Fractal and complex network analyses of protein molecular dynamics

Based on protein molecular dynamics, we investigate the fractal properties of energy, pressure and volume time series using the multifractal detrended fluctuation analysis (MF-DFA) and the topological and fractal properties of their converted horizontal visibility graphs (HVGs). The energy parameters of protein dynamics we considered are bonded potential, angle potential, dihedral potential, improper potential, kinetic energy, Van der Waals potential, electrostatic potential, total energy and potential energy. The shape of the h(q)h(q) curves from MF-DFA indicates that these time series are multifractal. The numerical values of the exponent h(2)h(2) of MF-DFA show that the series of total energy and potential energy are non-stationary and anti-persistent; the other time series are stationary and persistent apart from series of pressure (with H≈0.5H≈0.5 indicating the absence of long-range correlation). The degree distributions of their converted HVGs show that these networks are exponential. The results of fractal analysis show that fractality exists in these converted HVGs. For each energy, pressure or volume parameter, it is found that the values of h(2)h(2) of MF-DFA on the time series, exponent λλ of the exponential degree distribution and fractal dimension dBdB of their converted HVGs do not change much for different proteins (indicating some universality). We also found that after taking average over all proteins, there is a linear relationship between 〈h(2)〉〈h(2)〉 (from MF-DFA on time series) and 〈dB〉〈dB〉 of the converted HVGs for different energy, pressure and volume.

Boxicity and Poset Dimension

Let G be a simple, undirected, finite graph with vertex set V(G) and edge set E(C). A k-dimensional box is a Cartesian product of closed intervals a(1), b(1)] x a(2), b(2)] x ... x a(k), b(k)]. The boxicity of G, box(G) is the minimum integer k such that G can be represented as the intersection graph of k-dimensional boxes, i.e. each vertex is mapped to a k-dimensional box and two vertices are adjacent in G if and only if their corresponding boxes intersect. Let P = (S, P) be a poset where S is the ground set and P is a reflexive, anti-symmetric and transitive binary relation on S. The dimension of P, dim(P) is the minimum integer l such that P can be expressed as the intersection of t total orders. Let G(P) be the underlying comparability graph of P. It is a well-known fact that posets with the same underlying comparability graph have the same dimension. The first result of this paper links the dimension of a poset to the boxicity of its underlying comparability graph. In particular, we show that for any poset P, box(G(P))/(chi(G(P)) - 1) <= dim(P) <= 2box(G(P)), where chi(G(P)) is the chromatic number of G(P) and chi(G(P)) not equal 1. The second result of the paper relates the boxicity of a graph G with a natural partial order associated with its extended double cover, denoted as G(c). Let P-c be the natural height-2 poset associated with G(c) by making A the set of minimal elements and B the set of maximal elements. We show that box(G)/2 <= dim(P-c) <= 2box(G) + 4. These results have some immediate and significant consequences. The upper bound dim(P) <= 2box(G(P)) allows us to derive hitherto unknown upper bounds for poset dimension. In the other direction, using the already known bounds for partial order dimension we get the following: (I) The boxicity of any graph with maximum degree Delta is O(Delta log(2) Delta) which is an improvement over the best known upper bound of Delta(2) + 2. (2) There exist graphs with boxicity Omega(Delta log Delta). This disproves a conjecture that the boxicity of a graph is O(Delta). (3) There exists no polynomial-time algorithm to approximate the boxicity of a bipartite graph on n vertices with a factor of O(n(0.5-epsilon)) for any epsilon > 0, unless NP=ZPP.

