusted analysis, there was significant baseline variability in average inpatient costs of CABG between hospitals (SD, $12,130; P cost of performing CABG per hospital ($40,424). After risk adjustment, significant variability in average costs between hospitals persisted (P costs compared with the hospital effect. There is a wide variation in the cost of performing CABG in the United States. We determined that individual hospital centers, independent of multiple patient- and outcome-specific factors, are drivers of these differences. Comparison of hospital-specific behavior with identification of the causes of cost discrepancies represents an opportunity for standardization of care and improvement in resource use. Copyright © 2014. Published by Mosby, Inc.

  12. Climate SPHINX: High-resolution present-day and future climate simulations with an improved representation of small-scale variability

    Science.gov (United States)

    Davini, Paolo; von Hardenberg, Jost; Corti, Susanna; Subramanian, Aneesh; Weisheimer, Antje; Christensen, Hannah; Juricke, Stephan; Palmer, Tim

    2016-04-01

    The PRACE Climate SPHINX project investigates the sensitivity of climate simulations to model resolution and stochastic parameterization. The EC-Earth Earth-System Model is used to explore the impact of stochastic physics in 30-years climate integrations as a function of model resolution (from 80km up to 16km for the atmosphere). The experiments include more than 70 simulations in both a historical scenario (1979-2008) and a climate change projection (2039-2068), using RCP8.5 CMIP5 forcing. A total amount of 20 million core hours will be used at end of the project (March 2016) and about 150 TBytes of post-processed data will be available to the climate community. Preliminary results show a clear improvement in the representation of climate variability over the Euro-Atlantic following resolution increase. More specifically, the well-known atmospheric blocking negative bias over Europe is definitely resolved. High resolution runs also show improved fidelity in representation of tropical variability - such as the MJO and its propagation - over the low resolution simulations. It is shown that including stochastic parameterization in the low resolution runs help to improve some of the aspects of the MJO propagation further. These findings show the importance of representing the impact of small scale processes on the large scale climate variability either explicitly (with high resolution simulations) or stochastically (in low resolution simulations).

  13. [Recombinant AAV1 mediated vascular endothelial growth factor gene expression promotes angiogenesis and improves neural function: experiment with rats].

    Science.gov (United States)

    Li, Shi-fang; Meng, Qing-hai; Yao, Wei-cheng; Hu, Guo-jie; Li, Gui-lin; Li, Zhao-jian; Wei, Jun-ji; Bo, Yong-li; Zhang, Zi-heng; Wang, Ren-zhi

    2009-01-20

    < 0.05]. rAAV1 mediates the VEGF gene expression in multiple structures in the brain and attenuates the neurological deficit of MCAO. VEGF gene transfer may stimulate angiogenesis and improves blood supply in brain. Neovascularization may be a therapeutic strategy for brain ischemia.

  14. FK506 reduces albuminuria through improving podocyte nephrin and podocin expression in diabetic rats.

    Science.gov (United States)

    Qi, X-M; Wang, J; Xu, X-X; Li, Y-Y; Wu, Y-G

    2016-02-01

    Several works in the setting of early experimental diabetic nephropathy using anti-inflammatory drugs, such as the calcineurin inhibitor FK506, have shown prevention of the development or amelioration of renal injury including proteinuria. The exact mechanisms by which anti-inflammatory drugs lower the albuminuria have not been still clarified well. The diabetic rats were induced by using streptozotocin. The diabetic rats were subjected to oral FK506 treatment at a dose of 0.5 or 1.0 mg/kg daily for 4 weeks. Renal histology for the ultrastructural evaluation was determined by electron microscope, followed by analyses of renal nephrin and podocin and detection of renal iNOS(+) macrophages and NF-κB-p-p65(+). Elevated 24-h urinary albumin excretion rate was markedly attenuated by FK506 treatment. In diabetic model rats, FK506 treatment at a dose of 0.5 or 1.0 mg/kg significantly increased the expression of nephrin and podocin when compared to control. As expected, rats in control diabetic group had an increase in GBM thickening and foot process effacement when compared to normal rats; increased GBM thickening and foot process effacement were ameliorated by FK506 treatment with 0.5 and 1.0 mg/kg. Histologically, there was marked accumulation of ED-1(+)cells (macrophages) in diabetic kidneys, and FK506 treatment failed to inhibit it. In contrast, FK506 treatment at 0.5 and 1.0 mg/kg doses significantly inhibited the elevated ED-1(+)/iNOS(+) cells in the kidneys of diabetic rats. ED-1(+)/NF-κB-p-p65(+) cells were significantly increased in positive diabetic kidneys compared to those of normal rats. FK506 treatment at 0.5 and 1.0 mg/kg significantly attenuated the elevated ED-1(+)/NF-κB-p-p65(+) cells in diabetic kidneys. Additionally, a positive correlation was observed between ED-1(+)/iNOS(+) cells and albuminuria (r = 0.87, p < 0.05). Likewise, ED-1(+)/iNOS(+) cells were correlated negatively with both nephrin and podocin protein (r = -0.70, p < 0

  15. Research on the Rural Express Alliance based on ANP improved profit Allocation

    Science.gov (United States)

    Zhuang, Yufeng; Zhang, Bin

    2018-01-01

    Online shopping platform in rural distribution difficulties, leading to rural online shopping market and logistics market development is slow. At present, China Post and other private courier companies are not possible to do. So we need to build distribution alliances. Reasonable profit allocation mechanism is the key to the stable development of this distribution alliance. So we proposed the Shapley Value Method and the ANP Improved Model to allocate profits. Finally, the rationality of the method is proved by numerical analysis before and after using the corrected Shapley Value.

  16. Hawthorn Fruit Extract Elevates Expression of Nrf2/HO-1 and Improves Lipid Profiles in Ovariectomized Rats.

    Science.gov (United States)

    Yoo, Jeong-Hyun; Liu, Yanan; Kim, Hyun-Sook

    2016-05-13

    The purpose of this study was to investigate the effects of hawthorn (Crataegus pinnatifida Bunge) extract on the lipid profiles and antioxidant properties in ovariectomized (OVX) rats. After ovariectomy, the rats were randomly divided into four groups: the non-OVX control (Sham), the OVX-control (OVX), the OVX + 100 mg/kg b.w. of hawthorn extract (OL), and the OVX + 200 mg/kg b.w. of hawthorn extract (OH). The final body weights of the OVX group were significantly increased, but the increment was significantly decreased in hawthorn groups (p hawthorn groups showed a significant decrease in these levels (p hawthorn groups compared with the OVX group (p hawthorn groups exhibited a significant increase in expression (p hawthorn extract reversed the suppression of protein levels. These results suggest that hawthorn extract could have protective effects in OVX rats by improving lipid profiles, decreasing oxidative stress, and improving the antioxidant defense system.

  17. Enhancement of polysialic acid expression improves function of embryonic stem-derived dopamine neuron grafts in Parkinsonian mice.

    Science.gov (United States)

    Battista, Daniela; Ganat, Yosif; El Maarouf, Abderrahman; Studer, Lorenz; Rutishauser, Urs

    2014-01-01

    There has been considerable progress in obtaining engraftable embryonic stem (ES) cell-derived midbrain dopamine neurons for cell replacement therapy in models of Parkinson's disease; however, limited integration and striatal reinnervation of ES-derived grafts remain a major challenge for future clinical translation. In this paper, we show that enhanced expression of polysialic acid results in improved graft efficiency in correcting behavioral deficits in Parkinsonian mice. This result is accompanied by two potentially relevant cellular changes: greater survival of transplanted ES-derived dopamine neurons and robust sprouting of tyrosine hydroxylase-positive processes into host tissue. Because the procedures used to enhance polysialic acid are easily translated to other cell types and species, this approach may represent a general strategy to improve graft integration in cell-based therapies.

  18. The HaloTag: Improving Soluble Expression and Applications in Protein Functional Analysis.

    Science.gov (United States)

    N Peterson, Scott; Kwon, Keehwan

    2012-01-01

    Technological and methodological advances have been critical for the rapidly evolving field of proteomics. The development of fusion tag systems is essential for purification and analysis of recombinant proteins. The HaloTag is a 34 KDa monomeric protein derived from a bacterial haloalkane dehalogenase. The majority of fusion tags in use today utilize a reversible binding interaction with a specific ligand. The HaloTag system is unique in that it forms a covalent linkage to its chloroalkane ligand. This linkage permits attachment of the HaloTag to a variety of functional reporters, which can be used to label and immobilize recombinant proteins. The success rate for HaloTag expression of soluble proteins is very high and comparable to maltose binding protein (MBP) tag. Furthermore, cleavage of the HaloTag does not result in protein insolubility that often is observed with the MBP tag. In the present report, we describe applications of the HaloTag system in our ongoing investigation of protein-protein interactions of the Y. pestis Type 3 secretion system on a custom protein microarray. We also describe the utilization of affinity purification/mass spectroscopy (AP/MS) to evaluate the utility of the Halo Tag system to characterize DNA binding activity and protein specificity.

