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PubMed2003

Predicting the carcinogenic potential of pharmaceuticals in rodents using molecular structural similarity and E-state indices.

MDL QSAR (formerly SciVision QSAR IS) software is one of the several software systems under evaluation by the Informatics and Computational Safety Analysis Staff (ICSAS) of the FDA Center for Drug Evaluation and Research for regulatory and scientific decision support applications. MDL QSAR software contains an integrated set of tools for similarity searching, compound clustering, and modeling molecular structure related parameters that includes 240 electrotopological E-state, connectivity, and other descriptors. These molecular descriptors can be statistically correlated with toxicological or biological endpoints. The goal of this research was to evaluate the feasibility of using MDL QSAR software to develop structure-activity relationship (SAR) models that can be used to predict the carcinogenic potential of pharmaceuticals and organic chemicals. A validation study of 108 compounds that include 86 pharmaceuticals and 22 chemicals that were not present in a control rodent carcinogenicity data set of 1275 compounds demonstrated that MDL QSAR models had excellent coverage (93%) and good sensitivity (72%) and specificity (72%) for rodent carcinogenicity. The software correctly predicted 72% of non-carcinogenic compounds and compounds with carcinogenic findings. E-state descriptors contributed to more than half of the SAR models used to predict carcinogenic activity. We believe that electrotopological E-state descriptors and QSAR IS (MDL QSAR) software are promising new in silico approaches for modeling and predicting rodent carcinogenicity and may have application for other toxicological endpoints.

Algorithms↗
PubMed1994

Data driven medical decision support based on Arden Syntax within the HELIOS environment.

Methods and tools for development of data driven decision support systems (DSSs) is an integral part of the HELIOS software engineering environment. The DSS development environment includes tools for knowledge acquisition and knowledge base construction, provides trigger mechanisms for evocation of the knowledge base and an inference engine for execution control of appropriate parts of the knowledge base during run-time. The tools are part of the HELIOS service components and are integrated within the HELIOS communication framework. The work is based on the Arden Syntax, a standard for knowledge representation, allowing medical logic modules (MLMs) to be shared and transferred between institutions.

Artificial Intelligence↗
PubMed2004

Removing a barrier to computer-based outbreak and disease surveillance--the RODS Open Source Project.

INTRODUCTION: Computer-based outbreak and disease surveillance requires high-quality software that is well-supported and affordable. Developing software in an open-source framework, which entails free distribution and use of software and continuous, community-based software development, can produce software with such characteristics, and can do so rapidly. OBJECTIVES: The objective of the Real-Time Outbreak and Disease Surveillance (RODS) Open Source Project is to accelerate the deployment of computer-based outbreak and disease surveillance systems by writing software and catalyzing the formation of a community of users, developers, consultants, and scientists who support its use. METHODS: The University of Pittsburgh seeded the Open Source Project by releasing the RODS software under the GNU General Public License. An infrastructure was created, consisting of a website, mailing lists for developers and users, designated software developers, and shared code-development tools. These resources are intended to encourage growth of the Open Source Project community. Progress is measured by assessing website usage, number of software downloads, number of inquiries, number of system deployments, and number of new features or modules added to the code base. RESULTS: During September--November 2003, users generated 5,370 page views of the project website, 59 software downloads, 20 inquiries, one new deployment, and addition of four features. CONCLUSIONS: Thus far, health departments and companies have been more interested in using the software as is than in customizing or developing new features. The RODS laboratory anticipates that after initial installation has been completed, health departments and companies will begin to customize the software and contribute their enhancements to the public code base.

Disease Outbreaks↗
PubMed1995

Multi-national, multi-lingual, multi-professional CATs: (Curriculum Analysis Tools).

