PathCase-SB architecture and database design

<p>Abstract</p> <p>Background</p> <p>Integration of metabolic pathways resources and regulatory metabolic network models, and deploying new tools on the integrated platform can help perform more effective and more efficient systems biology research on understanding the regulation in metabolic networks. Therefore, the tasks of (a) integrating under a single database environment regulatory metabolic networks and existing models, and (b) building tools to help with modeling and analysis are desirable and intellectually challenging computational tasks.</p> <p>Description</p> <p>PathCase Systems Biology (PathCase-SB) is built and released. The PathCase-SB database provides data and API for multiple user interfaces and software tools. The current PathCase-SB system provides a database-enabled framework and web-based computational tools towards facilitating the development of kinetic models for biological systems. PathCase-SB aims to integrate data of selected biological data sources on the web (currently, BioModels database and KEGG), and to provide more powerful and/or new capabilities via the new web-based integrative framework. This paper describes architecture and database design issues encountered in PathCase-SB's design and implementation, and presents the current design of PathCase-SB's architecture and database.</p> <p>Conclusions</p> <p>PathCase-SB architecture and database provide a highly extensible and scalable environment with easy and fast (real-time) access to the data in the database. PathCase-SB itself is already being used by researchers across the world.</p

Analysis of Serum Cytokine Levels in Larynx Squamous Cell Carcinoma and Dysplasia Patients

ABSTRACT Background: Although the imbalance of cytokines in Head and Neck Squamous Cell Carcinoma (HNSCC) is well known, there is scarce data regarding its occurrence during dysplasia, before the malignant transformation. Objective: To determine whether laryngeal dysplasia patients show a different cytokine profile than patients with cancer and healthy controls. Methods: Seventeen newly diagnosed, untreated larynx squamous cell carcinoma (SCC) and six laryngeal dysplasia patients as well as 22 healthy controls were analyzed for circulating cytokines. A flowcytometry Th1/Th2 cytokine array kit was used to quantitatively measure Interleukin-2 (IL-2), IL-4, IL-6, IL-10, Tumor Necrosis Factor-α (TNF-α) and Interferon-γ (IFN-γ) levels. Additionally, IL-8 levels were determined through ELISA. Results: IL-6, IL-8 and IL-10 were determined to be statistically increased in SCC patients (p&lt;0.05). IL-8 and IL-10 levels were also higher in SCC patients than dysplasia patients (p&lt;0.05). Additionally, IL-6 and IL-10 were all found to be markedly increased in dysplasia patients compared with controls (p&lt;0.05). Conclusion: Our results demonstrate an imbalance of IL-6 and IL-10 not only in HNSCC but also in laryngeal dysplasia

Evaluation of the ICT Tuberculosis test for the routine diagnosis of tuberculosis

BACKGROUND: Rapid and accurate diagnosis of tuberculosis (TB) is crucial to facilitate early treatment of infectious cases and thus to reduce its spread. To improve the diagnosis of TB, more rapid diagnostic techniques such as antibody detection methods including enzyme-linked immunosorbent assay (ELISA)-based serological tests and immunochromatographic methods were developed. This study was designed to evaluate the validity of an immunochromatographic assay, ICT Tuberculosis test for the serologic diagnosis of TB in Antalya, Turkey. METHODS: Sera from 72 patients with active pulmonary (53 smear-positive and 19 smear-negative cases) and eight extrapulmonary (6 smear-positive and 2 smear-negative cases) TB, and 54 controls from different outpatient clinics with similar demographic characteristics as patients were tested by ICT Tuberculosis test. RESULTS: The sensitivity, specificity, and negative predictive value of the ICT Tuberculosis test for pulmonary TB were 33.3%, 100%, and 52.9%, respectively. Smear-positive pulmonary TB patients showed a higher positivity rate for antibodies than smear-negative patients, but the difference was not statistically significant. Of the eight patients with extrapulmonary TB, antibody was detected in four patients. CONCLUSION: Our results suggest that ICT Tuberculosis test can be used to aid TB diagnosis in smear-positive patients until the culture results are available

LANGUAGE AND A PHYSICAL ORGANIZATION TECHNIQUE FOR SUMMARY TABLES.