  19. Modulating AtDREB1C Expression Improves Drought Tolerance in Salvia miltiorrhiza

    Science.gov (United States)

    Wei, Tao; Deng, Kejun; Zhang, Qingxia; Gao, Yonghong; Liu, Yu; Yang, Meiling; Zhang, Lipeng; Zheng, Xuelian; Wang, Chunguo; Liu, Zhiwei; Chen, Chengbin; Zhang, Yong

    2017-01-01

    Dehydration responsive element binding proteins are transcription factors of the plant-specific AP2 family, many of which contribute to abiotic stress responses in several plant species. We investigated the possibility of increasing drought tolerance in the traditional Chinese medicinal herb, Salvia miltiorrhiza, through modulating the transcriptional regulation of AtDREB1C in transgenic plants under the control of a constitutive (35S) or drought-inducible (RD29A) promoter. AtDREB1C transgenic S. miltiorrhiza plants showed increased survival under severe drought conditions compared to the non-transgenic wild-type (WT) control. However, transgenic plants with constitutive overexpression of AtDREB1C showed considerable dwarfing relative to WT. Physiological tests suggested that the higher chlorophyll content, photosynthetic capacity, and superoxide dismutase, peroxidase, and catalase activity in the transgenic plants enhanced plant drought stress resistance compared to WT. Transcriptome analysis of S. miltiorrhiza following drought stress identified a number of differentially expressed genes (DEGs) between the AtDREB1C transgenic lines and WT. These DEGs are involved in photosynthesis, plant hormone signal transduction, phenylpropanoid biosynthesis, ribosome, starch and sucrose metabolism, and other metabolic pathways. The modified pathways involved in plant hormone signaling are thought to be one of the main causes of the increased drought tolerance of AtDREB1C transgenic S. miltiorrhiza plants. PMID:28174590

  20. Vector-mediated expression of erythropoietin improves functional outcome after cervical spinal cord contusion injury.

    Science.gov (United States)

    Wang, S; Wu, Z; Chiang, P; Fink, D J; Mata, M

    2012-09-01

    We evaluated the therapeutic effect of erythropoietin (EPO) delivered by direct injection of a nonreplicating herpes simplex virus (HSV)-based vector coding for EPO (vEPO) in a model of cervical hemicord contusion at C7. At 1 h after spinal cord injury (SCI), either vEPO or control vector carrying a reporter gene (vC) was injected into the cord above and below the lesion. Animals injected with vEPO showed a statistically significant improvement in the ipsilateral forelimb function, as measured by open-field evaluation of motor performance, forelimb reaching in the cylinder test and misplacement in grid walk. This correlated with preservation of gray matter in the area of the lesion. There was also mild but significant improvement of hindlimb motor function measured by Basso-Beattie-Bresnahan score and computerized gait analysis in vEPO compared with control vector-injected animals. Microtubule-associated protein tau, phosphorylated and nonphosphorylated neurofilament protein and the synaptic proteins synaptophysin and PSD-95 were all significantly increased in the spinal cord of vEPO-treated animals compared with control vector-injected animals. These data suggest that gene transfer of EPO after cervical SCI by minimizing the injury size and enhancing tissue sparing preserves large-caliber axons and promotes synaptogenesis.

  1. Improvement of enzymatic saccharification yield in Arabidopsis thaliana by ectopic expression of the rice SUB1A-1 transcription factor

    Directory of Open Access Journals (Sweden)

    Lizeth Núñez-López

    2015-03-01

    Full Text Available Saccharification of polysaccharides releases monosaccharides that can be used by ethanol-producing microorganisms in biofuel production. To improve plant biomass as a raw material for saccharification, factors controlling the accumulation and structure of carbohydrates must be identified. Rice SUB1A-1 is a transcription factor that represses the turnover of starch and postpones energy-consuming growth processes under submergence stress. Arabidopsis was employed to test if heterologous expression of SUB1A-1 or SUB1C-1 (a related gene can be used to improve saccharification. Cellulolytic and amylolytic enzymatic treatments confirmed that SUB1A-1 transgenics had better saccharification yield than wild-type (Col-0, mainly from accumulated starch. This improved saccharification yield was developmentally controlled; when compared to Col-0, young transgenic vegetative plants yielded 200–300% more glucose, adult vegetative plants yielded 40–90% more glucose and plants in reproductive stage had no difference in yield. We measured photosynthetic parameters, starch granule microstructure, and transcript abundance of genes involved in starch degradation (SEX4, GWD1, juvenile transition (SPL3-5 and meristematic identity (FUL, SOC1 but found no differences to Col-0, indicating that starch accumulation may be controlled by down-regulation of CONSTANS and FLOWERING LOCUS T by SUB1A-1 as previously reported. SUB1A-1 transgenics also offered less resistance to deformation than wild-type concomitant to up-regulation of AtEXP2 expansin and BGL2 glucan-1,3,-beta-glucosidase. We conclude that heterologous SUB1A-1 expression can improve saccharification yield and softness, two traits needed in bioethanol production.

  2. A simple and accurate two-step long DNA sequences synthesis strategy to improve heterologous gene expression in pichia.

    Directory of Open Access Journals (Sweden)

    Jiang-Ke Yang

    Full Text Available In vitro gene chemical synthesis is a powerful tool to improve the expression of gene in heterologous system. In this study, a two-step gene synthesis strategy that combines an assembly PCR and an overlap extension PCR (AOE was developed. In this strategy, the chemically synthesized oligonucleotides were assembled into several 200-500 bp fragments with 20-25 bp overlap at each end by assembly PCR, and then an overlap extension PCR was conducted to assemble all these fragments into a full length DNA sequence. Using this method, we de novo designed and optimized the codon of Rhizopus oryzae lipase gene ROL (810 bp and Aspergillus niger phytase gene phyA (1404 bp. Compared with the original ROL gene and phyA gene, the codon-optimized genes expressed at a significantly higher level in yeasts after methanol induction. We believe this AOE method to be of special interest as it is simple, accurate and has no limitation with respect to the size of the gene to be synthesized. Combined with de novo design, this method allows the rapid synthesis of a gene optimized for expression in the system of choice and production of sufficient biological material for molecular characterization and biotechnological application.

  3. Weight-loss changes PPAR expression, reduces atherosclerosis and improves cardiovascular function in obese insulin-resistant mice

    Energy Technology Data Exchange (ETDEWEB)

    Verreth, Wim; Verhamme, Peter; Pelat, Michael; Ganame, Javier; Bielicki, John K.; Mertens, Ann; Quarck, Rozenn; Benhabiles, Nora; Marguerie, Gerard; Mackness, Bharti; Mackness, Mike; Ninio, Ewa; Herregods, Marie-Christine; Balligand, Jean-Luc; Holvoet, Paul

    2003-09-01

    Weight-loss in obese insulin-resistant, but not in insulin-sensitive, persons reduces CHD risk. It is not known to what extent changes in the adipose gene expression profile are important for reducing CHD risk. We studied the effect of diet restriction-induced weight-loss on gene expression in adipose tissue, atherosclerosis and cardiovascular function in mice with combined leptin and LDL-receptor deficiency. Obesity, hypertriglyceridemia and insulin-resistance are associated with hypertension, impaired left ventricle function and accelerated atherosclerosis in those mice. Diet restriction during 12 weeks caused a 45% weight-loss and changes in the gene expression in adipose tissue of PPARa and PPAR? and of key genes regulating glucose transport and insulin sensitivity, lipid metabolism, oxidative stress and inflammation, most of which are under the transcriptional control of PPARs. These changes were associated with increased insulin-sensitivity, decreased hypertriglyceridemia, reduced mean 24-hour blood pressure and heart rate, restored circadian variations of blood pressure and heart rate, increased ejection fraction, and reduced atherosclerosis. Thus, induction of PPARa and PPAR? in adipose tissue is a key mechanism for reducing atherosclerosis and improving cardiovascular function resulting from weight-loss. Our observations point to the critical role of PPARs in the pathogenesis of cardiovascular features of the metabolic syndrome.

  4. A Moderate Low-Carbohydrate Low-Calorie Diet Improves Lipid Profile, Insulin Sensitivity and Adiponectin Expression in Rats

    Directory of Open Access Journals (Sweden)

    Jie-Hua Chen

    2015-06-01

    Full Text Available Calorie restriction (CR via manipulating dietary carbohydrates has attracted increasing interest in the prevention and treatment of metabolic syndrome. There is little consensus about the extent of carbohydrate restriction to elicit optimal results in controlling metabolic parameters. Our study will identify a better carbohydrate-restricted diet using rat models. Rats were fed with one of the following diets for 12 weeks: Control diet, 80% energy (34% carbohydrate-reduced and 60% energy (68% carbohydrate-reduced of the control diet. Changes in metabolic parameters and expressions of adiponectin and peroxisome proliferator activator receptor γ (PPARγ were identified. Compared to the control diet, 68% carbohydrate-reduced diet led to a decrease in serum triglyceride and increases inlow density lipoprotein-cholesterol (LDL-C, high density lipoprotein-cholesterol (HDL-C and total cholesterol; a 34% carbohydrate-reduced diet resulted in a decrease in triglycerides and an increase in HDL-cholesterol, no changes however, were shown in LDL-cholesterol and total cholesterol; reductions in HOMA-IR were observed in both CR groups. Gene expressions of adiponectin and PPARγ in adipose tissues were found proportionally elevated with an increased degree of energy restriction. Our study for the first time ever identified that a moderate-carbohydrate restricted diet is not only effective in raising gene expressions of adiponectin and PPARγ which potentially lead to better metabolic conditions but is better at improving lipid profiles than a low-carbohydrate diet in rats.