A consortium of dental schools and allied dental programs was established in 1991 with the expressed purpose of creating a curriculum database program that was end-user modifiable [1]. In April of 1994, a beta version (Beta 2.5 written in FoxPro(TM) 2.5) of the software CATs, an acronym for Curriculum Analysis Tools, was released for use by over 30 of the consortium's 60 member institutions, while the remainder either waited for the Macintosh (TM) or Windows (TM) versions of the program or were simply not ready to begin an institutional curriculum analysis project. Shortly after this release, the design specifications were rewritten based on a thorough critique of the Beta 2.5 design and coding structures and user feedback. The result was Beta 3.0 which has been designed to accommodate any health professions curriculum, in any country that uses English or French as one of its languages. Given the program's extensive use of screen generation tools, it was quite easy to offer screen displays in a second language. As more languages become available as part of the Unified Medical Language System, used to document curriculum content, the program's design will allow their incorporation. When the software arrives at a new institution, the choice of language and health profession will have been preselected, leaving the Curriculum Database Manager to identify the country where the member institution is located. With these 'macro' end-user decisions completed, the database manager can turn to a more specific set of end-user questions including: 1) will the curriculum view selected for analysis be created by the course directors (provider entry of structured course outlines) or by the students (consumer entry of class session summaries)?; 2) which elements within the provided course outline or class session modules will be used?; 3) which, if any, internal curriculum validation measures will be included?; and 4) which, if any, external validation measures will be included. External measures can include accreditation standards, entry-level practitioner competencies, an index of learning behaviors, an index of discipline integration, or others defined by the institution. When data entry, which is secure to the course level, is complete users may choose to browse a variety of graphic representations of their curriculum, or either preview or print a variety of reports that offer more detail about the content and adequacy of their curriculum. The progress of all data entry can be monitored by the database manager over the course of an academic year, and all reports contain extensive missing data reports to ensure that the user knows whether they are studying complete or partial data. Institutions using the beta version of the program have reported considerable satisfaction with its functionality and have also offered a variety of design and interface enhancements. The anticipated release date for Curriculum Analysis Tools (CATs) is the first quarter of 1995.

Curriculum↗
PubMed1990

PRIST: a fourth-generation tool for medical information systems.

PRIST is a fourth-generation software package purposely oriented to development and management of medical applications, running under MS/DOS IBM compatible personal computers. The tool has been developed on the top of DBIII Plus language utilizing the Clipper Compiler networking features for the integration in a LAN environment. Several routines written in C and BASIC Microsoft languages integrated this DBMS-kernel system providing I/O, graphics, statistics, retrieval utilities. To increase the interactivity of the system both menu-driven and windowing interfaces have been implemented. PRIST has been utilized to develop a wide variety of small medical applications ranging from research laboratories to intensive care units. The great majority of reactions from the use of these applications were positive, confirming that PRIST is able to assist in practice management and patient care as well as research purposes.

Hospital Information Systems↗
PubMed2003

Evaluation of dietary assessment instruments in adolescents.

PURPOSE OF REVIEW: The obesity epidemic, the increasing occurrence of adult diseases in childhood, and the growing awareness of a connection between adult diseases and the diet of children and adolescents have led to increased interest in what our youth are eating. Designing an instrument to evaluate adolescents' eating habits requires addressing not only the typical requirements for a diet assessment tool but also the unique concerns of the adolescent population. We reviewed current dietary instruments for adolescents. RECENT FINDINGS: New nutrient assessment methods fall into one of two groups: instruments limited to a specific nutrient/food or those designed for a specific population. The new tools range from Food Intake Recording Software System, a computer program to assist individuals under 10 years of age in reporting their diets, to short food-frequency questionnaires specifically designed to assess fruits and vegetables or fat. Another new instrument uses picture cards to evaluate the entire diet of low-income, overweight African-Americans. The Youth Adolescent Questionnaire, although not a new tool, has been evaluated in new populations (multi-ethnic, multi-income, and multi-education) and with doubly labeled water. SUMMARY: A limited number of dietary assessment instruments that are specifically designed for adolescents have been found to be reproducible and validated. There is a demand for a short, easily administered, inexpensive, accurate instrument that can be used in a broad range of adolescent subpopulations. Future tools will need to meet these criteria and evaluate the 'new' nutrients, foods, and other factors that lead our youth to eat the foods they do.

