DVMS 1.5: A user manual (the data visualization and modeling system)

The data available during the drug discovery process is vast in amount and diverse in nature. To gain useful information from such data, an effective visualisation tool is required. To provide better visualisation facilities to the domain experts (screening scientist, biologist, chemist, etc.),we developed a software which is based on recently developed principled visualisation algorithms such as Generative Topographic Mapping (GTM) and Hierarchical Generative Topographic Mapping (HGTM). The software also supports conventional visualisation techniques such as Principal Component Analysis, NeuroScale, PhiVis, and Locally Linear Embedding (LLE). The software also provides global and local regression facilities . It supports regression algorithms such as Multilayer Perceptron (MLP), Radial Basis Functions network (RBF), Generalised Linear Models (GLM), Mixture of Experts (MoE), and newly developed Guided Mixture of Experts (GME). This user manual gives an overview of the purpose of the software tool, highlights some of the issues to be taken care while creating a new model, and provides information about how to install & use the tool. The user manual does not require the readers to have familiarity with the algorithms it implements. Basic computing skills are enough to operate the software.

miniDVMS v1.8 : A user manual(The data visualization and modeling system)

Today, the data available to tackle many scientific challenges is vast in quantity and diverse in nature. The exploration of heterogeneous information spaces requires suitable mining algorithms as well as effective visual interfaces. miniDVMS v1.8 provides a flexible visual data mining framework which combines advanced projection algorithms developed in the machine learning domain and visual techniques developed in the information visualisation domain. The advantage of this interface is that the user is directly involved in the data mining process. Principled projection methods, such as generative topographic mapping (GTM) and hierarchical GTM (HGTM), are integrated with powerful visual techniques, such as magnification factors, directional curvatures, parallel coordinates, and user interaction facilities, to provide this integrated visual data mining framework. The software also supports conventional visualisation techniques such as principal component analysis (PCA), Neuroscale, and PhiVis. This user manual gives an overview of the purpose of the software tool, highlights some of the issues to be taken care while creating a new model, and provides information about how to install and use the tool. The user manual does not require the readers to have familiarity with the algorithms it implements. Basic computing skills are enough to operate the software.

First in-vivo trials of a fibre Bragg grating based temperature profiling system

We describe the results of in-vivo trials of a portable fiber Bragg grating based temperature profile monitoring system. The probe incorporates five Bragg gratings along a single fiber and prevents the gratings from being strained. Illumination is provided by a superluminescent diode, and a miniature CCD based spectrometer is used for demultiplexing. The CCD signal is read into a portable computer through a small A/D interface; the computer then calculates the positions of the center wavelengths of the Bragg gratings, providing a resolution of 0.2°C. Tests were carried out on rabbits undergoing hyperthermia treatment of the kidney and liver via inductive heating of metallic implants and comparison was made with a commercial Fluoroptic thermometry system.

First in-vivo trials of a fibre Bragg grating based temperature profiling system

We describe the results of in-vivo trials of a portable fiber Bragg grating based temperature profile monitoring system. The probe incorporates five Bragg gratings along a single fiber and prevents the gratings from being strained. Illumination is provided by a superluminescent diode, and a miniature CCD based spectrometer is used for demultiplexing. The CCD signal is read into a portable computer through a small A/D interface; the computer then calculates the positions of the center wavelengths of the Bragg gratings, providing a resolution of 0.2 °C. Tests were carried out on rabbits undergoing hyperthermia treatment of the kidney and liver via inductive heating of metallic implants and comparison was made with a commercial Fluoroptic thermometry system.

Models, Techniques and Applications of e-Learning Personalization

In recent years Web has become mainstream medium for communication and information dissemination. This paper presents approaches and methods for adaptive learning implementation, which are used in some contemporary web-interfaced Learning Management Systems (LMSs). The problem is not how to create electronic learning materials, but how to locate and utilize the available information in personalized way. Different attitudes to personalization are briefly described in section 1. The real personalization requires a user profile containing information about preferences, aims, and educational history to be stored and used by the system. These issues are considered in section 2. A method for development and design of adaptive learning content in terms of learning strategy system support is represented in section 3. Section 4 includes a set of innovative personalization services that are suggested by several very important research projects (SeLeNe project, ELENA project, etc.) dated from the last few years. This section also describes a model for role- and competency-based learning customization that uses Web Services approach. The last part presents how personalization techniques are implemented in Learning Grid-driven applications.