  5. The porcine circovirus type 1 capsid gene promoter improves antigen expression and immunogenicity in a HIV-1 plasmid vaccine

    Directory of Open Access Journals (Sweden)

    Burger Marieta

    2011-02-01

    Full Text Available Abstract Background One of the promising avenues for development of vaccines against Human immunodeficiency virus type 1 (HIV-1 and other human pathogens is the use of plasmid-based DNA vaccines. However, relatively large doses of plasmid must be injected for a relatively weak response. We investigated whether genome elements from Porcine circovirus type 1 (PCV-1, an apathogenic small ssDNA-containing virus, had useful expression-enhancing properties that could allow dose-sparing in a plasmid vaccine. Results The linearised PCV-1 genome inserted 5' of the CMV promoter in the well-characterised HIV-1 plasmid vaccine pTHgrttnC increased expression of the polyantigen up to 2-fold, and elicited 3-fold higher CTL responses in mice at 10-fold lower doses than unmodified pTHgrttnC. The PCV-1 capsid gene promoter (Pcap alone was equally effective. Enhancing activity was traced to a putative composite host transcription factor binding site and a "Conserved Late Element" transcription-enhancing sequence previously unidentified in circoviruses. Conclusions We identified a novel PCV-1 genome-derived enhancer sequence that significantly increased antigen expression from plasmids in in vitro assays, and improved immunogenicity in mice of the HIV-1 subtype C vaccine plasmid, pTHgrttnC. This should allow significant dose sparing of, or increased responses to, this and other plasmid-based vaccines. We also report investigations of the potential of other circovirus-derived sequences to be similarly used.

  6. Melatonin improved anthocyanin accumulation by regulating gene expressions and resulted in high reactive oxygen species scavenging capacity in cabbage

    Directory of Open Access Journals (Sweden)

    Na eZhang

    2016-03-01

    Full Text Available In this work, we found that exogenous melatonin pretreatment improved anthocyanin accumulation (1- to 2-fold in cabbage. To verify the relationship with melatonin and anthocyanin, an Arabidopsis mutant, snat, which expresses a defective form of the melatonin biosynthesis enzyme SNAT (Serotonin N-acetyl transferase, was employed. Under cold conditions, the foliage of wild-type Arabidopsis exhibited a deeper red color than the snat mutant. This finding further proved that exogenous melatonin treatment was able to affect anthocyanin accumulation. To gain a better understanding of how exogenous melatonin upregulates anthocyanin, we measured gene expression in cabbage samples treated with melatonin and untreated controls. We found that the transcript levels of anthocyanin biosynthetic genes were upregulated by melatonin treatment. Moreover, melatonin treatment increased the expression levels of the transcription factors MYB, bHLH, and WD40, which constitute the transcriptional activation complex responsible for coordinative regulation of anthocyanin biosynthetic genes. We found that free radical generation was downregulated, whereas the osmotic adjustment and antioxidant capacities were upregulated in exogenous melatonin-treated cabbage plants. We concluded that melatonin increases anthocyanin production and benefits cabbage growth.

  7. The accuracy of survival time prediction for patients with glioma is improved by measuring mitotic spindle checkpoint gene expression.

    Directory of Open Access Journals (Sweden)

    Li Bie

    Full Text Available Identification of gene expression changes that improve prediction of survival time across all glioma grades would be clinically useful. Four Affymetrix GeneChip datasets from the literature, containing data from 771 glioma samples representing all WHO grades and eight normal brain samples, were used in an ANOVA model to screen for transcript changes that correlated with grade. Observations were confirmed and extended using qPCR assays on RNA derived from 38 additional glioma samples and eight normal samples for which survival data were available. RNA levels of eight major mitotic spindle assembly checkpoint (SAC genes (BUB1, BUB1B, BUB3, CENPE, MAD1L1, MAD2L1, CDC20, TTK significantly correlated with glioma grade and six also significantly correlated with survival time. In particular, the level of BUB1B expression was highly correlated with survival time (p<0.0001, and significantly outperformed all other measured parameters, including two standards; WHO grade and MIB-1 (Ki-67 labeling index. Measurement of the expression levels of a small set of SAC genes may complement histological grade and other clinical parameters for predicting survival time.

  8. Spotlight on Express Lane Eligibility (ELE): A Tool to Improve Enrollment and Renewal.

    Science.gov (United States)

    Hoag, Sheila D

    2015-01-01

    We examine a new simplification policy, Express Lane Eligibility (ELE), introduced by the Children's Health Insurance Program Reauthorization Act of 2009 (CHIPRA), to understand ELE's effects on enrollment, renewal, and administrative costs. Beginning in January 2012 and lasting through June 2013, we conducted 2 rounds of phone interviews with 38 state administrators and staff in 8 states that implemented ELE in Medicaid, Children's Health Insurance Program (CHIP), or both; we also conducted case studies in these same states, resulting in 136 in-person interviews. We collected administrative data on enrollments and renewals processed through ELE methods from the 8 states. ELE was adopted in different ways; the method of adoption influenced how many children were served and administrative savings. Automatic ELE processes, which enable states to use eligibility findings from partner agencies to automatically enroll or renew children, serve the most children and generate, on average, $1 million annually in administrative savings. Given the size of renewal caseloads and the recurring nature of renewal, using ELE for renewals holds substantial promise for administrative savings and keeping children covered. Automatic ELE processes are a best practice for using ELE. However, because Congress has not yet made ELE a permanent policy option, states are discouraged from adopting this more efficient method of eligibility determination and redeterminations. Making ELE permanent would support states that have already adopted the policy; in addition, ELE could support the transition of children to Medicaid or exchanges should CHIP not be funded after September 30, 2015. Copyright © 2015 Academic Pediatric Association. All rights reserved.

  9. Targeting SR proteins improves SMN expression in spinal muscular atrophy cells.

    Directory of Open Access Journals (Sweden)

    Claribel D Wee

    Full Text Available Spinal muscular atrophy (SMA is one of the most common inherited causes of pediatric mortality. SMA is caused by deletions or mutations in the survival of motor neuron 1 (SMN1 gene, which results in SMN protein deficiency. Humans have a centromeric copy of the survival of motor neuron gene, SMN2, which is nearly identical to SMN1. However, SMN2 cannot compensate for the loss of SMN1 because SMN2 has a single-nucleotide difference in exon 7, which negatively affects splicing of the exon. As a result, most mRNA produced from SMN2 lacks exon 7. SMN2 mRNA lacking exon 7 encodes a truncated protein with reduced functionality. Improving SMN2 exon 7 inclusion is a goal of many SMA therapeutic strategies. The identification of regulators of exon 7 inclusion may provide additional therapeutic targets or improve the design of existing strategies. Although a number of regulators of exon 7 inclusion have been identified, the function of most splicing proteins in exon 7 inclusion is unknown. Here, we test the role of SR proteins and hnRNP proteins in SMN2 exon 7 inclusion. Knockdown and overexpression studies reveal that SRSF1, SRSF2, SRSF3, SRSF4, SRSF5, SRSF6, SRSF7, SRSF11, hnRNPA1/B1 and hnRNP U can inhibit exon 7 inclusion. Depletion of two of the most potent inhibitors of exon 7 inclusion, SRSF2 or SRSF3, in cell lines derived from SMA patients, increased SMN2 exon 7 inclusion and SMN protein. Our results identify novel regulators of SMN2 exon 7 inclusion, revealing potential targets for SMA therapeutics.

  10. MO-DE-207B-03: Improved Cancer Classification Using Patient-Specific Biological Pathway Information Via Gene Expression Data

    Energy Technology Data Exchange (ETDEWEB)

    Young, M; Craft, D [Massachusetts General Hospital and Harvard Medical School, Boston, MA (United States)

    2016-06-15

    Purpose: To develop an efficient, pathway-based classification system using network biology statistics to assist in patient-specific response predictions to radiation and drug therapies across multiple cancer types. Methods: We developed PICS (Pathway Informed Classification System), a novel two-step cancer classification algorithm. In PICS, a matrix m of mRNA expression values for a patient cohort is collapsed into a matrix p of biological pathways. The entries of p, which we term pathway scores, are obtained from either principal component analysis (PCA), normal tissue centroid (NTC), or gene expression deviation (GED). The pathway score matrix is clustered using both k-means and hierarchical clustering, and a clustering is judged by how well it groups patients into distinct survival classes. The most effective pathway scoring/clustering combination, per clustering p-value, thus generates various ‘signatures’ for conventional and functional cancer classification. Results: PICS successfully regularized large dimension gene data, separated normal and cancerous tissues, and clustered a large patient cohort spanning six cancer types. Furthermore, PICS clustered patient cohorts into distinct, statistically-significant survival groups. For a suboptimally-debulked ovarian cancer set, the pathway-classified Kaplan-Meier survival curve (p = .00127) showed significant improvement over that of a prior gene expression-classified study (p = .0179). For a pancreatic cancer set, the pathway-classified Kaplan-Meier survival curve (p = .00141) showed significant improvement over that of a prior gene expression-classified study (p = .04). Pathway-based classification confirmed biomarkers for the pyrimidine, WNT-signaling, glycerophosphoglycerol, beta-alanine, and panthothenic acid pathways for ovarian cancer. Despite its robust nature, PICS requires significantly less run time than current pathway scoring methods. Conclusion: This work validates the PICS method to improve

  11. The over-expression of Chrysanthemum crassum CcSOS1 improves the salinity tolerance of chrysanthemum.

    Science.gov (United States)

    An, Juan; Song, Aiping; Guan, Zhiyong; Jiang, Jiafu; Chen, Fadi; Lou, Wanghuai; Fang, Weimin; Liu, Zhaolei; Chen, Sumei

    2014-06-01

    Soil salinity represents a major constraint on plant growth. Here, we report that the over-expression of the Chrysanthemum crassum plasma membrane Na(+)/H(+) antiporter gene CcSOS1, driven by the CaMV 35S promoter, improved the salinity tolerance of chrysanthemum 'Jinba'. In salinity-stressed transgenic plants, both the proportion of the leaf area suffering damage and the electrical conductivity of the leaf were lower in the transgenic lines than in salinity-stressed wild type plants. After a 6 day exposure to 200 mM NaCl, the leaf content of both chlorophyll (a+b) and proline was higher in the transgenic than in the wild type plants. The activity of both superoxide dismutase and peroxidase was higher in the transgenic than in the wild type plants throughout the period of NaCl stress. The transgenic plants had a stronger control over the ingress of Na(+) into the plant, particularly with respect to the youngest leaves, and so maintained a more favorable K(+)/Na(+) ratio. The result suggests that a possible strategy for improving the salinity tolerance of chrysanthemum could target the restriction of Na(+) accumulation. This study is the first to report the transgenic expression of a Na(+) efflux carrier in chrysanthemum.