Adolescent↗
PubMed2004

CAAT-Box, Contigs-Assembly and Annotation Tool-Box for genome sequencing projects.

MOTIVATION: Contigs-Assembly and Annotation Tool-Box (CAAT-Box) is a software package developed for the computational part of a genome project where the sequence is obtained by a shotgun strategy. CAAT-Box contains new tools to predict links between contigs by using similarity searches with other whole genome sequences. Most importantly, it allows annotation of a genome to commence during the finishing phase using a gene-oriented strategy. For this purpose, CAAT-Box creates an Individual Protein file (IPF) for each ORF of an assembly. The nucleotide sequence reported in an IPF corresponds to the sequence of the ORF with 500 additional bases before the ORF and 200 bases after. For annotation, additional information like Blast results can be added or linked to the IPFs as well as automatic and/or manual annotations. When a new assembly is performed, CAAT-Box creates new IPFs according to the old IPF panel. CAAT-Box recognizes the modified IPFs which are the only ones used for a new automatic analysis after each assembly. Using this strategy, the user works with a group of IPFs independently of the closure phase progression. The IPFs are accessible by a web server and can therefore be modified and commented by different groups. RESULT: CAAT-Box was used to obtain and to annotate several complete genomes like Listeria monocytogenes or Streptococcus agalactiae. AVAILABILITY: The program may be obtained from the authors and is freely available to non-profit organisations.

Algorithms↗
PubMed1998

Broadsheet number 46: Internet for pathologists.

The Internet, and its most user-friendly manifestation, the World Wide Web (WWW), has undergone an exponential growth in the last few years. The volume of medical and pathology related information available has kept pace, making the Internet invaluable tool for the practising pathologist, supplementing traditional hard-copy textbooks and professional journals. E-mail, newsgroups, mailing lists, access to libraries, Medline, atlases, case studies and tutorials are only some of the additional features to which the net offers rapid access from your work-station. To make optimal use of electronic resources, a basic understanding of the hardware, software, communication protocols and information retrieval tools underlying the Internet is desirable. This paper is intended only as a brief introduction to what the Net has to offer to pathology in particular, and medicine in general, it is not meant to supplement the many excellent and more detailed reviews already available (see references). Parallel with the information explosion on the Net, concerns for the quality of posted material and possibility of misinformation have arisen. These issues will be addressed. Website addresses are given in parentheses in the text [e.g.: the website address of the Royal College of Pathologists of Australasia (RCPA) is given as (http:/(/)www.rcpa.edu.au/)] for easy retrieval on your Web browser. Because of the constantly evolving nature of the Web, I apologise in advance if some of the listed sites are no longer current.

Australia↗
PubMed2005

[Electronic surveillance of nosocomial infections in head and neck surgery and stapes surgery].

BACKGROUND: Nosocomial infection is generally regarded as the most important postoperative complication. Therefore, on 28 December 2002 a German law was implemented requiring the surveillance of postoperative infections in all hospitals. METHODS: The authors propose using stapes and thyroid surgery to monitor the infection rate in a typical Head and Neck Department. A versatile software (CISS) based on MS Word and MS Excel was developed for this purpose. RESULTS: Postoperative infections were retrospectively analyzed for three subsequent years. The present data confirm the results of previous studies that surveillance itself is a powerful tool in reducing the postoperative infection rate. CONCLUSION: The newly developed software provided an easy tool for the collection of infection data. The reported infection rates in stapes and thyroid surgery are representative of ENT clinics in Germany.

Cross Infection↗
PubMed1992

Application of an essential data set based computer system in support of maternal and child care.