Preparation of pH-sensitive polymer by thermal initiation polymerization and its application in fluorescence immunoassay

A fluorescence immunoassay for human IgG (Ag) was developed using a pH-sensitive polymer prepared by thermal initiation or redox initiation polymerization as a carrier. In the competitive immunoassay, appropriate quantity of Ag was immobilized on the polymer and the standard Ag (or sample) solution, and a constant amount of fluorescein isothiocyanate labeled goat anti-human IgG antibody (Ab-FITC) was added. Immobilized Ag and the standard (or sample) Ag competed for binding to the Ab-FITC in 37 C in homogeneous format. After changing the pH to separate the polymer-immune complex precipitate, it was re-dissolved and determined by fluorescence method. The results showed that the immobilization efficiency, immunological reaction activities of immobilized Au and phase transition pH range were improved as Ag was immobilized by thermal initiation instead of redox initiation polymerization. Under optimum conditions, the calibration graphs for the Ag in both methods, thermal initiation and redox initiation, were linear over the concentration range of 0.0-1000 ng mL(-1), with detection limits 8 (thermal initiation) and 12 ng mL(1) (redox initiation), respectively. Moreover, some pH-sensitive polymer prepared only in organic solvent or under high temperature could also be used as an immunoreaction carrier by thermal initiation polymerization. Thermal initiation polymerization was a better immobilization mode. (C) 2004 Elsevier B.V. All rights reserved.

Rétro ingénierie des modèles d’objets dynamiques pour JavaScript

La compréhension des objets dans les programmes orientés objet est une tâche impor- tante à la compréhension du code. JavaScript (JS) est un langage orienté-objet dyna- mique, et son dynamisme rend la compréhension du code source très difficile. Dans ce mémoire, nous nous intéressons à l’analyse des objets pour les programmes JS. Notre approche construit de façon automatique un graphe d’objets inspiré du diagramme de classes d’UML à partir d’une exécution concrète d’un programme JS. Le graphe résul- tant montre la structure des objets ainsi que les interactions entre eux. Notre approche utilise une transformation du code source afin de produire cette in- formation au cours de l’exécution. Cette transformation permet de recueillir de l’infor- mation complète au sujet des objets crées ainsi que d’intercepter toutes les modifications de ces objets. À partir de cette information, nous appliquons plusieurs abstractions qui visent à produire une représentation des objets plus compacte et intuitive. Cette approche est implémentée dans l’outil JSTI. Afin d’évaluer l’utilité de l’approche, nous avons mesuré sa performance ainsi que le degré de réduction dû aux abstractions. Nous avons utilisé les dix programmes de réfé- rence de V8 pour cette comparaison. Les résultats montrent que JSTI est assez efficace pour être utilisé en pratique, avec un ralentissement moyen de 14x. De plus, pour 9 des 10 programmes, les graphes sont suffisamment compacts pour être visualisés. Nous avons aussi validé l’approche de façon qualitative en inspectant manuellement les graphes gé- nérés. Ces graphes correspondent généralement très bien au résultat attendu. Mots clés: Analyse de programmes, analyse dynamique, JavaScript, profilage.

Bioactivity Profile of Polyunsaturated Fattyacid extracts from Sardinella longiceps and Sardinella fimbriata – A comparative study