  12. Improved Variable Selection Algorithm Using a LASSO-Type Penalty, with an Application to Assessing Hepatitis B Infection Relevant Factors in Community Residents

    Science.gov (United States)

    Guo, Pi; Zeng, Fangfang; Hu, Xiaomin; Zhang, Dingmei; Zhu, Shuming; Deng, Yu; Hao, Yuantao

    2015-01-01

    Objectives In epidemiological studies, it is important to identify independent associations between collective exposures and a health outcome. The current stepwise selection technique ignores stochastic errors and suffers from a lack of stability. The alternative LASSO-penalized regression model can be applied to detect significant predictors from a pool of candidate variables. However, this technique is prone to false positives and tends to create excessive biases. It remains challenging to develop robust variable selection methods and enhance predictability. Material and methods Two improved algorithms denoted the two-stage hybrid and bootstrap ranking procedures, both using a LASSO-type penalty, were developed for epidemiological association analysis. The performance of the proposed procedures and other methods including conventional LASSO, Bolasso, stepwise and stability selection models were evaluated using intensive simulation. In addition, methods were compared by using an empirical analysis based on large-scale survey data of hepatitis B infection-relevant factors among Guangdong residents. Results The proposed procedures produced comparable or less biased selection results when compared to conventional variable selection models. In total, the two newly proposed procedures were stable with respect to various scenarios of simulation, demonstrating a higher power and a lower false positive rate during variable selection than the compared methods. In empirical analysis, the proposed procedures yielding a sparse set of hepatitis B infection-relevant factors gave the best predictive performance and showed that the procedures were able to select a more stringent set of factors. The individual history of hepatitis B vaccination, family and individual history of hepatitis B infection were associated with hepatitis B infection in the studied residents according to the proposed procedures. Conclusions The newly proposed procedures improve the identification of

  13. Genetic improvement of fiber length and coarseness based on paper product performance and material variability - a review

    Science.gov (United States)

    Brian K. Via; Michael Stine; Todd F. Shupe; Chi-Leung So; Leslie Groom

    2004-01-01

    Improvement of specific gravity through tree breeding was an early choice made in the mid 20th century due to its ease of measurement and impact on pulp yield and lumber strength and stiffness. This was often the first, and in many cases, the only wood quality trait selected for. However, from a product standpoint, increased specific gravity has shown to lower many...

  14. Hawthorn Fruit Extract Elevates Expression of Nrf2/HO-1 and Improves Lipid Profiles in Ovariectomized Rats

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    Jeong-Hyun Yoo

    2016-05-01

    Full Text Available The purpose of this study was to investigate the effects of hawthorn (Crataegus pinnatifida Bunge extract on the lipid profiles and antioxidant properties in ovariectomized (OVX rats. After ovariectomy, the rats were randomly divided into four groups: the non-OVX control (Sham, the OVX-control (OVX, the OVX + 100 mg/kg b.w. of hawthorn extract (OL, and the OVX + 200 mg/kg b.w. of hawthorn extract (OH. The final body weights of the OVX group were significantly increased, but the increment was significantly decreased in hawthorn groups (p < 0.05. The serum total and low-density lipoprotein (LDL cholesterol levels were significantly elevated in the OVX group, whereas the hawthorn groups showed a significant decrease in these levels (p < 0.05. The hepatic triglyceride (TG and malondialdehyde (MDA levels were significantly reduced in the hawthorn groups compared with the OVX group (p < 0.05. The mRNA expression of nuclear factor erythroid 2–related factor (Nrf2, heme oxygenase-1 (HO-1, and glutathione peroxidase (GPx were significantly decreased in the OVX group, whereas the hawthorn groups exhibited a significant increase in expression (p < 0.05. The protein expressions of Nrf2, HO-1, and GPx were lower in the OVX group than the Sham group (p < 0.05. The oral administration of hawthorn extract reversed the suppression of protein levels. These results suggest that hawthorn extract could have protective effects in OVX rats by improving lipid profiles, decreasing oxidative stress, and improving the antioxidant defense system.

  15. Phosphodiesterase-4 inhibition alters gene expression and improves isoniazid-mediated clearance of Mycobacterium tuberculosis in rabbit lungs.

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    Selvakumar Subbian

    2011-09-01

    Full Text Available Tuberculosis (TB treatment is hampered by the long duration of antibiotic therapy required to achieve cure. This indolent response has been partly attributed to the ability of subpopulations of less metabolically active Mycobacterium tuberculosis (Mtb to withstand killing by current anti-TB drugs. We have used immune modulation with a phosphodiesterase-4 (PDE4 inhibitor, CC-3052, that reduces tumor necrosis factor alpha (TNF-α production by increasing intracellular cAMP in macrophages, to examine the crosstalk between host and pathogen in rabbits with pulmonary TB during treatment with isoniazid (INH. Based on DNA microarray, changes in host gene expression during CC-3052 treatment of Mtb infected rabbits support a link between PDE4 inhibition and specific down-regulation of the innate immune response. The overall pattern of host gene expression in the lungs of infected rabbits treated with CC-3052, compared to untreated rabbits, was similar to that described in vitro in resting Mtb infected macrophages, suggesting suboptimal macrophage activation. These alterations in host immunity were associated with corresponding down-regulation of a number of Mtb genes that have been associated with a metabolic shift towards dormancy. Moreover, treatment with CC-3052 and INH resulted in reduced expression of those genes associated with the bacterial response to INH. Importantly, CC-3052 treatment of infected rabbits was associated with reduced ability of Mtb to withstand INH killing, shown by improved bacillary clearance, from the lungs of co-treated animals compared to rabbits treated with INH alone. The results of our study suggest that changes in Mtb gene expression, in response to changes in the host immune response, can alter the responsiveness of the bacteria to antimicrobial agents. These findings provide a basis for exploring the potential use of adjunctive immune modulation with PDE4 inhibitors to enhance the efficacy of existing anti-TB treatment.

  16. Joint analysis of expression profiles from multiple cancers improves the identification of microRNA–gene interactions

    Science.gov (United States)

    Chen, Xiaowei; Slack, Frank J.; Zhao, Hongyu

    2013-01-01

    Motivation: MicroRNAs (miRNAs) play a crucial role in tumorigenesis and development through their effects on target genes. The characterization of miRNA–gene interactions will lead to a better understanding of cancer mechanisms. Many computational methods have been developed to infer miRNA targets with/without expression data. Because expression datasets are in general limited in size, most existing methods concatenate datasets from multiple studies to form one aggregated dataset to increase sample size and power. However, such simple aggregation analysis results in identifying miRNA–gene interactions that are mostly common across datasets, whereas specific interactions may be missed by these methods. Recent releases of The Cancer Genome Atlas data provide paired expression profiling of miRNAs and genes in multiple tumors with sufficiently large sample size. To study both common and cancer-specific interactions, it is desirable to develop a method that can jointly analyze multiple cancers to study miRNA–gene interactions without combining all the data into one single dataset. Results: We developed a novel statistical method to jointly analyze expression profiles from multiple cancers to identify miRNA–gene interactions that are both common across cancers and specific to certain cancers. The benefit of this joint analysis approach is demonstrated by both simulation studies and real data analysis of The Cancer Genome Atlas datasets. Compared with simple aggregate analysis or single sample analysis, our method can effectively use the shared information among different but related cancers to improve the identification of miRNA–gene interactions. Another useful property of our method is that it can estimate similarity among cancers through their shared miRNA–gene interactions. Availability and implementation: The program, MCMG, implemented in R is available at http://bioinformatics.med.yale.edu/group/. Contact: hongyu.zhao@yale.edu PMID:23772050

  17. Nanopolymers improve delivery of exon skipping oligonucleotides and concomitant dystrophin expression in skeletal muscle of mdx mice.

