MAPI: towards the integrated exploitation of bioinformatics Web Services.

BACKGROUND. Bioinformatics is commonly featured as a well assorted list of available web resources. Although diversity of services is positive in general, the proliferation of tools, their dispersion and heterogeneity complicate the integrated exploitation of such data processing capacity. RESULTS. To facilitate the construction of software clients and make integrated use of this variety of tools, we present a modular programmatic application interface (MAPI) that provides the necessary functionality for uniform representation of Web Services metadata descriptors including their management and invocation protocols of the services which they represent. This document describes the main functionality of the framework and how it can be used to facilitate the deployment of new software under a unified structure of bioinformatics Web Services. A notable feature of MAPI is the modular organization of the functionality into different modules associated with specific tasks. This means that only the modules needed for the client have to be installed, and that the module functionality can be extended without the need for re-writing the software client. CONCLUSIONS. The potential utility and versatility of the software library has been demonstrated by the implementation of several currently available clients that cover different aspects of integrated data processing, ranging from service discovery to service invocation with advanced features such as workflows composition and asynchronous services calls to multiple types of Web Services including those registered in repositories (e.g. GRID-based, SOAP, BioMOBY, R-bioconductor, and others).

The TT genotype of the STAT4 rs7574865 polymorphism is associated with high disease activity and disability in patients with early arthritis

BACKGROUND The number of copies of the HLA-DRB1 shared epitope, and the minor alleles of the STAT4 rs7574865 and the PTPN22 rs2476601 polymorphisms have all been linked with an increased risk of developing rheumatoid arthritis. In the present study, we investigated the effects of these genetic variants on disease activity and disability in patients with early arthritis. METHODOLOGY AND RESULTS We studied 640 patients with early arthritis (76% women; median age, 52 years), recording disease-related variables every 6 months during a 2-year follow-up. HLA-DRB1 alleles were determined by PCR-SSO, while rs7574865 and rs2476601 were genotyped with the Taqman 5' allelic discrimination assay. Multivariate analysis was performed using generalized estimating equations for repeated measures. After adjusting for confounding variables such as gender, age and ACPA, the TT genotype of rs7574865 in STAT4 was associated with increased disease activity (DAS28) as compared with the GG genotype (β coefficient [95% confidence interval] = 0.42 [0.01-0.83], p = 0.044). Conversely, the presence of the T allele of rs2476601 in PTPN22 was associated with diminished disease activity during follow-up in a dose-dependent manner (CT genotype = -0.27 [-0.56- -0.01], p = 0.042; TT genotype = -0.68 [-1.64- -0.27], p = 0.162). After adjustment for gender, age and disease activity, homozygosity for the T allele of rs7574865 in STAT4 was associated with greater disability as compared with the GG genotype. CONCLUSIONS Our data suggest that patients with early arthritis who are homozygous for the T allele of rs7574865 in STAT4 may develop a more severe form of the disease with increased disease activity and disability.

Fluorodeoxyglucose-positron emission tomography scan-positive recurrent papillary thyroid cancer and the prognosis and implications for surgical management.

BACKGROUND To compare outcomes for patients with recurrent or persistent papillary thyroid cancer (PTC) who had metastatic tumors that were fluorodeoxyglucose-positron emission tomography (FDG-PET) positive or negative, and to determine whether the FDG-PET scan findings changed the outcome of medical and surgical management. METHODS From a prospective thyroid cancer database, we retrospectively identified patients with recurrent or persistent PTC and reviewed data on demographics, initial stage, location and extent of persistent or recurrent disease, clinical management, disease-free survival and outcome. We further identified subsets of patients who had an FDG-PET scan or an FDG-PET/CT scan and whole-body radioactive iodine scans and categorized them by whether they had one or more FDG-PET-avid (PET-positive) lesions or PET-negative lesions. The medical and surgical treatments and outcome of these patients were compared. RESULTS Between 1984 and 2008, 41 of 141 patients who had recurrent or persistent PTC underwent FDG-PET (n = 11) or FDG-PET/CT scans (n = 30); 22 patients (54%) had one or more PET-positive lesion(s), 17 (41%) had PET-negative lesions, and two had indeterminate lesions. Most PET-positive lesions were located in the neck (55%). Patients who had a PET-positive lesion had a significantly higher TNM stage (P = 0.01), higher age (P = 0.03), and higher thyroglobulin (P = 0.024). Only patients who had PET-positive lesions died (5/22 vs. 0/17 for PET-negative lesions; P = 0.04). In two of the seven patients who underwent surgical resection of their PET-positive lesions, loco-regional control was obtained without evidence of residual disease. CONCLUSION Patients with recurrent or persistent PTC and FDG-PET-positive lesions have a worse prognosis. In some patients loco-regional control can be obtained without evidence of residual disease by reoperation if the lesion is localized in the neck or mediastinum.