A summary table is a tabular representation of summary data, and is a useful data structure for statistical databases. Primitive summary tables are basic building blocks of summary tables, and can be represented as relations with set-valued attributes. In this paper, we propose a set of summary table manipulation operators that, together with an algebra of set-valued relations, form an algebraic language for manipulating set-valued relations and arbitrary summary tables. We then describe a physical organization technique for summary tables, and discuss an implementation for summary table operators utilizing this technique.Case Western Reserve University // // United State

The Level of Knowledge of Parkinson’s Disease among Nonprofessional Caregivers in a Movement Disorders Center in Turkey

Introduction. Only a few studies have been conducted to determine the level of knowledge among caregivers about Parkinson’s disease (PD). The aim of the current study was to determine the knowledge of PD among caregivers at a movement disorder clinic in Turkey. Methods. We conducted a questionnaire based interview with the subjects in a tertiary care neurology facility in Turkey. The questions were divided into two parts covering the symptomatology and treatment of PD. A questionnaire consisting of 10 questions was applied to the subjects who had to mark the correct option in a stipulated time. Results. Eighty caregivers were included in the study. The caregivers’ mean age was 47.94 years (SD = 12.40). There were 47 female caregivers (58.8%). The most well-known question was that the number of drugs given to the patient may vary with time (76.3%), whereas “the benefit noted in the patient’s treatment decreases over time” was the least known question (11.3%). Discussion. This study is the first in our country and shows the necessity to increase the knowledge of PD among caregivers and the public. Education programs may have a positive role in imparting knowledge to the caregivers of PD patients

A web-based data source for metabolomics

Abstract—With the development of improved and cost-effective technologies, it is now possible to detect thousands of metabolites in biofluids or specific organs, and reliably quantify their amounts. Metabolomics focuses on studying the concentrations of metabolites in a cell or a tissue. In this paper, we describe a prototype web-based metabolomics data analysis system, PathCase MAW (PathCase Metabolomics Analysis Workbench), which features (1) A web-accessible metabolic pathway database that supports online browsing and querying, and is novel in that it includes tissue and subcompartment information for pathways, and models transport processes, (2) Tissue-aware visualization support for viewing processes, pathways, or groups of pathways in PathCase MAW database, and (3) An online metabolomics data analysis tool, called Automated Consequence Prediction Tool, which allows users to upload their own observed/measured metabolite level changes, and computationally invalidates or M(aybe)-validates those biological mechanisms that produce the observed metabolite changes

On Automated Lesson Construction from Electronic Textbooks

Abstract—An electronic book may be viewed as an application with a multimedia database. We define an electronic textbook as an electronic book that is used in conjunction with instructional resources such as lectures. In this paper, we propose an electronic textbook data model with topics, topic sources, metalinks (relationships among topics), and instructional modules which are multimedia presentations possibly capturing real-life lectures of instructors. Using the data model, the system provides users a topic-guided multimedia lesson construction. This paper concentrates, in detail, on the use of one metalink type in lesson construction, namely, prerequisite dependencies, and provides a sound and complete axiomatization of prerequisite dependencies. We present a simple automated way of constructing lessons for users where the user lists a set of topic names (s)he is interested in, and the system automatically constructs and delivers the “best ” user-tailored lesson as a multimedia presentation, where “best ” is characterized in terms of both topic closures with respect to prerequisite dependencies and what the user knows about topics. We model and present sample lesson construction requests for users, discuss their complexity, and give algorithms that evaluate such requests. For expensive lesson construction requests, we list heuristics and empirically evaluate their performance. We also discuss the worst-case performance guarantees of lesson request algorithms. Index Terms—Electronic textbooks, electronic textbook data models, instructional modules, topics, lesson construction, lesson construction heuristics, lesson complexity.