    Science.gov (United States)

    Williams, Jason H; Schray, Rebecca C; Sirsi, Shashank R; Lutz, Gordon J

    2008-04-02

    Exon skipping oligonucleotides (ESOs) of 2'O-Methyl (2'OMe) and morpholino chemistry have been shown to restore dystrophin expression in muscle fibers from the mdx mouse, and are currently being tested in phase I clinical trials for Duchenne Muscular Dystrophy (DMD). However, ESOs remain limited in their effectiveness because of an inadequate delivery profile. Synthetic cationic copolymers of poly(ethylene imine) (PEI) and poly(ethylene glycol) (PEG) are regarded as effective agents for enhanced delivery of nucleic acids in various applications. We examined whether PEG-PEI copolymers can facilitate ESO-mediated dystrophin expression after intramuscular injections into tibialis anterior (TA) muscles of mdx mice. We utilized a set of PEG-PEI copolymers containing 2 kDa PEI and either 550 Da or 5 kDa PEG, both of which bind 2'OMe ESOs with high affinity and form stable nanoparticulates with a relatively low surface charge. Three weekly intramuscular injections of 5 microg of ESO complexed with PEI2K-PEG550 copolymers resulted in about 500 dystrophin-positive fibers and about 12% of normal levels of dystrophin expression at 3 weeks after the initial injection, which is significantly greater than for injections of ESO alone, which are known to be almost completely ineffective. In an effort to enhance biocompatibility and cellular uptake, the PEI2K-PEG550 and PEI2K-PEG5K copolymers were functionalized by covalent conjugation with nanogold (NG) or adsorbtion of colloidal gold (CG), respectively. Surprisingly, using the same injection and dosing regimen, we found no significant difference in dystrophin expression by Western blot between the NG-PEI2K-PEG550, CG-PEI2K-PEG5K, and non-functionalized PEI2K-PEG550 copolymers. Dose-response experiments using the CG-PEI2K-PEG5K copolymer with total ESO ranging from 3-60 microg yielded a maximum of about 15% dystrophin expression. Further improvements in dystrophin expression up to 20% of normal levels were found at 6 weeks after

  18. Nanopolymers improve delivery of exon skipping oligonucleotides and concomitant dystrophin expression in skeletal muscle of mdx mice

    Directory of Open Access Journals (Sweden)

    Sirsi Shashank R

    2008-04-01

    Full Text Available Abstract Background Exon skipping oligonucleotides (ESOs of 2'O-Methyl (2'OMe and morpholino chemistry have been shown to restore dystrophin expression in muscle fibers from the mdx mouse, and are currently being tested in phase I clinical trials for Duchenne Muscular Dystrophy (DMD. However, ESOs remain limited in their effectiveness because of an inadequate delivery profile. Synthetic cationic copolymers of poly(ethylene imine (PEI and poly(ethylene glycol (PEG are regarded as effective agents for enhanced delivery of nucleic acids in various applications. Results We examined whether PEG-PEI copolymers can facilitate ESO-mediated dystrophin expression after intramuscular injections into tibialis anterior (TA muscles of mdx mice. We utilized a set of PEG-PEI copolymers containing 2 kDa PEI and either 550 Da or 5 kDa PEG, both of which bind 2'OMe ESOs with high affinity and form stable nanoparticulates with a relatively low surface charge. Three weekly intramuscular injections of 5 μg of ESO complexed with PEI2K-PEG550 copolymers resulted in about 500 dystrophin-positive fibers and about 12% of normal levels of dystrophin expression at 3 weeks after the initial injection, which is significantly greater than for injections of ESO alone, which are known to be almost completely ineffective. In an effort to enhance biocompatibility and cellular uptake, the PEI2K-PEG550 and PEI2K-PEG5K copolymers were functionalized by covalent conjugation with nanogold (NG or adsorbtion of colloidal gold (CG, respectively. Surprisingly, using the same injection and dosing regimen, we found no significant difference in dystrophin expression by Western blot between the NG-PEI2K-PEG550, CG-PEI2K-PEG5K, and non-functionalized PEI2K-PEG550 copolymers. Dose-response experiments using the CG-PEI2K-PEG5K copolymer with total ESO ranging from 3–60 μg yielded a maximum of about 15% dystrophin expression. Further improvements in dystrophin expression up to 20% of normal

  19. Estimation of Paddy Rice Variables with a Modified Water Cloud Model and Improved Polarimetric Decomposition Using Multi-Temporal RADARSAT-2 Images

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    Zhi Yang

    2016-10-01

    Full Text Available Rice growth monitoring is very important as rice is one of the staple crops of the world. Rice variables as quantitative indicators of rice growth are critical for farming management and yield estimation, and synthetic aperture radar (SAR has great advantages for monitoring rice variables due to its all-weather observation capability. In this study, eight temporal RADARSAT-2 full-polarimetric SAR images were acquired during rice growth cycle and a modified water cloud model (MWCM was proposed, in which the heterogeneity of the rice canopy in the horizontal direction and its phenological changes were considered when the double-bounce scattering between the rice canopy and the underlying surface was firstly considered as well. Then, three scattering components from an improved polarimetric decomposition were coupled with the MWCM, instead of the backscattering coefficients. Using a genetic algorithm, eight rice variables were estimated, such as the leaf area index (LAI, rice height (h, and the fresh and dry biomass of ears (Fe and De. The accuracy validation showed the MWCM was suitable for the estimation of rice variables during the whole growth season. The validation results showed that the MWCM could predict the temporal behaviors of the rice variables well during the growth cycle (R2 > 0.8. Compared with the original water cloud model (WCM, the relative errors of rice variables with the MWCM were much smaller, especially in the vegetation phase (approximately 15% smaller. Finally, it was discussed that the MWCM could be used, theoretically, for extensive applications since the empirical coefficients in the MWCM were determined in general cases, but more applications of the MWCM are necessary in future work.

  20. Age differences in coupling of intraindividual variability in mnemonic strategies and practice-related associative recall improvements.

    Science.gov (United States)

    Hertzog, Christopher; Lövdén, Martin; Lindenberger, Ulman; Schmiedek, Florian

    2017-09-01

    The importance of encoding strategies for associative recall is well established, but there have been no studies of aging and intraindividual variability (IAV) in strategy use during extended practice. We observed strategy use and cued-recall test performance over 101 days of practice in 101 younger adults (M = 25.6 years) and 103 older adults (M = 71.3 years) sandwiched by a pretest and posttest battery including an associative recall test. Each practice session included 2 lists of 12 number-noun paired-associate (PA) items (e.g., 23-DOGS), presented for brief exposures titrated to maintain below-ceiling performance throughout practice. Participants reported strategy use (e.g., rote repetition, imagery) after each test. Substantial IAV in strategy use was detected that was coupled with performance; lists studied with normatively effective strategies (e.g., imagery) generated higher PA recall than lists studied with less effective strategies (e.g., rote repetition). In comparison to younger adults, older adults' practice (a) relied more on repetition and less on effective strategies, (b) showed lower levels of IAV in effective strategy use, and (c) had lower within-person strategy-recall coupling, especially late in practice. Individual differences in pretest-posttest gains in PA recall were predicted by average level of effective strategy use in young adults but by strategy-recall coupling in older adults. Results are consistent with the hypothesis that experiencing variability in strategic outcomes during practice helps hone the effectiveness of strategic encoding behavior, and that older adults' reduced degree of pretest-posttest gains is influenced by lower likelihood of using and optimizing effective strategies through practice. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  1. Fumarate Production by Torulopsis glabrata: Engineering Heterologous Fumarase Expression and Improving Acid Tolerance.

    Science.gov (United States)

    Chen, Xiulai; Song, Wei; Gao, Cong; Qin, Wen; Luo, Qiuling; Liu, Jia; Liu, Liming

    2016-01-01

    Fumarate is a well-known biomass building block compound. However, the poor catalytic efficiency of fumarase is one of the major factors preventing its widespread production. To address this issue, we selected residues 159HPND162 of fumarase from Rhizopus oryzae as targets for site-directed mutagenesis based on molecular docking analysis. Twelve mutants were generated and characterized in detail. Kinetic studies showed that the Km values of the P160A, P160T, P160H, N161E, and D162W mutants were decreased, whereas Km values of H159Y, H159V, H159S, N161R, N161F, D162K, and D162M mutants were increased. In addition, all mutants displayed decreased catalytic efficiency except for the P160A mutant, whose kcat/Km was increased by 33.2%. Moreover, by overexpressing the P160A mutant, the engineered strain T.G-PMS-P160A was able to produce 5.2 g/L fumarate. To further enhance fumarate production, the acid tolerance of T.G-PMS-P160A was improved by deleting ade12, a component of the purine nucleotide cycle, and the resulting strain T.G(△ade12)-PMS-P160A produced 9.2 g/L fumarate. The strategy generated in this study opens up new avenues for pathway optimization and efficient production of natural products.

  2. Fumarate Production by Torulopsis glabrata: Engineering Heterologous Fumarase Expression and Improving Acid Tolerance.

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    Xiulai Chen

    Full Text Available Fumarate is a well-known biomass building block compound. However, the poor catalytic efficiency of fumarase is one of the major factors preventing its widespread production. To address this issue, we selected residues 159HPND162 of fumarase from Rhizopus oryzae as targets for site-directed mutagenesis based on molecular docking analysis. Twelve mutants were generated and characterized in detail. Kinetic studies showed that the Km values of the P160A, P160T, P160H, N161E, and D162W mutants were decreased, whereas Km values of H159Y, H159V, H159S, N161R, N161F, D162K, and D162M mutants were increased. In addition, all mutants displayed decreased catalytic efficiency except for the P160A mutant, whose kcat/Km was increased by 33.2%. Moreover, by overexpressing the P160A mutant, the engineered strain T.G-PMS-P160A was able to produce 5.2 g/L fumarate. To further enhance fumarate production, the acid tolerance of T.G-PMS-P160A was improved by deleting ade12, a component of the purine nucleotide cycle, and the resulting strain T.G(△ade12-PMS-P160A produced 9.2 g/L fumarate. The strategy generated in this study opens up new avenues for pathway optimization and efficient production of natural products.