Searching patterns in painting images with computer vision techniques

This paper presents a pattern recognition method focused on paintings images. The purpose is construct a system able to recognize authors or art styles based on common elements of his work (here called patterns). The method is based on comparing images that contain the same or similar patterns. It uses different computer vision techniques, like SIFT and SURF, to describe the patterns in descriptors, K-Means to classify and simplify these descriptors, and RANSAC to determine and detect good results. The method are good to find patterns of known images but not so good if they are not.

Comparison of Work Scheduling Using Constraint Programming or Auctions

Business processes designers take into account the resources that the processes would need, but, due to the variable cost of certain parameters (like energy) or other circumstances, this scheduling must be done when business process enactment. In this report we formalize the energy aware resource cost, including time and usage dependent rates. We also present a constraint programming approach and an auction-based approach to solve the mentioned problem including a comparison of them and a comparison of the proposed algorithms for solving them

Human-Computer Interaction with older people through ethnographical lenses: everyday interactions with ICT

Report for the scientific sojourn carried out at the School of Computing of the University of Dundee, United Kingdom, from 2010 to 2012. This document is a scientific report of the work done, main results, publications and accomplishment of the objectives of the 2-year post-doctoral research project with reference number BP-A 00239. The project has addressed the topic of older people (60+) and Information and Communication Technologies (ICT), which is a topic of growing social and research interest, from a Human-Computer Interaction perspective. Over a 2-year period (June 2010-June 2012), we have conducted classical ethnography of ICT use in a computer clubhouse in Scotland, addressing interaction barriers and strategies, social sharing practices in Social Network Sites, and ICT learning, and carried out rapid ethnographical studies related to geo-enabled ICT and e-government services towards supporting independent living and active ageing. The main results have provided a much deeper understanding of (i) the everyday use of Computer-Mediated Communication tools, such as video-chats and blogs, and its evolution as older people’s experience with ICT increases over time, (ii) cross-cultural aspects of ICT use in the north and south of Europe, (iii) the relevance of cognition over vision in interacting with geographical information and a wide range of ICT tools, despite common stereotypes (e.g. make things bigger), (iv) the important relationship offline-online to provide older people with socially inclusive and meaningful eservices for independent living and active ageing, (v) how older people carry out social sharing practices in the popular YouTube, (vi) their user experiences and (vii) the challenges they face in ICT learning and the strategies they use to become successful ICT learners over time. The research conducted in this project has been published in 17 papers, 4 in journals – two of which in JCR, 5 in conferences, 4 in workshops and 4 in magazines. Other public output consists of 10 invited talks and seminars.

Deployment of self-expandable stents in aneurysmatic cerebral vessels: comparison of different computational approaches for interventional planning

In the last few years, there has been a growing focus on faster computational methods to support clinicians in planning stenting procedures. This study investigates the possibility of introducing computational approximations in modelling stent deployment in aneurysmatic cerebral vessels to achieve simulations compatible with the constraints of real clinical workflows. The release of a self-expandable stent in a simplified aneurysmatic vessel was modelled in four different initial positions. Six progressively simplified modelling approaches (based on Finite Element method and Fast Virtual Stenting – FVS) have been used. Comparing accuracy of the results, the final configuration of the stent is more affected by neglecting mechanical properties of materials (FVS) than by adopting 1D instead of 3D stent models. Nevertheless, the differencesshowed are acceptable compared to those achieved by considering different stent initial positions. Regarding computationalcosts, simulations involving 1D stent features are the only ones feasible in clinical context.

