Multiscale analysis of protein functions and stochastic modelling of gene transcriptional regulatory networks

Genomic and proteomic analyses have attracted a great deal of interests in biological research in recent years. Many methods have been applied to discover useful information contained in the enormous databases of genomic sequences and amino acid sequences. The results of these investigations inspire further research in biological fields in return. These biological sequences, which may be considered as multiscale sequences, have some specific features which need further efforts to characterise using more refined methods. This project aims to study some of these biological challenges with multiscale analysis methods and stochastic modelling approach. The first part of the thesis aims to cluster some unknown proteins, and classify their families as well as their structural classes. A development in proteomic analysis is concerned with the determination of protein functions. The first step in this development is to classify proteins and predict their families. This motives us to study some unknown proteins from specific families, and to cluster them into families and structural classes. We select a large number of proteins from the same families or superfamilies, and link them to simulate some unknown large proteins from these families. We use multifractal analysis and the wavelet method to capture the characteristics of these linked proteins. The simulation results show that the method is valid for the classification of large proteins. The second part of the thesis aims to explore the relationship of proteins based on a layered comparison with their components. Many methods are based on homology of proteins because the resemblance at the protein sequence level normally indicates the similarity of functions and structures. However, some proteins may have similar functions with low sequential identity. We consider protein sequences at detail level to investigate the problem of comparison of proteins. The comparison is based on the empirical mode decomposition (EMD), and protein sequences are detected with the intrinsic mode functions. A measure of similarity is introduced with a new cross-correlation formula. The similarity results show that the EMD is useful for detection of functional relationships of proteins. The third part of the thesis aims to investigate the transcriptional regulatory network of yeast cell cycle via stochastic differential equations. As the investigation of genome-wide gene expressions has become a focus in genomic analysis, researchers have tried to understand the mechanisms of the yeast genome for many years. How cells control gene expressions still needs further investigation. We use a stochastic differential equation to model the expression profile of a target gene. We modify the model with a Gaussian membership function. For each target gene, a transcriptional rate is obtained, and the estimated transcriptional rate is also calculated with the information from five possible transcriptional regulators. Some regulators of these target genes are verified with the related references. With these results, we construct a transcriptional regulatory network for the genes from the yeast Saccharomyces cerevisiae. The construction of transcriptional regulatory network is useful for detecting more mechanisms of the yeast cell cycle.

Qualitative analysis and eating disorders : Discourse analytic research on anorexia nervosa

The absence of qualitative analysis in mainstream research on eating disorders is discussed in the following article as being a weakness in developing theory and clinical practice. This article includes an analysis of interviews with British healthcare workers who manage anorexic patients. This analysis presents an example of qualitative methodology in the form of discourse analysis, which is argued to provide a systematic, yet flexible approach to research on eating disorders. The overwhelming prevalence of anorexia nervosa in women is specifically examined within the context of the identification of the "discourse of femininity. " The research findings are discussed in relation to the use of discursive practices that contribute to the maintenance and reproduction of clinical processes and their relative efficacy.

Marx as a Critical Discourse Analyst : The Genesis of a Critical Method and its Relevance to the Critique of Global Capital (with Phil Graham)

In this paper we identify elements in Marx’s economic and political writings that are relevant to contemporary critical discourse analysis (CDA). We argue that Marx can be seen to be engaging in a form of discourse analysis. We identify the elements in Marx’s historical materialist method that support such a perspective, and exemplify these in longitudinal comparison of Marx’s texts.

Analysis of differential gene expression based on Bayesian estimation of variance

Gene expression is arguably the most important indicator of biological function. Thus identifying differentially expressed genes is one of the main aims of high throughout studies that use microarray and RNAseq platforms to study deregulated cellular pathways. There are many tools for analysing differentia gene expression from transciptomic datasets. The major challenge of this topic is to estimate gene expression variance due to the high amount of ‘background noise’ that is generated from biological equipment and the lack of biological replicates. Bayesian inference has been widely used in the bioinformatics field. In this work, we reveal that the prior knowledge employed in the Bayesian framework also helps to improve the accuracy of differential gene expression analysis when using a small number of replicates. We have developed a differential analysis tool that uses Bayesian estimation of the variance of gene expression for use with small numbers of biological replicates. Our method is more consistent when compared to the widely used cyber-t tool that successfully introduced the Bayesian framework to differential analysis. We also provide a user-friendly web based Graphic User Interface for biologists to use with microarray and RNAseq data. Bayesian inference can compensate for the instability of variance caused when using a small number of biological replicates by using pseudo replicates as prior knowledge. We also show that our new strategy to select pseudo replicates will improve the performance of the analysis. - See more at: http://www.eurekaselect.com/node/138761/article#sthash.VeK9xl5k.dpuf