The oceans have proved to be an interminable source of new and effective drugs. Innumerable studies have proved that specific compounds isolated from marine organisms have great nutritional and pharmaceutical value. Polyunsaturated fattyacids (PUFA) in general are known for their dietary benefits in preventing and curing several critical ailments including Coronary heart disease (CHD) and cancers of various kinds. Eicosapentaenoic Acid (EPA) and Docosahexaenoic Acid (DHA) are two PUFA which are entirely marine in origin – and small Clupeoid fishes like sardines are known to be excellent sources of these two compounds. In this study, we selected two widely available Sardine species in the west coast, Sardinella longiceps and Sardinella fimbriata, for a comparative analysis of their bioactive properties. Both these sardines are known to be rich in EPA and DHA, however considerable seasonal variation in its PUFA content was expected and these variations studied. An extraction procedure to isolate PUFA at high purity levels was identified and the extracts obtained thus were studied for anti-bacterial, anti-diabetic and anti-cancerous properties.Samples of both the sardines were collected from landing centre, measured and their gut content analysed in four different months of the year – viz. June, September, December and March. The fish samples were analyzed for fattyacid using FAME method using gas chromatography to identify the full range of fattyacids and their respective concentration in each of the samples. The fattyacids were expressed in mg/g meat and later converted to percentage values against total fatty acids and total PUFA content. Fattyacids during winter season (Dec-Mar) were found to be generally higher than spawning season (June-Sept). PUFA dominated the profiles of both species and average PUFA content was also higher during winter. However, it was found that S. longiceps had proportionately higher EPA as compared to S. fimbriata which was DHA rich. Percentage of EPA and DHA also varied across months for both species – the spawning season seemed to show higher EPA content in S. longiceps and higher DHA content in S. fimbriata. Gut content analysis indicate that adult S. fimbriata is partial to zooplanktons which are DHA rich while adult S. longiceps feed mainly on EPA rich phytoplankton. Juveniles of both species, found mainly in winter, had a gut content showing more mixed diet. This difference in the feeding pattern reflect clearly in their PUFA profile – adult S. longiceps, which dominate the catch during the spawn season, feeding mostly on phytoplankton is concentrated with EPA while the juveniles which are found mostly in the winter season has slightly less EPA proportion as compared to adults. The same is true for S. fimbriata adults that are caught mostly in the spawning season; being rich in DHA as they feed mainly on zooplankton while the juveniles caught during winter season has a relatively lower concentration of DHA in their total PUFA.Various extraction procedures are known to obtain PUFA from fish oil. However, most of them do not give high purity and do not use materials indicated as safe. PUFA extracts have to be edible and should not have harmful substances for applying on mice and human subjects. Some PUFA extraction procedures, though pure and non-toxic, might induce cis-trans conversions during the extraction process. This conversion destroys the benefits of PUFA and at times is harmful to human body. A method free from these limitations has been standardized for this study. Gas Chromatography was performed on the extracts thus made to ensure that it is substantially pure. EPA: DHA ratios for both samples were derived - for S. longiceps this ratio was 3:2, while it was 3:8 for S. fimbriata.Eight common strains of gram positive and gram negative bacterial strains were subjected to the PUFA extracts from both species dissolved in acetone solution using Agar Well Diffusion method. The activity was studied against an acetone control. At the end of incubation period, zones of inhibition were measured to estimate the activity. Minimum inhibitory concentration for each of the active combinations was calculated by keeping p < 0.01 as significant. Four of the bacteria including multi-resistant Staphylococcus aureus were shown to be inhibited by the fish extracts. It was also found that the extracts from S. fimbriata were better than the one from S. longiceps in annihilating harmful bacteria.Four groups of mice subjects were studied to evaluate the antidiabetic properties of the PUFA extracts. Three groups were induced diabetes by administration of alloxan tetra hydrate. One group without diabetes was kept as control and another with diabetes was kept as diabetic control. For two diabetic groups, a prescribed amount of fish extracts were fed from each of the extracts. The biochemical parameters like serum glucose, total cholesterol, LDL & HDL cholesterol, triglycerides, urea and creatinine were sampled from all four groups at regular intervals of 7 days for a period of 28 days. It was found that groups fed with fish extracts had marked improvement in the levels of total LDL & HDL cholesterol, triglycerides and creatinine. Groups fed with extracts from S. fimbriata seem to have fared better as compared to S. longiceps. However, both groups did not show any marked improvement in blood glucose levels or levels of urea.Cell lines of MCF-7 (Breast Cancer) and DU-145 (Prostate Cancer) were used to analyse the cytotoxicity of the PUFA extracts. Both cell lines were subjected to MTT Assay and later the plates were read using an ELISA reader at a wavelength of 570nm. It was found that both extracts had significant cytotoxic effects against both cell lines and a peak cytotoxicity of 85-90% was apparent. IC50 values were calculated from the graphs and it was found that S. longiceps extracts had a slightly lower IC50 value indicating that it is toxic even at a lower concentration as compared to extracts from S. fimbriata.This study summarizes the bioactivity profile of PUFA extracts and provides recommendation for dietary intake; fish based nutritional industry and indigenous pharmaceutical industry. Possible future directions of this study are also elaborated.

