Biomedical subjects

Francesco Pinciroli

Publications and source records attributed to Francesco Pinciroli.

At least 19 recordsLinked to original sources

PubMed2006

A web management service applied to a comprehensive characterization of Visible Human Dataset colour images.

Visible Human Dataset (VHD) is a remarkable piece of raw digital anatomical knowledge still to be fully exploited. Colours of VHD anatomic images are the natural targets of different algorithmic approaches devoted to understanding the content of the complex digital medical images, but they have never been analysed exhaustively. A full colorimetric characterization of all 9000 VHD colour images may help to take advantage of implicit available information in raw data. This study describes a novel colorimetric characterization and a Visual Knowledge Discovery tool, using methods from database field, data visualization, and image analysis. The applied heterogeneous methods allowed us to develop a histogram meta database and make it available remotely. It consists of a histogram-based colorimetric characterization of the all VHD 24-bit colour images. A user-friendly, interactive, and intuitive 3D framework providing 3D services was built and made freely available. It allows real-time analysis of colour component characteristics of a user-defined set of VHD images providing 3D interactive navigation of the histogram meta database. New knowledge can be discovered using our tool and the histogram meta database provided. This work allowed us to propose novel methods for colour image characterization and obtained results using developed service on VHD colour images let us to partially understand the not fully satisfactorily results achieved so far analysing these images.

Anatomy↗

PubMed2005

Inherited disorder phenotypes: controlled annotation and statistical analysis for knowledge mining from gene lists.

BACKGROUND: Analysis of inherited diseases and their associated phenotypes is of great importance to gain knowledge of underlying genetic interactions and could ultimately give clinically useful insights into disease processes, including complex diseases influenced by multiple genetic loci. Nevertheless, to date few computational contributions have been proposed for this purpose, mainly due to lack of controlled clinical information easily accessible and structured for computational genome-wise analyses. To allow performing phenotype analyses of inherited disorder related genes we implemented new original modules within GFINDer http://www.bioinformatics.polimi.it/GFINDer/, a Web system we previously developed that dynamically aggregates functional annotations of user uploaded gene lists and allows performing their statistical analysis and mining. RESULTS: New GFINDer modules allow annotating large numbers of user classified biomolecular sequence identifiers with morbidity and clinical information, classifying them according to genetic disease phenotypes and their locations of occurrence, and statistically analyzing the obtained classifications. To achieve this we exploited, normalized and structured the information present in textual form in the Clinical Synopsis sections of the Online Mendelian Inheritance in Man (OMIM) databank. Such valuable information delineates numerous signs and symptoms accompanying many genetic diseases and it is divided into phenotype location categories, either by organ system or type of finding. CONCLUSION: Supporting phenotype analyses of inherited diseases and biomolecular functional evaluations, GFINDer facilitates a genomic approach to the understanding of fundamental biological processes and complex cellular mechanisms underlying patho-physiological phenotypes.

Computational Biology↗

PubMed2005

MicroGen: a MIAME compliant web system for microarray experiment information and workflow management.

BACKGROUND: Improvements of bio-nano-technologies and biomolecular techniques have led to increasing production of high-throughput experimental data. Spotted cDNA microarray is one of the most diffuse technologies, used in single research laboratories and in biotechnology service facilities. Although they are routinely performed, spotted microarray experiments are complex procedures entailing several experimental steps and actors with different technical skills and roles. During an experiment, involved actors, who can also be located in a distance, need to access and share specific experiment information according to their roles. Furthermore, complete information describing all experimental steps must be orderly collected to allow subsequent correct interpretation of experimental results. RESULTS: We developed MicroGen, a web system for managing information and workflow in the production pipeline of spotted microarray experiments. It is constituted of a core multi-database system able to store all data completely characterizing different spotted microarray experiments according to the Minimum Information About Microarray Experiments (MIAME) standard, and of an intuitive and user-friendly web interface able to support the collaborative work required among multidisciplinary actors and roles involved in spotted microarray experiment production. MicroGen supports six types of user roles: the researcher who designs and requests the experiment, the spotting operator, the hybridisation operator, the image processing operator, the system administrator, and the generic public user who can access the unrestricted part of the system to get information about MicroGen services. CONCLUSION: MicroGen represents a MIAME compliant information system that enables managing workflow and supporting collaborative work in spotted microarray experiment production.

Computational Biology↗

PubMed2005

The unexpected high practical value of medical ontologies.