Distortion control for delay-sensitive sources

We investigate the problem of finding minimum-distortion policies for streaming delay-sensitive but distortion-tolerant data. We consider cross-layer approaches which exploit the coupling between presentation and transport layers. We make the natural assumption that the distortion function is convex and decreasing. We focus on a single source-destination pair and analytically find the optimum transmission policy when the transmission is done over an error-free channel. This optimum policy turns out to be independent of the exact form of the convex and decreasing distortion function. Then, for a packet-erasure channel, we analytically find the optimum open-loop transmission policy, which is also independent of the form of the convex distortion function. We then find computationally efficient closed-loop heuristic policies and show, through numerical evaluation, that they outperform the open-loop policy and have near optimal performance.

Hierachy-based methodology for producing educational contents with maximal reutilization

Computer based training or distance education are facing dramatic changes withthe advent of standardization efforts, some of them concentrating in maximal reuse.This is of paramount importance for a sustainable -cost affordable- production ofeducational materials. Reuse in itself should not be a goal, though, since manymethodological aspects might be lost. In this paper we propose two contentproduction approaches for the InterMediActor platform under a competence-basedmethodology: either a bottom-up approach where content is designed from scratchor a top-down methodology where existing material can be gradually adapted tofulfil requisites to be used with maximal flexibility into InterMediActor.

The cooperative induction of hypoxia-inducible factor-1 alpha and STAT3 during hypoxia induced an impairment of tumor susceptibility to CTL-mediated cell lysis.

Hypoxia is an essential component of tumor microenvironment. In this study, we investigated the influence of hypoxia (1% PO(2)) on CTL-mediated tumor cell lysis. We demonstrate that exposure of target tumor cells to hypoxia has an inhibitory effect on the CTL clone (Heu171)-induced autologous target cell lysis. Such inhibition correlates with hypoxia-inducible factor-1alpha (HIF-1alpha) induction but is not associated with an alteration of CTL reactivity as revealed by granzyme B polarization or morphological change. Western blot analysis indicates that although hypoxia had no effect on p53 accumulation, it induced the phosphorylation of STAT3 in tumor cells by a mechanism at least in part involving vascular endothelial growth factor secretion. We additionally show that a simultaneous nuclear translocation of HIF-1alpha and phospho-STAT3 was observed. Interestingly, gene silencing of STAT3 by small interfering RNA resulted in HIF-1alpha inhibition and a significant restoration of target cell susceptibility to CTL-induced killing under hypoxic conditions by a mechanism involving at least in part down-regulation of AKT phosphorylation. Moreover, knockdown of HIF-1alpha resulted in the restoration of target cell lysis under hypoxic conditions. This was further supported by DNA microarray analysis where STAT3 inhibition resulted in a partly reversal of the hypoxia-induced gene expression profile. The present study demonstrates that the concomitant hypoxic induction of phospho-STAT3 and HIF-1alpha are functionally linked to the alteration of non-small cell lung carcinoma target susceptibility to CTL-mediated killing. Considering the eminent functions of STAT3 and HIF-1alpha in the tumor microenvironment, their targeting may represent novel strategies for immunotherapeutic intervention.

Development of a Computer Controlled Underbody Plow: TR412, Final Report, January 2006

Underbody plows can be very useful tools in winter maintenance, especially when compacted snow or hard ice must be removed from the roadway. By the application of significant down-force, and the use of an appropriate cutting edge angle, compacted snow and ice can be removed very effectively by such plows, with much greater efficiency than any other tool under those circumstances. However, the successful operation of an underbody plow requires considerable skill. If too little down pressure is applied to the plow, then it will not cut the ice or compacted snow. However, if too much force is applied, then either the cutting edge may gouge the road surface, causing significant damage often to both the road surface and the plow, or the plow may ride up on the cutting edge so that it is no longer controllable by the operator. Spinning of the truck in such situations is easily accomplished. Further, excessive down force will result in rapid wear of the cutting edge. Given this need for a high level of operator skill, the operation of an underbody plow is a candidate for automation. In order to successfully automate the operation of an underbody plow, a control system must be developed that follows a set of rules that represent appropriate operation of such a plow. These rules have been developed, based upon earlier work in which operational underbody plows were instrumented to determine the loading upon them (both vertical and horizontal) and the angle at which the blade was operating.These rules have been successfully coded into two different computer programs, both using the MatLab® software. In the first program, various load and angle inputs are analyzed to determine when, whether, and how they violate the rules of operation. This program is essentially deterministic in nature. In the second program, the Simulink® package in the MatLab® software system was used to implement these rules using fuzzy logic. Fuzzy logic essentially replaces a fixed and constant rule with one that varies in such a way as to improve operational control. The development of the fuzzy logic in this simulation was achieved simply by using appropriate routines in the computer software, rather than being developed directly. The results of the computer testing and simulation indicate that a fully automated, computer controlled underbody plow is indeed possible. The issue of whether the next steps toward full automation should be taken (and by whom) has also been considered, and the possibility of some sort of joint venture between a Department of Transportation and a vendor has been suggested.