  3. Treatment with vitamin B3 improves functional recovery and reduces GFAP expression following traumatic brain injury in rats.

    Science.gov (United States)

    Hoane, Michael R; Akstulewicz, Stacy L; Toppen, James

    2003-11-01

    Previous studies have shown that administration of vitamin B(3) (B(3)) in animal models of ischemia significantly reduced the size of infarction and improved functional recovery. The present study evaluated the effect of administration of B(3) on recovery of function following traumatic brain injury (TBI), incorporating the bilateral medial frontal cortex contusion injury model. Groups of rats were assigned to B(3) (500 mg/kg) or saline (1.0 ml/kg) treatment conditions and received contusion injuries or sham surgeries. Drug treatment was administered 15 min and 24 h following injury. Rats were examined on a variety of tests to measure sensorimotor performance (bilateral tactile adhesive removal), skilled forelimb use (staircase test), and cognitive ability (reference and working memory) in the Morris Water Maze. Administration of B(3) following injury significantly reduced the behavioral impairments observed on the bilateral tactile removal test, but not on skilled forelimb use. The acquisition of reference and working memory tests were also significantly improved compared to saline-treated rats. Examination of the brains revealed that administration of B(3) significantly reduced the size of the lesion compared to treatment with saline. In addition, examination of glial fibrillary acidic protein (GFAP) expression around the lesion revealed that B(3) significantly reduced the number of GFAP(+) astrocytes. These results indicate that B(3) administration significantly improved behavioral outcome following injury, reduced the size of the lesion, and reduced the expression of GFAP. The current findings suggest that B(3) may have therapeutic potential for the treatment of TBI.

  4. Improvement in latent variable indirect response modeling of multiple categorical clinical endpoints: application to modeling of guselkumab treatment effects in psoriatic patients.

    Science.gov (United States)

    Hu, Chuanpu; Randazzo, Bruce; Sharma, Amarnath; Zhou, Honghui

    2017-10-01

    Exposure-response modeling plays an important role in optimizing dose and dosing regimens during clinical drug development. The modeling of multiple endpoints is made possible in part by recent progress in latent variable indirect response (IDR) modeling for ordered categorical endpoints. This manuscript aims to investigate the level of improvement achievable by jointly modeling two such endpoints in the latent variable IDR modeling framework through the sharing of model parameters. This is illustrated with an application to the exposure-response of guselkumab, a human IgG1 monoclonal antibody in clinical development that blocks IL-23. A Phase 2b study was conducted in 238 patients with psoriasis for which disease severity was assessed using Psoriasis Area and Severity Index (PASI) and Physician's Global Assessment (PGA) scores. A latent variable Type I IDR model was developed to evaluate the therapeutic effect of guselkumab dosing on 75, 90 and 100% improvement of PASI scores from baseline and PGA scores, with placebo effect empirically modeled. The results showed that the joint model is able to describe the observed data better with fewer parameters compared with the common approach of separately modeling the endpoints.

  5. Efficient heterologous expression and secretion in Aspergillus oryzae of a llama variable heavy-chain antibody fragment V(HH) against EGFR.

    Science.gov (United States)

    Okazaki, Fumiyoshi; Aoki, Jun-ichi; Tabuchi, Soichiro; Tanaka, Tsutomu; Ogino, Chiaki; Kondo, Akihiko

    2012-10-01

    We have constructed a filamentous fungus Aspergillus oryzae that secretes a llama variable heavy-chain antibody fragment (V(HH)) that binds specifically to epidermal growth factor receptor (EGFR) in a culture medium. A major improvement in yield was achieved by fusing the V(HH) with a Taka-amylase A signal sequence (sTAA) and a segment of 28 amino acids from the N-terminal region of Rhizopus oryzae lipase (N28). The yields of secreted, immunologically active anti-EGFR V(HH) reached 73.8 mg/1 in a Sakaguchi flask. The V(HH) fragments were released from the sTAA or N28 proteins by an indigenous A. oryzae protease during cultivation. The purified recombinant V(HH) fragment was specifically recognized and could bind to the EGFR with a high affinity.

  6. Expression and Functional Properties of an Anti-Triazophos High-Affinity Single-Chain Variable Fragment Antibody with Specific Lambda Light Chain

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    Rui Liu

    2016-06-01

    Full Text Available Triazophos is a widely used organophosphorous insecticide that has potentially adverse effects to organisms. In the present study, a high-affinity single-chain variable fragment (scFv antibody with specific lambda light chain was developed for residue monitoring. First, the specific variable regions were correctly amplified from a hybridoma cell line 8C10 that secreted monoclonal antibody (mAb against triazophos. The regions were then assembled as scFv via splicing by overlap extension polymerase chain reaction. Subsequently, the recombinant anti-triazophos scFv-8C10 was successfully expressed in Escherichia coli strain HB2151 in soluble form, purified through immobilized metal ion affinity chromatography, and verified via Western blot and peptide mass fingerprinting analyses. Afterward, an indirect competitive enzyme-linked immunosorbent assay was established based on the purified anti-triazophos scFv-8C10 antibody. The assay exhibited properties similar to those based on the parent mAb, with a high sensitivity (IC50 of 1.73 ng/mL to triazophos and no cross reaction for other organophosphorus pesticides; it was reliable in detecting triazophos residues in spiked water samples. Moreover, kinetic measurement using a surface plasmon resonance biosensor indicated that the purified scFv-8C10 antibody had a high affinity of 1.8 × 10−10 M and exhibited good binding stability. Results indicated that the recombinant high-affinity scFv-8C10 antibody was an effective detection material that would be promising for monitoring triazophos residues in environment samples.

  7. Response of CYP1A Gene expression in fish liver of catfish (Ariopsis felis) from Gulf of Mexico and their relationship with the genetic variability.

    Science.gov (United States)

    Zapata-Perez, Omar; Sanchez-Teyer, Lorenzo F; Perez-Nunez, Maria T; Arroyo-Herrera, Ana L; Moreno, Adriana Quiroz; Albores-Medina, Arnulfo

    2010-01-01

    We determined the hepatic Cytochrome P4501A (CYP1A) mRNA and Ethoxyresorufin-O-deethylase (EROD) activities in the fish, Ariopsis felis, from highly polluted to relatively pristine regions in the southwest Gulf of Mexico and their relationship with the genetic polymorphisms of the same fish. We hypothesized that a high genetic variation reflects interindividual variability in levels of CYP1A mRNA underlying the pathway culminating in EROD induction caused by the environmental contaminants. Catfish from Laguna de Mecoacan exhibited marked induction of CYP1A mRNA and high levels of hepatic EROD activities, whereas fish from Laguna de Celestun showed no induction of CYP1A mRNA and moderately low levels of EROD activities. In contrast, the similarity index considering all samples varied from 0.4 to 0.87, showing a wide range of variation. A dendrogram showed a clear grouping of fish collected from the Laguna de Terminos, Rio Coatzacoalcos and Laguna de Celestun, with discrete subgroups according to region. In contrast, fish from Laguna de Mecoacan were grouped together completely separate from the rest of the fish. Despite the low number of fish from Mecoacan (a high bootstrap support was observed in this group), the results indicated a significant genetic variability in comparison with the other ecosystems included. The differential level of expression of CYP1A and the EROD activity observed among the ecosystems analyzed could be due to the high range of genetic variation, with special emphasis on fish collected in Mecoacan where it is possible to find a subspecies of Ariopsis felis.

  8. Integrated cell and process engineering for improved transient production of a "difficult-to-express" fusion protein by CHO cells.

    Science.gov (United States)

    Johari, Yusuf B; Estes, Scott D; Alves, Christina S; Sinacore, Marty S; James, David C

    2015-12-01

    Based on an optimized electroporation protocol, we designed a rapid, milliliter-scale diagnostic transient production assay to identify limitations in the ability of Chinese hamster ovary (CHO) cells to produce a model "difficult-to-express" homodimeric Fc-fusion protein, Sp35Fc, that exhibited very low volumetric titer and intracellular formation of disulfide-bonded oligomeric aggregates post-transfection. As expression of Sp35Fc induced an unfolded protein response in transfected host cells, we utilized the transient assay to compare, in parallel, multiple functionally diverse strategies to engineer intracellular processing of Sp35Fc in order to increase production and reduce aggregation as two discrete design objectives. Specifically, we compared the effect of (i) co-expression of ER-resident molecular chaperones (BiP, PDI, CypB) or active forms of UPR transactivators (ATF6c, XBP1s) at varying recombinant gene load, (ii) addition of small molecules known to act as chemical chaperones (PBA, DMSO, glycerol, betaine, TMAO) or modulate UPR signaling (PERK inhibitor GSK2606414) at varying concentration, (iii) a reduction in culture temperature to 32°C. Using this information, we designed a biphasic, Sp35Fc-specific transient manufacturing process mediated by lipofection that utilized CypB co-expression at an optimal Sp35Fc:CypB gene ratio of 5:1 to initially maximize transfected cell proliferation, followed by addition of a combination of PBA (0.5 mM) and glycerol (1% v/v) at the onset of stationary phase to maximize cell specific production and eliminate Sp35Fc aggregation. Using this optimal, engineered process transient Sp35Fc production was significantly increased sixfold over a 12 day production process with no evidence of disulfide-bonded aggregates. Finally, transient production in clonally derived sub-populations (derived from parental CHO host) screened for a heritably improved capability to produce Sp35Fc was also significantly improved by the optimized

  9. Locomotor training with body weight support in SCI: EMG improvement is more optimally expressed at a low testing speed.