A simple functional application software has been developed to support care providers in information management related to perinatal care activities, family planning encounters and the immunization of infants. This was distributed to some sites and was implemented with no organizational change, though the methods differed. An early assessment of the software after a period of implementation is made based on the observations and experiences reported. This is presented in a framework outlined earlier as the OUST model. The systems objective to enhance the value of information was observed to have been partially achieved. The utility to the users is observed in the ability of the end-users at the sites to identify the local community needs and adopt accordingly suitable strategies. The social impact was seen in the assistance provided by the sentinel action of the system in tracking dropouts from the immunization programme at a site, thereby ensuring quality in care and also economic benefits. From a technical standpoint, the application software was small yet functional and in it were incorporated features that ensured data quality. The application software was designed to generate a unique identity code to assist in follow-up of the target population. Based on the data entered it compiled reports to meet administrative requirements, reports that gave the care providers feedback and lists to coordinate in the follow-up of the target population. The application software is a common data collection tool that can assist in building a data registry for health outcomes research.

Adult↗
PubMed2005

A web-based tool for principal component and significance analysis of microarray data.

UNLABELLED: We have developed a program for microarray data analysis, which features the false discovery rate for testing statistical significance and the principal component analysis using the singular value decomposition method for detecting the global trends of gene-expression patterns. Additional features include analysis of variance with multiple methods for error variance adjustment, correction of cross-channel correlation for two-color microarrays, identification of genes specific to each cluster of tissue samples, biplot of tissues and corresponding tissue-specific genes, clustering of genes that are correlated with each principal component (PC), three-dimensional graphics based on virtual reality modeling language and sharing of PC between different experiments. The software also supports parameter adjustment, gene search and graphical output of results. The software is implemented as a web tool and thus the speed of analysis does not depend on the power of a client computer. AVAILABILITY: The tool can be used on-line or downloaded at http://lgsun.grc.nia.nih.gov/ANOVA/

Algorithms↗
PubMed2005

[Development of high speed UV-Vis spectrophotometer].

A high speed spectrophotometer based on a linear CCD was developed. The function and structure of the hardware and the software for the instrument were discussed. The elementary performance was tested as follows: wavelength range 200-820 nm, full spectrum scan time < 0.1 s, spectral bandwidth 0.7 nm, wavelength accuracy +/-1 nm, photometric accuracy +/- 0.005 AU, baseline flatness < 0.001 AU (rms), and stray light < 0.1%. Results showed that this instrument is easy to use, fast and with high analytical performance. In addition, it has internet function of remote control and remote access. With the powerful data processing and spectrum analyzing software, it will provide a strong tool for routine analysis and the research on dynamic reaction in chemistry and biology fields.

Equipment Design↗
PubMed2004

Micellar electrokinetic capillary chromatography and data alignment analysis: a new tool in urine profiling.

The complex nature of biofluids demands efficient, sensitive and high-resolution analytical methodologies to examine how the 'metabolic fingerprint' changes during disease. This paper describes how sulphated beta-cyclodextrin-modified micellar electrokinetic capillary chromatography (SbetaCD-MECC) has been combined with data alignment analysis and may prove a useful new tool in urine profiling, allowing for separation of over 80 urinary analytes in under 25 min. The optimised and validated SbetaCD-MECC methodology combined with data alignment analysis provides rapid identification of 'mismatches' between urine profiles which are not easily detected with the naked eye as well as a 'similarity score' which indicates the total sum of differences between one profile and another. The combination of SbetaCD-MECC with data alignment software should prove a useful alternative tool in metabonomic studies for rapid comparison of urine profiles.

Acetaminophen↗
PubMed2002

Does pornography-blocking software block access to health information on the Internet?