Ontology is no longer a mere research topic, but its relevance has been recognized in several practical fields. Current applications areas include natural language translation, e-commerce, geographic information systems, legal information systems and biology and medicine. It is the backbone of solid and effective applications in health care and can help to build more powerful and more interoperable medical information systems. The design and implementation of ontologies in medicine is mainly focused on the re-organization of medical terminologies. This is obviously a difficult task and requires a deep analysis of the structure and the concepts of such terminologies, in order to define domain ontologies able to provide both flexibility and consistency to medical information systems. The aim of this special issue of Computers in Biology and Medicine is to report the current evolution of research in biomedical ontologies, presenting both papers devoted to methodological issues and works with a more applicative emphasis.

Computational Biology↗

PubMed2005

Using Gene Ontology and genomic controlled vocabularies to analyze high-throughput gene lists: three tool comparison.

In genomic and molecular biology domains, controlled vocabularies and ontologies are becoming of paramount importance to integrate and correlate the massive amount of information increasingly accumulating in heterogeneous and distributed databanks. Although at present they are still few and present some issues, they can effectively be used also to biologically annotate genes on a genomic scale and across different species, and to evaluate the relevance of such annotations. Here, we compare three tools using the Gene Ontology and genomic controlled vocabularies to statistically highlight significant biological characteristics of gene sets to help in the biological interpretation of high-throughput experiment results and knowledge discovery from data.

Computational Biology↗

PubMed2005

GFINDer: genetic disease and phenotype location statistical analysis and mining of dynamically annotated gene lists.

Phenotype analysis is commonly recognized to be of great importance for gaining insight into genetic interaction underlying inherited diseases. However, few computational contributions have been proposed for this purpose, mainly owing to lack of controlled clinical information easily accessible and structured for computational genome-wise analyses. We developed and made available through GFINDer web server an original approach for the analysis of genetic disorder related genes by exploiting the information on genetic diseases and their clinical phenotypes present in textual form within the Online Mendelian Inheritance in Man (OMIM) database. Because several synonyms for the same name and different names for overlapping concepts are often used in OMIM, we first normalized phenotype location descriptions reducing them to a list of unique controlled terms representing phenotype location categories. Then, we hierarchically structured them and the correspondent genetic diseases according to their topology and granularity of description, respectively. Thus, in GFINDer we could implement specific Genetic Disorders modules for the analysis of these structured data. Such modules allow to automatically annotate user-classified gene lists with updated disease and clinical information, classify them according to the genetic syndrome and the phenotypic location categories, and statistically identify the most relevant categories in each gene class. GFINDer is available for non-profit use at http://www.bioinformatics.polimi.it/GFINDer/.

Data Interpretation, Statistical↗

PubMed2005

He@lthCo-op: a web-based system to support distributed healthcare co-operative work.

Healthcare is characterized by close collaboration and information sharing among many distinct actors, who co-operate for the patient care in different temporal moments, also at a distance. In this context, availability to care givers of all relevant patient health data and of specific healthcare co-operative work supporting tools is fundamental for best patient treatment. We designed and implemented He@lthCo-op, a web-based modular system supporting co-operative work and patient information secure sharing among healthcare personnel also from remotely located sites. He@lthCo-op enables easily gathering, storing, and accessing patient clinical and personal data anytime and from anywhere an Internet connection is available.

Computer Communication Networks↗

PubMed2005

Understanding telecardiology success and pitfalls by a systematic review.

Cardiology is the clinical area where death causes are more frequent than in any other clinical area, and it could benefit from telemedicine. At present, assessment about telecardiology application are hard to find, and sometimes can be found in review article about telemedicine, but there is a lack of review on telecardiology application literature. So we reviewed studies regarding telemedicine applications on cardiology specialty.Sixty-one articles were selected, searching the PubMed database for all years the database were available. All considered articles were published on peer reviewed telemedicine and biomedical journals, from 1992 to 2004. We defined an evaluation grid for the articles in our research result set. Each article was reviewed and catalogued, identifying: 1) Article identification, 2) Content description, 3) Telemedicine manifesto classification, 4) Telemedicine system paradigm, 5) Involved actors.Most of the analysed literature referred only to feasibility studies, pilot projects and to short-term outcomes, for example only 21 cases reported a project duration greater than one year. The method proposed can be used to analyse literature on others telemedicine specialties.

Cardiology↗

PubMed2005

PubMiur: a tool for on-line assisted bibliographic researches.