Integrating service user and practitioner expertise within a web-based system for collaborative mental-health risk and safety management

Objectives: To develop a decision support system (DSS), myGRaCE, that integrates service user (SU) and practitioner expertise about mental health and associated risks of suicide, self-harm, harm to others, self-neglect, and vulnerability. The intention is to help SUs assess and manage their own mental health collaboratively with practitioners. Methods: An iterative process involving interviews, focus groups, and agile software development with 115 SUs, to elicit and implement myGRaCE requirements. Results: Findings highlight shared understanding of mental health risk between SUs and practitioners that can be integrated within a single model. However, important differences were revealed in SUs' preferred process of assessing risks and safety, which are reflected in the distinctive interface, navigation, tool functionality and language developed for myGRaCE. A challenge was how to provide flexible access without overwhelming and confusing users. Conclusion: The methods show that practitioner expertise can be reformulated in a format that simultaneously captures SU expertise, to provide a tool highly valued by SUs. A stepped process adds necessary structure to the assessment, each step with its own feedback and guidance. Practice Implications: The GRiST web-based DSS (www.egrist.org) links and integrates myGRaCE self-assessments with GRiST practitioner assessments for supporting collaborative and self-managed healthcare.

User Effects on Wearable Conformal SCMR System

The performance of a compact, wearable Conformal Strongly Coupled Magnetic Resonance (CSCMR) system is studied when the antenna is in the air and is worn on a user’s arm. The wireless powering system consists of the receiver and load elements designed on a printed circuit board that is attached to a polyester fabric band. The wearable antenna achieves high efficiency, has a small volume, and can be easily printed on substrates. Although the user effect on mobile terminal antennas has been studied in detail, absorption losses in wearable antennas have not been widely investigated. Our results show that efficiency of the antenna in free space is 70% and on a user’s arm is 50%. Human tissue in the close proximity of our wearable Conformal SCMR caused a decrease in radiated efficiency and total efficiency. This undesired degradation in antenna efficiency might be attributed to body loss and absorption losses. Our findings can be used as a reference for future studies on wearable devices and their applications, such as health and sports monitoring.

Enzymatic profiling of cellulosomal enzymes from the human gut bacterium, Ruminococcus champanellensis, reveals a fine-tuned system for cohesin-dockerin recognition

Funded by United States-Israel Binational Science Foundation (BSF), Jerusalem, Israel Israel Science Foundation (ISF). Grant Number: 1349 Israel Science Foundation Israel Strategic Alternative Energy Foundation (I-SAEF) BBSRC. Grant Number: BB/L009951/1 Scottish Government Food, Land and People program Society for Applied Microbiology

Enzymatic profiling of cellulosomal enzymes from the human gut bacterium, Ruminococcus champanellensis, reveals a fine-tuned system for cohesin-dockerin recognition

Funded by United States-Israel Binational Science Foundation (BSF), Jerusalem, Israel Israel Science Foundation (ISF). Grant Number: 1349 Israel Science Foundation Israel Strategic Alternative Energy Foundation (I-SAEF) BBSRC. Grant Number: BB/L009951/1 Scottish Government Food, Land and People program Society for Applied Microbiology

Fuzzy logic-based implicit authentication for mobile access control

In order to address the increasing compromise of user privacy on mobile devices, a Fuzzy Logic based implicit authentication scheme is proposed in this paper. The proposed scheme computes an aggregate score based on selected features and a threshold in real-time based on current and historic data depicting user routine. The tuned fuzzy system is then applied to the aggregated score and the threshold to determine the trust level of the current user. The proposed fuzzy-integrated implicit authentication scheme is designed to: operate adaptively and completely in the background, require minimal training period, enable high system accuracy while provide timely detection of abnormal activity. In this paper, we explore Fuzzy Logic based authentication in depth. Gaussian and triangle-based membership functions are investigated and compared using real data over several weeks from different Android phone users. The presented results show that our proposed Fuzzy Logic approach is a highly effective, and viable scheme for lightweight real-time implicit authentication on mobile devices.

An Artificial Immune System Based Recommender

The immune system is a complex biological system with a highly distributed, adaptive and self-organising nature. This paper presents an artificial immune system (AIS) that exploits some of these characteristics and is applied to the task of film recommendation by collaborative filtering (CF). Natural evolution and in particular the immune system have not been designed for classical optimisation. However, for this problem, we are not interested in finding a single optimum. Rather we intend to identify a sub-set of good matches on which recommendations can be based. It is our hypothesis that an AIS built on two central aspects of the biological immune system will be an ideal candidate to achieve this: Antigen - antibody interaction for matching and antibody - antibody interaction for diversity. Computational results are presented in support of this conjecture and compared to those found by other CF techniques. Notes: Uwe Aickelin, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, UK

Iis--integrated Interactome System: A Web-based Platform For The Annotation, Analysis And Visualization Of Protein-metabolite-gene-drug Interactions By Integrating A Variety Of Data Sources And Tools.