Experimental analysis and computer prediction of CTF/NFI transcription factor DNA binding sites.

Accurate prediction of transcription factor binding sites is needed to unravel the function and regulation of genes discovered in genome sequencing projects. To evaluate current computer prediction tools, we have begun a systematic study of the sequence-specific DNA-binding of a transcription factor belonging to the CTF/NFI family. Using a systematic collection of rationally designed oligonucleotides combined with an in vitro DNA binding assay, we found that the sequence specificity of this protein cannot be represented by a simple consensus sequence or weight matrix. For instance, CTF/NFI uses a flexible DNA binding mode that allows for variations of the binding site length. From the experimental data, we derived a novel prediction method using a generalised profile as a binding site predictor. Experimental evaluation of the generalised profile indicated that it accurately predicts the binding affinity of the transcription factor to natural or synthetic DNA sequences. Furthermore, the in vitro measured binding affinities of a subset of oligonucleotides were found to correlate with their transcriptional activities in transfected cells. The combined computational-experimental approach exemplified in this work thus resulted in an accurate prediction method for CTF/NFI binding sites potentially functioning as regulatory regions in vivo.

Micro-Computer Based Linear Scheduling Application for Highway Construction Project Control, HR-339A, 1995

This report describes a new approach to the problem of scheduling highway construction type projects. The technique can accurately model linear activities and identify the controlling activity path on a linear schedule. Current scheduling practices are unable to accomplish these two tasks with any accuracy for linear activities, leaving planners and manager suspicious of the information they provide. Basic linear scheduling is not a new technique, and many attempts have been made to apply it to various types of work in the past. However, the technique has never been widely used because of the lack of an analytical approach to activity relationships and development of an analytical approach to determining controlling activities. The Linear Scheduling Model (LSM) developed in this report, completes the linear scheduling technique by adding to linear scheduling all of the analytical capabilities, including computer applications, present in CPM scheduling today. The LSM has tremendous potential, and will likely have a significant impact on the way linear construction is scheduled in the future.

A Computer Based Information System for County Equipment Cost Records, Interim Report, HR-173, 1975

This report describes the work accomplished to date on research project HR-173, A Computer Based Information System for County Equipment Cost Records, and presents the initial design for this system. The specific topics discussed here are findings from the analysis of information needs, the system specifications developed from these findings, and the proposed system design based upon the system specifications. The initial system design will include tentative input designs for capturing input data, output designs to show the output formats and the items to be output for use in decision making, file design showing the organization of information to be kept on each piece of equipment in the computer data file, and general system design explaining how the entire system will operate. The Steering Committee appointed by Iowa Highway Research Board is asked to study this report, make appropriate suggestions, and give approval to the proposed design subject to any suggestions made. This approval will permit the designer to proceed promptly with the development of the computer program implementation phase of the design.

Reconfigurable Architecture To Estimate The Motion Of An Underwater Vehicle

This work proposes a parallel architecture for a motion estimation algorithm. It is well known that image processing requires a huge amount of computation, mainly at low level processing where the algorithms are dealing with a great numbers of data-pixel. One of the solutions to estimate motions involves detection of the correspondences between two images. Due to its regular processing scheme, parallel implementation of correspondence problem can be an adequate approach to reduce the computation time. This work introduces parallel and real-time implementation of such low-level tasks to be carried out from the moment that the current image is acquired by the camera until the pairs of point-matchings are detected