Introduction to Matlab - a self-study tutorial

Matlab is a high level language that is very easy to use and very powerful. It comes with a wealth of libraries and toolboxes, that you can use directly, so that you don't need to program low level functions. It enables you to display results very easily on graphs and images. To get started with it, you need to understand how to manipulate and represent data, and how to find information about the available functions. During this self-study tutorial, you will learn: 1- How to start Matlab. 2- How you can find out all the information you need. 3- How to create simple vectors and matrices. 4- What functions are available and how to find them. 5- How to plot graphs of functions. 6- How to write a script. After this (should take about an hour), you will know most of what you need to know about Matlab and should definitely know how to go on learning about it on your own…

Matlab self study tutorial - Graphing

These resources are designed to support students in gaining more confidence with using Matlab. The PDFs provide guidance and information; Objectives: Introduce basic syntax and data preparation for graphing with Matlab by providing some data, examples of code and some background documents. Outcomes: -how to write an m file script -the importance of syntax -how to load files -how to produce simple graphs -where to get help and further examples There are also some data files to provide example data for students to work with in producing Matlab resources.

Social Networks and Small World phenomena

Social Networking tools like Facebook yield recognisable small world phenomena, that is particular kinds of social graphs that facilitate particular kinds of interaction and information exchange.

Lecture notes

Lecture notes in LaTex

Sostenibilidad del proyecto industrial del plástico .

El reciclaje se ha caracterizado por ser un tema importante en la última década, por el desarrollo económico, social y tecnológico que tiene consigo. Evidentemente, el sector de reciclaje se ha convertido en un sector con visión para poder conseguir un nuevo sector. Por este motivo lo que se ha querido con este trabajo de investigación es buscar nuevas manera de ver los recursos que se encuentran en cualquier lugar de las ciudades. La tesis cuenta con un sin número de argumentos que ayudarán a que las personas que lean el documento se interesen cada vez más en reutilizar los materiales que día a día encuentran. De esta manera, se puede ver una cadena de suministro, que llevará a que la materia prima que se haya mejorado sirva para realizar otro tipo de productos y genere un sostenimiento significativo a miles de personas que pueden sacarle provecho a estos materiales. Nuestros hábitos más cotidianos tienen mucho que ver con la degradación global del planeta. Actos tan rutinarios como tirar la basura sin separarla, comprar utensilios de usar y tirar o adquirir los alimentos envasados en materiales anti ecológicos o no reciclables contribuyen en gran medida a la contaminación medioambiental (Inzillo, 2000).

Lecture notes pdf

Lecture notes in PDF

WAIS seminar: Provenance Analytics and Crowdsourcing

Wednesday 26th March 2014 Speaker(s): Dr Trung Dong Huynh Organiser: Dr Tim Chown Time: 26/03/2014 11:00-11:50 Location: B32/3077 File size: 349Mb Abstract Understanding the dynamics of a crowdsourcing application and controlling the quality of the data it generates is challenging, partly due to the lack of tools to do so. Provenance is a domain-independent means to represent what happened in an application, which can help verify data and infer their quality. It can also reveal the processes that led to a data item and the interactions of contributors with it. Provenance patterns can manifest real-world phenomena such as a significant interest in a piece of content, providing an indication of its quality, or even issues such as undesirable interactions within a group of contributors. In this talk, I will present an application-independent methodology for analysing provenance graphs, constructed from provenance records, to learn about such patterns and to use them for assessing some key properties of crowdsourced data, such as their quality, in an automated manner. I will also talk about CollabMap (www.collabmap.org), an online crowdsourcing mapping application, and show how we applied the approach above to the trust classification of data generated by the crowd, achieving an accuracy over 95%.

A violência no âmbito de escolas públicas do ensino fundamental do Município de Aracaju