High-throughput screening of physical, genetic and chemical-genetic interactions brings important perspectives in the Systems Biology field, as the analysis of these interactions provides new insights into protein/gene function, cellular metabolic variations and the validation of therapeutic targets and drug design. However, such analysis depends on a pipeline connecting different tools that can automatically integrate data from diverse sources and result in a more comprehensive dataset that can be properly interpreted. We describe here the Integrated Interactome System (IIS), an integrative platform with a web-based interface for the annotation, analysis and visualization of the interaction profiles of proteins/genes, metabolites and drugs of interest. IIS works in four connected modules: (i) Submission module, which receives raw data derived from Sanger sequencing (e.g. two-hybrid system); (ii) Search module, which enables the user to search for the processed reads to be assembled into contigs/singlets, or for lists of proteins/genes, metabolites and drugs of interest, and add them to the project; (iii) Annotation module, which assigns annotations from several databases for the contigs/singlets or lists of proteins/genes, generating tables with automatic annotation that can be manually curated; and (iv) Interactome module, which maps the contigs/singlets or the uploaded lists to entries in our integrated database, building networks that gather novel identified interactions, protein and metabolite expression/concentration levels, subcellular localization and computed topological metrics, GO biological processes and KEGG pathways enrichment. This module generates a XGMML file that can be imported into Cytoscape or be visualized directly on the web. We have developed IIS by the integration of diverse databases following the need of appropriate tools for a systematic analysis of physical, genetic and chemical-genetic interactions. IIS was validated with yeast two-hybrid, proteomics and metabolomics datasets, but it is also extendable to other datasets. IIS is freely available online at: http://www.lge.ibi.unicamp.br/lnbio/IIS/.

Two-component System Vicrk Regulates Functions Associated With Establishment Of Streptococcus Sanguinis In Biofilms.

Streptococcus sanguinis is a commensal pioneer colonizer of teeth and an opportunistic pathogen of infectious endocarditis. The establishment of S. sanguinis in host sites likely requires dynamic fitting of the cell wall in response to local stimuli. In this study, we investigated the two-component system (TCS) VicRK in S. sanguinis (VicRKSs), which regulates genes of cell wall biogenesis, biofilm formation, and virulence in opportunistic pathogens. A vicK knockout mutant obtained from strain SK36 (SKvic) showed slight reductions in aerobic growth and resistance to oxidative stress but an impaired ability to form biofilms, a phenotype restored in the complemented mutant. The biofilm-defective phenotype was associated with reduced amounts of extracellular DNA during aerobic growth, with reduced production of H2O2, a metabolic product associated with DNA release, and with inhibitory capacity of S. sanguinis competitor species. No changes in autolysis or cell surface hydrophobicity were detected in SKvic. Reverse transcription-quantitative PCR (RT-qPCR), electrophoretic mobility shift assays (EMSA), and promoter sequence analyses revealed that VicR directly regulates genes encoding murein hydrolases (SSA_0094, cwdP, and gbpB) and spxB, which encodes pyruvate oxidase for H2O2 production. Genes previously associated with spxB expression (spxR, ccpA, ackA, and tpK) were not transcriptionally affected in SKvic. RT-qPCR analyses of S. sanguinis biofilm cells further showed upregulation of VicRK targets (spxB, gbpB, and SSA_0094) and other genes for biofilm formation (gtfP and comE) compared to expression in planktonic cells. This study provides evidence that VicRKSs regulates functions crucial for S. sanguinis establishment in biofilms and identifies novel VicRK targets potentially involved in hydrolytic activities of the cell wall required for these functions.

Emprego de regras de associação para extração de padrões mercadológicos de touros Nelore com avaliação genética

Objetivou-se com este trabalho utilizar regras de associação para identificar forças de mercado que regem a comercialização de touros com avaliação genética pelo programa Nelore Brasil. Essas regras permitem evidenciar padrões implícitos nas transações de grandes bases de dados, indicando causas e efeitos determinantes da oferta e comercialização de touros. Na análise foram considerados 19.736 registros de touros comercializados, 17 fazendas e 15 atributos referentes às diferenças esperadas nas progênies dos reprodutores, local e época da venda. Utilizou-se um sistema com interface gráfica usuário-dirigido que permite geração e seleção interativa de regras de associação. Análise de Pareto foi aplicada para as três medidas objetivas (suporte, confiança e lift) que acompanham cada uma das regras de associação, para validação das mesmas. Foram geradas 2.667 regras de associação, 164 consideradas úteis pelo usuário e 107 válidas para lift ≥ 1,0505. As fazendas participantes do programa Nelore Brasil apresentam especializações na oferta de touros, segundo características para habilidade materna, ganho de peso, fertilidade, precocidade sexual, longevidade, rendimento e terminação de carcaça. Os perfis genéticos dos touros são diferentes para as variedades padrão e mocho. Algumas regiões brasileiras são nichos de mercado para touros sem registro genealógico. A análise de evolução de mercado sugere que o mérito genético total, índice oficial do programa Nelore Brasil, tornou-se um importante índice para comercialização dos touros. Com o uso das regras de associação, foi possível descobrir forças do mercado e identificar combinações de atributos genéticos, geográficos e temporais que determinam a comercialização de touros no programa Nelore Brasil.