Using Flory-Huggins phase diagrams as a pre-formulation tool for the production of amorphous solid dispersions; a comparison between hot-melt extrusion and spray drying

Objectives: Amorphous drug forms provide a useful method of enhancing the dissolution performance of poorly water-soluble drugs; however, they are inherently unstable. In this article, we have used Flory–Huggins theory to predict drug solubility and miscibility in polymer candidates, and used this information to compare spray drying and melt extrusion as processes to manufacture solid dispersions.
Method:  Solid dispersions were characterised using a combination of thermal (thermogravimetric analysis and differential scanning calorimetry) and spectroscopic (Fourier transform infrared spectroscopy (FTIR) and X-ray diffraction methods. 
Key Findings: Spray drying permitted generation of amorphous solid dispersions to be produced across a wider drug concentration than melt extrusion. Melt extrusion provided sufficient energy for more intimate mixing to be achieved between drug and polymer, which may improve physical stability. It was also confirmed that stronger drug–polymer interactions might be generated through melt extrusion. Remixing and dissolution of recrystallised felodipine into the polymeric matrices did occur during the modulated differential scanning calorimetry analysis, but the complementary information provided from FTIR confirms that all freshly prepared spray-dried samples were amorphous with the existence of amorphous drug domains within high drug-loaded samples. 
Conclusion: Using temperature–composition phase diagrams to probe the relevance of temperature and drug composition in specific polymer candidates facilitates polymer screening for the purpose of formulating solid dispersions.

Effects of computer-mediated communication and face-to-face communication on the quantity and quality of discourse produced by English as a second language students /

The effects oftwo types of small-group communication, synchronous computer-mediated and face-to-face, on the quantity and quality of verbal output were con^ared. Quantity was deiSned as the number of turns taken per minute, the number of Analysis-of-Speech units (AS-units) produced per minute, and the number ofwords produced per minute. Quality was defined as the number of words produced per AS-unit. In addition, the interaction of gender and type of communication was explored for any differences that existed in the output produced. Questionnaires were also given to participants to determine attitudes toward computer-mediated and face-to-face communication. Thirty intermediate-level students fi-om the Intensive English Language Program (lELP) at Brock University participated in the study, including 15 females and 15 males. Nonparametric tests, including the Wilcoxon matched-pairs test, Mann-Whitney U test, and Friedman test were used to test for significance at the p < .05 level. No significant differences were found in the effects of computer-mediated and face-to-face communication on the output produced during follow-up speaking sessions. However, the quantity and quality of interaction was significantly higher during face-to-face sessions than computer-mediated sessions. No significant differences were found in the output produced by males and females in these 2 conditions. While participants felt that the use of computer-mediated communication may aid in the development of certain language skills, they generally preferred face-to-face communication. These results differed fi-om previous studies that found a greater quantity and quality of output in addition to a greater equality of interaction produced during computer-mediated sessions in comparison to face-to-face sessions (Kern, 1995; Warschauer, 1996).

On the health and wellbeing of single working women without children : an analysis of scientific and lay discourse

Cette thèse examine la façon dont on interprète la santé et le bien-être des travailleuses célibataires et sans enfant au sein de deux types de récits : ceux provenant d’études publiées dans des périodiques (récits scientifiques) et ceux provenant d’entrevues qualitatives avec des membres de ce groupe (récits profanes). Sur le plan démographique, leur nombre est significatif; elles représentent 28% des employées canadiennes. Par contre, leur santé/bien-être est peu visible dans les écrits de recherche. Dans les sciences sociales, plusieurs études portent sur l’expérience parfois éprouvante d’être un adulte célibataire vivant dans une culture orientée sur le couple et la famille. Elles mettent l’accent sur le stigma associé à ce statut. Certains suggèrent même que les pratiques de recherche peuvent contribuer à la perpétuation de représentations négatives à l’égard des célibataires. En ayant un profil qui pourrait être symbolique d’une déviation vis-à-vis des attentes normatives entourant la vie de couple ou de famille, les travailleuses célibataires et sans enfant semblent un point de repère utile pour évaluer cette dernière possibilité. S’attarder autant aux récits scientifiques que profanes permettrait d’explorer les tensions et convergences entre eux. Suivant cet objectif, un échantillon de 32 articles scientifiques et de 22 retranscriptions d’entrevues ont été analysés selon une approche d’analyse de discours guidée par les concepts de répertoire interprétatif (une façon cohérente d’aborder un sujet donné) et de position du sujet (une identité mise en évidence par une façon de parler ou d’écrire). Trois articles ont émergé de cette recherche. Suite à une analyse des thèmes communs utilisés dans l’interprétation de la santé/du bien-être du groupe en question, un répertoire interprétatif surnommé la famille comme référence a été identifié. Ce répertoire expliquerait notamment la tendance observée d’expliquer leur santé/bien-être en référant aux états et aux charactéristiques d’être parent ou partenaire. Cette pratique peut avoir l’effet de voiler leur vie privée ou de la construire comme étant relativement appauvrie. L’article 2 examine comment les membres de ce groupe construisent leur propre bien-être. Il identifie la notion d’équilibre entre plusieurs sphères de vie et une identité de femme dynamique comme éléments centraux aux récits sur leur bien-être. Ces derniers vont à l’encontre de la perception des célibataires ou des personnes sans enfant comme ayant des vies moins épanouies ou enrichies et qui ne sont pas touchées par des questions de conciliation travail-vie personnelle. Le troisième article rassemble les deux types de récits autour des sujets de l’emploi et du statut de célibataire en lien avec le bien-être. Il met en évidence de nombreuses similarités et divergences, et théorise la fonction de ces diverses constructions. En conclusion, j’avance qu’une perspective plus critique face au statut de couple ou familial et de ses aspects normatifs pourrait offrir à la recherche en santé publique un point de réflexivité à développer davantage.