Several kinds of user can be interested in scientific publication references produced by academic organizations. Sometimes references are arranged in HTML pages, separated one for an year, and a database containing them can not be available. Results of executed query using this framework couldn't be satisfying. We developed a web-based system to assist user making query, inside web pages, using different search criteria. The constrain on querying one year at a time and the lack of a database is so overcame.

Databases, Bibliographic↗

PubMed2004

MyWEST: my Web Extraction Software Tool for effective mining of annotations from web-based databanks.

MOTIVATION: High-throughput technologies create the necessity to mine large amounts of gene annotations from diverse databanks, and to integrate the resulting data. Most databanks can be interrogated only via Web, for a single gene at a time, and query results are generally available only in the HTML format. Although some databanks provide batch retrieval of data via FTP, this requires expertise and resources for locally reimplementing the databank. RESULTS: We developed MyWEST, a tool aimed at researchers without extensive informatics skills or resources, which exploits user-defined templates to easily mine selected annotations from different Web-interfaced databanks, and aggregates and structures results in an automatically updated database. Using microarray results from a model system of retinoic acid-induced differentiation, MyWEST effectively gathered relevant annotations from various biomolecular databanks, highlighted significant biological characteristics and supported a global approach to the understanding of complex cellular mechanisms. AVAILABILITY: MyWEST is freely available for non-profit use at http://www.medinfopoli.polimi.it/MyWEST/

Algorithms↗

PubMed2004

GFINDer: Genome Function INtegrated Discoverer through dynamic annotation, statistical analysis, and mining.

Statistical and clustering analyses of gene expression results from high-density microarray experiments produce lists of hundreds of genes regulated differentially, or with particular expression profiles, in the conditions under study. Independent of the microarray platforms and analysis methods used, these lists must be biologically interpreted to gain a better knowledge of the patho-physiological phenomena involved. To this end, numerous biological annotations are available within heterogeneous and widely distributed databases. Although several tools have been developed for annotating lists of genes, most of them do not give methods for evaluating the relevance of the annotations provided, or for estimating the functional bias introduced by the gene set on the array used to identify the gene list considered. We developed Genome Functional INtegrated Discoverer (GFINDer), a web server able to automatically provide large-scale lists of user-classified genes with functional profiles biologically characterizing the different gene classes in the list. GFINDer automatically retrieves annotations of several functional categories from different sources, identifies the categories enriched in each class of a user-classified gene list and calculates statistical significance values for each category. Moreover, GFINDer enables the functional classification of genes according to mined functional categories and the statistical analysis is of the classifications obtained, aiding better interpretation of microarray experiment results. GFINDer is available online at http://www.medinfopoli.polimi.it/GFINDer/.

Computational Biology↗

PubMed2004

Chief medical officer actions on information security in an Italian rehabilitation centre.

In a multi-speciality rehabilitation centre, where child neuropsychiatrists, neurologists, physical rehabilitators, psychologists, nurses, therapists and other health care professionals actively care for patients, the moment will arrive when information security takes high priority on the chief medical officer (CMO) agenda. This has happened at the La Nostra Famiglia Institution. Local push to high priority arose from several concurrent forces, like privacy both on the patient and on the doctor side, legal and ethical aspects. Recommendations on the protection of medical data require appropriate technical and organisational measures to be taken to protect personal data against unauthorised access, alterations or any other form of inappropriate processing. In the same time quick and easy access to patient information should be granted to authorised personnel to ensure proper and in time treatment of patients. A long lasting sequence of co-operative negotiation meetings between the CMO and the chief information officer (CIO) led to appropriate outline of policies. We developed a suitable and modular architecture for designing systems that can simultaneously manage an increasing number of healthcare actors, objects and related access levels taking into account temporal conditions. Actions for keeping the prototype in use on an everyday basis are directly taken by the CMO.

Access to Information↗

PubMed2004

Information security concepts and practices: the case of a provincial multi-specialty hospital.

In recent years, major and widely accepted information security understandings and achievements confirm that the problem is complex. They clarify that technologies are fundamental tools, but management processes have even bigger relevance, as also prestigious international magazines dossier clearly explained recently. Such a magazine attention outlines the wide impact that the subject has on watchful decision makers. ISO17799 is an emerging standard in information security. In principle there are no reasons for considering it not applicable to the health care sector. In practice, because of both the just conceptual level of the standard and the peculiarities of the health care data and institutions, a lot of analysis and design work need to be invested any time a health care institution decides to deal with the subject. CEN/ENV 12924 is another emerging standard certainly more on the spot of the health care. Nevertheless, it also asks for evident further investigation. The practical case of information security design, implementation, management, and auditing inside a multi-specialty provincial Italian hospital will be described.