    Science.gov (United States)

    Meyns, P; Van de Crommert, H W A A; Rijken, H; van Kuppevelt, D H J M; Duysens, J

    2014-12-01

    Case series. To determine the optimal testing speed at which the recovery of the EMG (electromyographic) activity should be assessed during and after body weight supported (BWS) locomotor training. Tertiary hospital, Sint Maartenskliniek, Nijmegen, The Netherlands. Four participants with incomplete chronic SCI were included for BWS locomotor training; one AIS-C and three AIS-D (according to the ASIA (American Spinal Injury Association) Impairment Scale or AIS). All were at least 5 years after injury. The SCI participants were trained three times a week for a period of 6 weeks. They improved their locomotor function in terms of higher walking speed, less BWS and less assistance needed. To investigate which treadmill speed for EMG assessment reflects the functional improvement most adequately, all participants were assessed weekly using the same two speeds (0.5 and 1.5 km h(-1), referred to as low and high speed, respectively) for 6 weeks. The change in root mean square EMG (RMS EMG) was assessed in four leg muscles; biceps femoris, rectus femoris, gastrocnemius medialis and tibialis anterior. The changes in RMS EMG occurred at similar phases of the step cycle for both walking conditions, but these changes were larger when the treadmill was set at a low speed (0.5 km h(-1)). Improvement in gait is feasible with BWS treadmill training even long after injury. The EMG changes after treadmill training are more optimally expressed using a low rather than a high testing treadmill speed.

  10. Improved process conditions for increasing expression of MHC class II protein from a stable Drosophila S2 cell line.

    Science.gov (United States)

    Shen, Xiao; Dojcinovic, Danijel; Baldi, Lucia; Hacker, David L; Luescher, Immanuel F; Wurm, Florian M

    2018-01-01

    To investigate the effects of operational process conditions on expression of MHC class II protein from a stable Drosophila S2 cell line. When the Drosophila S2 cells were grown in vented orbitally shaken TubeSpin bioreactor 600 containers, cell growth was improved three-fold and the yield of recombinant major histocompatibility (MHC) class II protein (HLA-DR1 2xHis ) increased four-fold over the levels observed for the same cells cultivated in roller bottles (RB) without vented caps. Culturing in RB with vented caps while increasing the rotation speed from 6 rpm to 18 rpm also improved cell growth five-fold and protein productivity three-fold which is comparable to the levels observed in the orbitally shaken containers. Protein activity was found to be almost identical between the two vessel systems tested. Optimized cell culture conditions and a more efficient vessel type can enhance gas transfer and mixing and lead to substantial improvement of recombinant product yields from S2 cells.

  11. Respiratory Muscle Training Improves Chemoreflex Response, Heart Rate Variability, and Respiratory Mechanics in Rats With Heart Failure.

    Science.gov (United States)

    Jaenisch, Rodrigo B; Quagliotto, Edson; Chechi, Chalyne; Calegari, Leonardo; Dos Santos, Fernando; Borghi-Silva, Audrey; Dal Lago, Pedro

    2017-04-01

    The aim of the present report was to evaluate respiratory muscle training (RMT) effects on hemodynamic function, chemoreflex response, heart rate variability, and respiratory mechanics in rats with heart failure (HF rats). Wistar rats were divided into 4 groups: sedentary-sham (Sed-Sham, n = 8), respiratory muscle trained-sham (RMT-Sham, n = 8), sedentary-HF (Sed-HF, n = 8) and respiratory muscle trained-HF (RMT-HF, n = 8). Animals were submitted to an RMT protocol performed 30 minutes per day, 5 days per week for 6 weeks, whereas the sedentary animals did not exercise. In HF rats, RMT promoted the reduction of left ventricular end-diastolic pressure, right ventricular hypertrophy, and pulmonary edema. Moreover, RMT produced a reduction in pressure response during chemoreflex activation, sympathetic modulation, and sympathetic vagal balance in addition to an increase in parasympathetic modulation. Also after RMT, HF rats demonstrated a reduction in respiratory system resistance, tissue resistance, Newtonian resistance, respiratory system compliance, and quasistatic compliance. These findings suggested that 6 weeks of RMT in HF rats promoted beneficial adaptations in hemodynamics, autonomic function, and respiratory mechanics and attenuated pressure response evoked by chemoreflex activation in HF rats. Copyright © 2016 Canadian Cardiovascular Society. Published by Elsevier Inc. All rights reserved.

  12. Auricular Acupressure to Improve Menstrual Pain and Menstrual Distress and Heart Rate Variability for Primary Dysmenorrhea in Youth with Stress

    Directory of Open Access Journals (Sweden)

    Yu-Jen Wang

    2013-01-01

    Full Text Available Background. Dysmenorrhea and accompanying symptoms can have a negative impact on academic achievement, physical activity and functioning, and quality of life. Unfortunately, stress increases the sensitivity and severity of pain, activating sympathetic responses while inhibiting parasympathetic responses. Objective. This study used objective, physiological measurements to evaluate the effects of auricular acupressure on menstrual pain and menstrual distress in young college students with primary dysmenorrhea across two menstrual cycles. The aim was to determine if significant differences could be detected between the intervention and follow-up phases after controlling life stress. Design. A one-group experimental research design was used, and repeated measurements and followups were done. Thirty-two women completed questionnaires and physiological parameters were measured. Results. Significant differences between the intervention and follow-up phases were found for high frequency (HF and blood pressure on day 1 and no significant differences in menstrual pain and menstrual distress, heart rate variability, low frequency (LF, LF/HF ratio, or heart rate. Conclusion. Auricular acupressure effectively increases parasympathetic activity to maintain autonomic function homeostasis in young women with primary dysmenorrhea and may have a value in alleviating menstrual pain and menstrual distress in a high-stress life. Future studies should consider stress, stimulus dose of auricular acupressure, severity of menstrual pain, and a longitudinal research design.

  13. Engineering Aspergillus oryzae A-4 through the chromosomal insertion of foreign cellulase expression cassette to improve conversion of cellulosic biomass into lipids.

    Directory of Open Access Journals (Sweden)

    Hui Lin

    Full Text Available A genetic modification scheme was designed for Aspergillus oryzae A-4, a natural cellulosic lipids producer, to enhance its lipid production from biomass by putting the spotlight on improving cellulase secretion. Four cellulase genes were separately expressed in A-4 under the control of hlyA promoter, with the help of the successful development of a chromosomal genetic manipulation system. Comparison of cellulase activities of PCR-positive transformants showed that these transformants integrated with celA gene and with celC gene had significantly (p<0.05 higher average FPAase activities than those strains integrated with celB gene and with celD gene. Through the assessment of cellulosic lipids accumulating abilities, celA transformant A2-2 and celC transformant D1-B1 were isolated as promising candidates, which could yield 101%-133% and 35.22%-59.57% higher amount of lipids than the reference strain A-4 (WT under submerged (SmF conditions and solid-state (SSF conditions, respectively. Variability in metabolism associated to the introduction of cellulase gene in A2-2 and D1-B1 was subsequently investigated. It was noted that cellulase expression repressed biomass formation but enhanced lipid accumulation; whereas the inhibitory effect on cell growth would be shielded during cellulosic lipids production owing to the essential role of cellulase in substrate utilization. Different metabolic profiles also existed between A2-2 and D1-B1, which could be attributed to not only different transgene but also biological impacts of different integration. Overall, both simultaneous saccharification and lipid accumulation were enhanced in A2-2 and D1-B1, resulting in efficient conversion of cellulose into lipids. A regulation of cellulase secretion in natural cellulosic lipids producers could be a possible strategy to enhance its lipid production from lignocellulosic biomass.

  14. Freight railway transport: Critical variables to improve the transport applied to infrastructure costs and its associated traffic flow

    Energy Technology Data Exchange (ETDEWEB)

    Zakowska, L.; Pulawska-Obiedowska, S.

    2016-07-01

    The developed societies have as challenge, among others, to achieve a mobility development based on economic models of low carbon and energy efficient, making it accessible to the entire population. In this context, the sustainable mobility seems to meet the economic, social and environmental needs, minimizing their negative impact. There are three factors that are relevant: (1) infrastructures; (2) modes of transport more ecological and safe, and (3) operations and services for passengers and freights.The objective of this research is to provide guidance to investment in sustainable transport infrastructures that are truly useful and effective. In particular we have studied the case of the railway, using the following information: details of the infrastructure; cost of construction (per kilometre); maintenance cost, and life cycle. This information may be relevant to consider their possible business models.The methodology of this research was focused in the detailed analysis of the infrastructure use and maintenance criteria, the market opportunities for freight development and the available data to validate the obtained results from the software tool reached in this work. Our research includes the different following aspects:• Evaluation of the supported traffic by the rail line.• Relevant items to be considered in the rail infrastructure. Defining the track, we can group items in two sets: civil and rail installations.• Rolling stock available. Locomotives and wagons are modelled to introduce the data as convenience for the user.Besides our research includes the development of software, Decision System Tool (DST), for studying the construction and maintenance cost of railway infrastructure. It is developed in a common and open source program, providing the user the interaction with the critical variable of the line. It has been adjusted using the following references: MOM PlanCargorail; EcoTransIT, and Projects funded by Framework Program of EU (New

  15. Reco level Smin and subsystem Smin: improved global inclusive variables for measuring the new physics mass scale in MET events at hadron colliders

    Energy Technology Data Exchange (ETDEWEB)

    Konar, Partha; /Florida U.; Kong, Kyoungchul; /SLAC; Matchev, Konstantin T.; Park, Myeonghun; /Florida U.