Proteomic analysis of redox- and ErbB2-dependent changes in mammary luminal epithelial cells using cysteine- and lysine-labelling two-dimensional difference gel electrophoresis

Differential protein expression analysis based on modification of selected amino acids with labelling reagents has become the major method of choice for quantitative proteomics. One such methodology, two-dimensional difference gel electrophoresis (2-D DIGE), uses a matched set of fluorescent N-hydroxysuccinimidyl (NHS) ester cyanine dyes to label lysine residues in different samples which can be run simultaneously on the same gels. Here we report the use of iodoacetylated cyanine (ICy) dyes (for labelling of cysteine thiols, for 2-D DIGE-based redox proteomics. Characterisation of ICy dye labelling in relation to its stoichiometry, sensitivity and specificity is described, as well as comparison of ICy dye with NHS-Cy dye labelling and several protein staining methods. We have optimised conditions for labelling of nonreduced, denatured samples and report increased sensitivity for a subset of thiol-containing proteins, allowing accurate monitoring of redox-dependent thiol modifications and expression changes. Cysteine labelling was then combined with lysine labelling in a multiplex 2-D DIGE proteomic study of redox-dependent and ErbB2-dependent changes in epithelial cells exposed to oxidative stress. This study identifies differentially modified proteins involved in cellular redox regulation, protein folding, proliferative suppression, glycolysis and cytoskeletal organisation, revealing the complexity of the response to oxidative stress and the impact that overexpression of ErbB2 has on this response.

Proteomic analysis of redox- and ErbB2-dependent changes in mammary luminal epithelial cells using cysteine- and lysine-labelling two-dimensional difference gel electrophoresis

Differential protein expression analysis based on modification of selected amino acids with labelling reagents has become the major method of choice for quantitative proteomics. One such methodology, two-dimensional difference gel electrophoresis (2-D DIGE), uses a matched set of fluorescent N-hydroxysuccinimidyl (NHS) ester cyanine dyes to label lysine residues in different samples which can be run simultaneously on the same gels. Here we report the use of iodoacetylated cyanine (ICy) dyes (for labelling of cysteine thiols, for 2-D DIGE-based redox proteomics. Characterisation of ICy dye labelling in relation to its stoichiometry, sensitivity and specificity is described, as well as comparison of ICy dye with NHS-Cy dye labelling and several protein staining methods. We have optimised conditions for labelling of nonreduced, denatured samples and report increased sensitivity for a subset of thiol-containing proteins, allowing accurate monitoring of redox-dependent thiol modifications and expression changes, Cysteine labelling was then combined with lysine labelling in a multiplex 2-D DIGE proteomic study of redox-dependent and ErbB2-dependent changes in epithelial cells exposed to oxidative stress. This study identifies differentially modified proteins involved in cellular redox regulation, protein folding, proliferative suppression, glycolysis and cytoskeletal organisation, revealing the complexity of the response to oxidative stress and the impact that overexpression of ErbB2 has on this response.