Computer Security↗

PubMed2004

A knowledge management system for new drug submission by pharma-industries.

The pharma-industries are facing a number of crucial business issues to improve operational excellence in product time-to-market and wide regulatory compliance. These organizations own, produce, and manipulate a lot of knowledge. The new regulations by Health Authorities (HA) to pharma-industries should make the content and format of new drug application uniform worldwide. In this paper we suggest a novel approach of a pharma-industry to capture, process, and transmit clinical data electronically. The approach begins with an analysis of the knowledge generation points, some of them being outside the company. Implementations are grounded on the use of a de facto standard platform being Microsoft, having acceptable cost levels. The proposed infrastructure is integrated into existing company environment and technological platform, minimizing cost and risks, but improving efficiency and efficacy of new drug dossier compilation.

Drug Approval↗

PubMed2004

A 3D interactive multimodal viewer as data mining tool for the Visible Human Dataset color image histograms.

An on-line virtual three-dimensional immersive environment to navigate through colorimetric characterization of the Visible Human Dataset (VHD) cryosectional cross-section color images is introduced. Real-time analysis of color component characteristics of a user defined set of VHD images is now possible. This is a potentially useful resource to many developers working on the VHD raw data, however it could be used in medical education.

Female↗

PubMed2004

BIRD: Bio-Image Referral Database. Design and implementation of a new web based and patient multimedia data focused system for effective medical diagnosis and therapy.

This paper presents a low cost software platform prototype supporting health care personnel in retrieving patient referral multimedia data. These information are centralized in a server machine and structured by using a flexible eXtensible Markup Language (XML) Bio-Image Referral Database (BIRD). Data are distributed on demand to requesting client in an Intranet network and transformed via eXtensible Stylesheet Language (XSL) to be visualized in an uniform way on market browsers. The core server operation software has been developed in PHP Hypertext Preprocessor scripting language, which is very versatile and useful for crafting a dynamic Web environment.

Database Management Systems↗

PubMed2004

Speak-eR: an audible web-based medical record for emergency patients.

Emergency conditions can inhibit the use of clinical data, even when it has been professionally collected and structured. Our aim is to improve the assessment of patients' medical histories in emergency situations. Under emergency conditions, when it may be impractical for health care providers to interact with a visual display of patient data, a "speaking" medical record may be useful. We are investigating the use of a voice synthesizer in conjunction with MyAngelWeb, an Italian web-based medical record service. Only the textual subset of patient medical records was considered and restructured according to the needs imposed by voice communication. The quality of the received messages was tested. Some quantitative features, including the number of words and time durations, were considered together with other subjective features, including intelligibility of single words and overall significance of the voice messages. Provided that the linguistic architecture of a medical records' text is arranged to minimize the number of choices presented to the user, and phrases are kept short with few acronyms, health care providers can satisfactorily interact with the service.. Audible medical record delivery may be considered as an effective enhancement to those datasets needed in emergencies.

Emergency Treatment↗

PubMed2004

Gene ontology application to genomic functional annotation, statistical analysis and knowledge mining.

While a massive amount of biomolecular information is increasingly accumulating in different databanks, on the other hand high-throughput technologies are generating a great quantity of data that need to be annotated with the genomic information available, and interpreted. To this aim, the use of specific ontologies can greatly help either in integrating different information stored within heterogeneous databanks, or in identifying and clustering sequence data sharing common characteristics. In the molecular biology domain, the Gene Ontology (GO) is the most developed and widely used ontology. To demonstrate its great utility in the annotation and biological interpretation of gene sets obtained by means of high-throughput experiments, we implemented the web application here described. It enables functional annotations of a given gene set on a genomic scale and across different species. Within our application the annotations provided by the GO vocabulary allow either to easily bind several information from different resources, or to cluster annotated genes according to their biological characteristics. Through the GO structure it is also possible to represent biological concepts with different specificity levels, from very general to very precise concepts. Furthermore, the statistical evaluation of the categorizations provided by the GO annotations enables to highlight the most significant biological characteristics of a gene set, and therefore to mine knowledge from data. Our created tool meets the need to manage a vast quantity of biological data with a simple user interface adapt also for users with limited informatics knowledge, leading them to evaluate the functional significance of experiment's results with graphical views and statistical indexes in a well-known web browser user interface.

Genomics↗