RESUMO: A violência escolar, entendida como todo ato praticado de maneira isolada ou em grupo nas instituições de ensino ou em suas redondezas, envolvendo o corpo discente e/ou docente desses estabelecimentos, é uma realidade vivenciada pelos mesmos e reconhecida por toda a sociedade. Nessa perspectiva, a presente pesquisa investigou a problemática nas instituições de ensino público da Cidade de Aracaju, capital de Sergipe, Brasil. A pesquisa possibilitou demonstrar algumas das causas e consequências da violência, e entender os motivos que permitem o seu desenvolvimento em escolas públicas, campo da pesquisa, com subsídios não somente na ciência da educação como também na ciência jurídica, visto que fundamenta suas ideias em Leis e Normas que orientam e tipificam o comportamento do indivíduo na sociedade. Nesta pesquisa – de caráter exploratório e descritivo, de cunho analítico, coerente com as questões e objetivos propostos ao objeto de estudo – recorreu-se a uma pesquisa de campo com análise quali-quantitativa com resultados apresentados em gráficos, quadros e registros de ocorrência, utilizando como universo pesquisado escolas públicas municipais de Aracaju, através de questionário aplicado aos diretores e funcionários em visita “in loco”. A pesquisa é baseada em teorias que fundamentam os resultados encontrados de que o “homem é produto do meio”, isto é, a sociedade em que vive e a família têm uma influência e um papel fundamental na formação da personalidade do indivíduo, seja ele bom ou ruim. ABSTRACT: The school violence, understood as any act performed in isolation or in groups in educational institutions or in its surroundings, involving the student body and / or teaching of these establishments, is a reality faced by them and recognized throughout society. From this perspective, this research investigated the issue in public education institutions in the city of Aracaju, capital of Sergipe, Brazil. The research allow us to demonstrate some of the causes and consequences of violence, and understand the reasons that allow its development in public schools, field of research, with subsidies not only in science education as well as in legal science, since it bases its ideas on Laws and Regulations that guide and typify the behavior of the individual in society. In this research, exploratory and descriptive character, of an analytical view, consistent with the proposed objectives and issues to the object of this study - resorted to a field research with quantitative and qualitative analysis with results presented in graphs, charts and records of occurrence, using as group studied public schools in Aracaju, through a questionnaire applied to directors and employees to visit in the place. The research is based on theories that motivate the results found that “the man is the product of the environment”, this means, the society in which they live and the family have an influence and a key role in shaping the character of the individual, be it good or bad. KEYWORDS: school

Molecular identification and anti-pathogenic activities of putative probiotic bacteria isolated from faeces of healthy elderly individuals

One hundred and nine lactic acid bacterial strains (56 bifidobacteria-like and 53 lactobacilli-like) were isolated from faecal samples donated by healthy elderly individuals (>65 years old). Isolates were identified to species level by phenotypic analysis (by API) and by 16S rDNA sequencing. Eleven species of Lactobacillus and six species of Bifidobacterium were identified. The most frequently isolated lactobacillus was L. fermentum and the most frequently isolated bifidobacterium was closely related to B. infantis by 16S rDNA sequence alignment. The isolates were characterized for their antimicrobial activity against Clostridium difficile, enteropathogenic Escherichia coli (EPEC), verocytotoxigenic E. coli (VTEC) and Campylobacter jejuni. The lactobacilli displayed variations in their antimicrobial activity with few strains showing inhibitory activity against all pathogens. The bifidobacteria displayed higher levels of inhibitory activity against C. jejuni and Cl. difficile than against the E. coli strains. Keywords: Lactobacillus, Bifidobacterium, elderly, gastrointestinal microbiota, inhibition, Clostridium difficile, enteropathogenic Escherichia coli (EPEC), verocytotoxigenic E. coli (VTEC), Campylobacter jejuni.

High functional coherence in k-partite protein cliques of protein interaction networks

We introduce a new topological concept called k-partite protein cliques to study protein interaction (PPI) networks. In particular, we examine functional coherence of proteins in k-partite protein cliques. A k-partite protein clique is a k-partite maximal clique comprising two or more nonoverlapping protein subsets between any two of which full interactions are exhibited. In the detection of PPI’s k-partite maximal cliques, we propose to transform PPI networks into induced K-partite graphs with proteins as vertices where edges only exist among the graph’s partites. Then, we present a k-partite maximal clique mining (MaCMik) algorithm to enumerate k-partite maximal cliques from K-partite graphs. Our MaCMik algorithm is applied to a yeast PPI network. We observe that there does exist interesting and unusually high functional coherence in k-partite protein cliques—most proteins in k-partite protein cliques, especially those in the same partites, share the same functions. Therefore, the idea of k-partite protein cliques suggests a novel approach to characterizing PPI networks, and may help function prediction for unknown proteins.