Thermodynamic analysis and comparison of downdraft gasifiers integrated with gas turbine, spark and compression ignition engines for distributed power generation

The objective of the present article is to assess and compare the performance of electricity generation systems integrated with downdraft biomass gasifiers for distributed power generation. A model for estimating the electric power generation of internal combustion engines and gas turbines powered by syngas was developed. First, the model determines the syngas composition and the lower heating value; and second, these data are used to evaluate power generation in Otto, Diesel, and Brayton cycles. Four synthesis gas compositions were tested for gasification with: air; pure oxygen; 60% oxygen with 40% steam; and 60% air with 40% steam. The results show a maximum power ratio of 0.567 kWh/Nm(3) for the gas turbine system, 0.647 kWh/Nm(3) for the compression ignition engine, and 0.775 kWh/Nm(3) for the spark-ignition engine while running on synthesis gas which was produced using pure oxygen as gasification agent. When these three systems run on synthesis gas produced using atmospheric air as gasification agent, the maximum power ratios were 0.274 kWh/Nm(3) for the gas turbine system, 0.302 kWh/Nm(3) for CIE, and 0.282 kWh/Nm(3) for SIE. The relationship between power output and synthesis gas flow variations is presented as is the dependence of efficiency on compression ratios. Since the maximum attainable power ratio of CIE is higher than that of SIE for gasification with air, more research should be performed on utilization of synthesis gas in CIE. (C) 2014 Elsevier Ltd. All rights reserved.

Linguistic gender identity construction in political discourse : a corpus-assisted analysis of the primary speeches of Barack Obama and Hillary Clinton

The present study is concerned with exploring the linguistic identity construction of Barack Obama and Hillary Clinton in the context of USA 2008 Democratic Party primaries. Thus, their speeches are examined in order to detect the aspects of identity that each politician resorted to in the process of projecting a political identity. The study, however, takes a special interest in the ways in which gender identity is projected by Obama and Clinton. Moreover, the notions of gender bias as well as gender representations are also investigated.

A call to arms at the end of history: a discourse-historical analysis of George W. Bush's declaration of war on terror

In this article we take a discourse-historical approach to illustrate the significance of George W Bush's (2001) declaration of a 'war on terror'. We present four exemplary 'call to arms' speeches by Pope Urban 11 (1095), Queen Elizabeth I (1588), Adolf Hitler (1938) and George W Bush (2001) to exemplify the structure, function, and historical significance of such texts in western societies over the last millennium. We identify four generic features that have endured in such texts throughout this period: (i) an appeal to a legitimate power source that is external to the orator, and which is presented as inherently good; (ii) an appeal to the historical importance of the culture in which the discourse is situated; (iii) the construction of a thoroughly evil Other; and (iv) an appeal for unification behind the legitimating external power source. We argue further that such texts typically appear in historical contexts characterized by deep crises in political legitimacy.

An analysis of police interview discourse and its role(s) in the judicial process

This study analyses the current role of police-suspect interview discourse in the England & Wales criminal justice system, with a focus on its use as evidence. A central premise is that the interview should be viewed not as an isolated and self-contained discursive event, but as one link in a chain of events which together constitute the criminal justice process. It examines: (1) the format changes undergone by interview data after the interview has taken place, and (2) how the other links in the chain – both before and after the interview – affect the interview-room interaction itself. It thus examines the police interview as a multi-format, multi-purpose and multi-audience mode of discourse. An interdisciplinary and multi-method discourse-analytic approach is taken, combining elements of conversation analysis, pragmatics, sociolinguistics and critical discourse analysis. Data from a new corpus of recent police-suspect interviews, collected for this study, are used to illustrate previously unaddressed problems with the current process, mainly in the form of two detailed case studies. Additional data are taken from the case of Dr. Harold Shipman. The analysis reveals several causes for concern, both in aspects of the interaction in the interview room, and in the subsequent treatment of interview material as evidence, especially in the light of s.34 of the Criminal Justice and Public Order Act 1994. The implications of the findings for criminal justice are considered, along with some practical recommendations for improvements. Overall, this study demonstrates the need for increased awareness within the criminal justice system of the many linguistic factors affecting interview evidence.

The conversation on political issues on Twitter: an analysis of the participation and frames in the debate on the 'Wert law' and evictions in Spain

The aim of this study is to determine which social agents are involved in the political debate on Twitter and whether the interpretive hegemony of actors that have traditionally been the most prominent is tempered by the challenge of framing shared with audiences. The relationship between the interpretations expressed and the profiles of participants is analyzed in comparison with the frames used by mainstream media. The chosen methodology combines content analysis and discourse analysis techniques on a sample of 1,504 relevant tweets posted on two political issues –the approval of the education law LOMCE and the evictions caused by the crisis, which have also been studied in the front pages of four leading newspapers in Spain. The results show a correlation between political issue singularities, frames and the type of discussion depending on the participants.