    2011-08-11

    The variable {radical}s{sub min} was originally proposed in [1] as a model-independent, global and fully inclusive measure of the new physics mass scale in missing energy events at hadron colliders. In the original incarnation of {radical}s{sub min}, however, the connection to the new physics mass scale was blurred by the effects of the underlying event, most notably initial state radiation and multiple parton interactions. In this paper we advertize two improved variants of the {radical}s{sub min} variable, which overcome this problem. First we show that by evaluating the {radical}s{sub min} variable at the RECO level, in terms of the reconstructed objects in the event, the effects from the underlying event are significantly diminished and the nice correlation between the peak in the {radical}s{sub min}{sup (reco)} distribution and the new physics mass scale is restored. Secondly, the underlying event problem can be avoided altogether when the {radical}s{sub min} concept is applied to a subsystem of the event which does not involve any QCD jets. We supply an analytic formula for the resulting subsystem {radical}s{sub min}{sup (sub)} variable and show that its peak exhibits the usual correlation with the mass scale of the particles produced in the subsystem. Finally, we contrast {radical}s{sub min} to other popular inclusive variables such as H{sub T}, M{sub Tgen} and M{sub TTgen}. We illustrate our discussion with several examples from supersymmetry, and with dilepton events from top quark pair production.

  16. Strigolactones Improve Plant Growth, Photosynthesis, and Alleviate Oxidative Stress under Salinity in Rapeseed (Brassica napus L. by Regulating Gene Expression

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    Ni Ma

    2017-09-01

    Full Text Available Rapeseed (Brassica napus L. is a very important edible oil crop in the world, and the production is inhibited by abiotic stresses, such as salinity. Plant hormones can alleviate the stress by regulating the physiological processes and gene expression. To study the plant responses to salinity in combination with GR24, a synthesized strigolactone, the oilseed rape variety (Zhongshuang 11 replications were grown in the pots in a controlled growth chamber under three levels of salinity (0, 100, and 200 mM NaCl and 0.18 μM GR24 treatments at the seedling stage for 7 days. The results showed that salinity depressed the shoots and roots growth, whereas GR24 improved the growth under salt stress. Leaf chlorophyll contents and gas exchange parameters (net photosynthetic rates, stomatal conductance, intercellular CO2 concentration, and transpiration rate were also reduced significantly with increasing salinity, and these effects could be partially reversed by GR24 application. Additionally, GR24 treatment significantly increased and decreased the photosystem II quantum yield and non-photochemical quenching, respectively, under salinity stress conditions. The activities of peroxidase and superoxide dismutase increased, and lipid peroxidation measured by the level of malondialdehyde reduced due to GR24 application. The transcriptome analysis of root and shoot was conducted. Three hundred and forty-two common differentially expressed genes (DEGs after GR24 treatment and 166 special DEGs after GR24 treatment under salinity stress were identified in root and shoot. The DEGs in root were significantly more than that in shoot. Quantitative PCR validated that the stress alleviation was mainly related to the gene expression of tryptophan metabolism, plant hormone signal transduction, and photosynthesis.

  17. Eugenosedin-A improves glucose metabolism and inhibits MAPKs expression in streptozotocin/nicotinamide-induced diabetic rats

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    Kuo-Ping Shen

    2018-03-01

    Full Text Available This study examined the effects of eugenosedin-A (Eu-A in a streptozotocin (STZ/nicotinamide-induced rat model of type II diabetes mellitus (T2DM. Six-week-old Sprague–Dawley rats were randomly divided into three groups: (1 RD group, normal rats fed a regular diet (RD, (2 DM group, T2DM rats fed a high-fat diet, and (3 Eu-A group, T2DM rats fed a high fat diet plus oral Eu-A (5 mg/kg/day. After 30 days, the DM group had higher body weight, higher blood glucose and lower insulin levels than the RD group. The DM group also had increased protein expression of glycogen synthase kinase (GSK in liver and skeletal muscle and decreased protein expression of insulin receptor (IR, insulin receptor substrate-1 (IRS-1, IRS-2, AMP-activated protein kinase (AMPK, glucose transporter-4 (GLUT-4, glucokinase (GCK, and peroxisome proliferator-activated receptor γ (PPAR-γ. STZ/nicotinamide-induced T2DM increased the expression of mitogen-activated protein kinases (MAPKs: p38, ERK, JNK and inflammatory p65 protein. In the Eu-A treated T2DM rats, however, blood glucose was attenuated and the insulin concentration stimulated. Changes in IR, IRS-1 and IRS-2 proteins as well as AMPK, GLUT-4, GCK, GSK, PPAR-γ, MAPKs, and inflammatory p65 proteins were ameliorated. These results suggested that Eu-A alleviates STZ/nicotinamide-induced hyperglycemia by improving insulin levels and glucose metabolism, and inhibiting the MAPKs- and p65-mediated inflammatory pathway.

  18. Ectopic Expression of Pumpkin NAC Transcription Factor CmNAC1 Improves Multiple Abiotic Stress Tolerance in Arabidopsis

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    Haishun Cao

    2017-11-01

    Full Text Available Drought, cold and salinity are the major environmental stresses that limit agricultural productivity. NAC transcription factors regulate the stress response in plants. Pumpkin (Cucurbita moschata is an important cucurbit vegetable crop and it has strong resistance to abiotic stress; however, the biological functions of stress-related NAC genes in this crop are largely unknown. This study reports the function of CmNAC1, a stress-responsive pumpkin NAC domain protein. The CmNAC1-GFP fusion protein was transiently expressed in tobacco leaves for subcellular localization analysis, and we found that CmNAC1 is localized in the nucleus. Transactivation assay in yeast cells revealed that CmNAC1 functions as a transcription activator, and its transactivation domain is located in the C-terminus. CmNAC1 was ubiquitously expressed in different organs, and its transcript was induced by salinity, cold, dehydration, H2O2, and abscisic acid (ABA treatment. Furthermore, the ectopic expression (EE of CmNAC1 in Arabidopsis led to ABA hypersensitivity and enhanced tolerance to salinity, drought and cold stress. In addition, five ABA-responsive elements were enriched in CmNAC1 promoter. The CmNAC1-EE plants exhibited different root architecture, leaf morphology, and significantly high concentration of ABA compared with WT Arabidopsis under normal conditions. Our results indicated that CmNAC1 is a critical factor in ABA signaling pathways and it can be utilized in transgenic breeding to improve the abiotic stress tolerance of crops.

  19. Flow analysis techniques as effective tools for the improved environmental analysis of organic compounds expressed as total indices.

    Science.gov (United States)

    Maya, Fernando; Estela, José Manuel; Cerdà, Víctor

    2010-04-15

    The scope of this work is the accomplishment of an overview about the current state-of-the-art flow analysis techniques applied to the environmental determination of organic compounds expressed as total indices. Flow analysis techniques are proposed as effective tools for the quick obtention of preliminary chemical information about the occurrence of organic compounds on the environment prior to the use of more complex, time-consuming and expensive instrumental techniques. Recently improved flow-based methodologies for the determination of chemical oxygen demand, halogenated organic compounds and phenols are presented and discussed in detail. The aim of the present work is to demonstrate the highlight of flow-based techniques as vanguard tools on the determination of organic compounds in environmental water samples. (c) 2010 Elsevier B.V. All rights reserved.

  20. Improving the phenotypic expression of rice genotypes: Rethinking “intensification” for production systems and selection practices for rice breeding

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    Norman Uphoff

    2015-06-01

    Full Text Available Intensification in rice crop production is generally understood as requiring increased use of material inputs: water, inorganic fertilizers, and agrochemicals. However, this is not the only kind of intensification available. More productive crop phenotypes, with traits such as more resistance to biotic and abiotic stresses and shorter crop cycles, are possible through modifications in the management of rice plants, soil, water, and nutrients, reducing rather than increasing material inputs. Greater factor productivity can be achieved through the application of new knowledge and more skill, and (initially more labor, as seen from the System of Rice Intensification (SRI, whose practices are used in various combinations by as many as 10 million farmers on about 4 million hectares in over 50 countries. The highest yields achieved with these management methods have come from hybrids and improved rice varieties, confirming the importance of making genetic improvements. However, unimproved varieties are also responsive to these changes, which induce better growth and functioning of rice root systems and more abundance, diversity, and activity of beneficial soil organisms. Some of these organisms as symbiotic endophytes can affect and enhance the expression of rice plants' genetic potential as well as their phenotypic resilience to multiple stresses, including those of climate change. SRI experience and data suggest that decades of plant breeding have been selecting for the best crop genetic endowments under suboptimal growing conditions, with crowding of plants that impedes their photosynthesis and growth, flooding of rice paddies that causes roots to degenerate and forgoes benefits derived from aerobic soil organisms, and overuse of agrochemicals that adversely affect these organisms as well as soil and human health. This review paper reports evidence from research in India and Indonesia that changes in crop and water management can improve the