CONTEXT: The Internet has become an important tool for finding health information, especially among adolescents. Many computers have software designed to block access to Internet pornography. Because pornography-blocking software cannot perfectly discriminate between pornographic and nonpornographic Web sites, such products may block access to health information sites, particularly those related to sexuality. OBJECTIVE: To quantify the extent to which pornography-blocking software used in schools and libraries limits access to health information Web sites. DESIGN AND SETTING: In a simulation of adolescent Internet searching, we compiled search results from 24 health information searches (n = 3206) and 6 pornography searches (n = 781). We then classified the content of each site as either health information (n = 2467), pornography (n = 516), or other (n = 1004). We also compiled a list of top teen health information sites (n = 586). We then tested 6 blocking products commonly used in schools and libraries and 1 blocking product used on home computers, each at 2 or 3 levels of blocking restrictiveness. MAIN OUTCOME MEASURE: Rates of health information and pornography blocking. RESULTS: At the least restrictive blocking setting, configured to block only pornography, the products blocked a mean of only 1.4% of health information sites. The differences between blocking products was small (range, 0.6%-2.3%). However, about 10% of health sites found using some search terms related to sexuality (eg, safe sex, condoms) and homosexuality (eg, gay) were blocked. The mean pornography blocking rate was 87% (range, 84%-90%). At moderate settings, the mean blocking rate was 5% for health information and 90% for pornography. At the most restrictive settings, health information blocking increased substantially (24%), but pornography blocking was only slightly higher (91%). CONCLUSIONS: Blocking settings have a greater impact than choice of blocking product on frequency of health information blocking. At their least restrictive settings, overblocking of general health information poses a relatively minor impediment. However, searches on some terms related to sexuality led to substantially more health information blocking. More restrictive blocking configurations blocked pornography only slightly more, but substantially increased blocking of health information sites.

Access to Information↗
PubMed2004

Going soft and SAD with manganese.

SAD phasing has been revisited recently, with experiments being carried out using previously unconventional sources of anomalous signal, particularly lighter atoms and softer X-rays. A case study is reported using the 75 kDa RNA-dependent RNA polymerase of the bacteriophase phi6, which binds a Mn atom and crystallizes with three molecules in the asymmetric unit. X-ray diffraction data were collected at a wavelength of 1.89 A and although the calculated anomalous signal from the three Mn atoms was only 1.2%, SHELXD and SOLVE were able to locate these atoms. SOLVE/RESOLVE used this information to obtain SAD phases and automatically build a model for the core region of the protein, which possessed the characteristic features of the right-hand polymerase motif. These results demonstrate that with modern synchrotron beamlines and software, manganese phasing is a practical tool for solving the structure of large proteins.

Amino Acid Motifs↗
PubMed1995

Human posture in microgravity: an experiment on EUROMIR '95 to verify and improve a simulation tool.

An anthropometric mannequin implemented in robotic modelling software has proved very useful in the simulation of static and semi-dynamic reachability envelopes. Its prediction of working postures has been verified to some extent during neutral buoyancy trials. While a robotic solution is useful for static analyses or rough estimates of simple movements, more realistic movement strategies need to be identified directly measuring astronauts' in-orbit behaviour. A set of experiments is to be performed as part of the EUROMIR '95 mission to the MIR orbiting station in which dynamic posture (i.e. posture and movement) measurements will be taken using the ELITE system. The data and analyses of the data will be used to animate the Alenia anthropometric mannequin and to develop movement algorithms more similar to those of a person in microgravity than the robotic solutions currently employed. This paper presents the experiments to be performed and the changes to Alenia's mannequin that will allow the model to effect movements according to the experimental results. It is aimed at expanding the dialog between the biomechanical and human factors disciplines started in this experiment to other potential end-users of the experimental results.

Adaptation, Physiological↗
PubMed2005

Randomised studies in general practice: how to integrate the electronic patient record.

The 'randomised database study' strategy was first proposed in 1997, with the aim of combining the generalisability of observational database studies based on electronic patient records (EPRs) with the validity of randomised clinical trials (RCTs). The key feature was to randomly assign treatments and to use routine care data, as available in the observational database, for patient identification and follow-up. To our knowledge, however, the idea of the randomised database study has not been implemented yet. The conduct of a randomised study in an observational database requires adjustments to methods of medical information processing in the general practice. We developed a software system that facilitates the conduct of an RCT with observational databases based on EPRs. It identifies eligible subjects and presents them one by one to the physician once their EPR is accessed. The general practitioner can then start an interactive recruitment process; after completion, the computer randomises the patients. Follow-up is documented by normal routine care in the EPR. Although the randomised database study has many methodological advantages, it has never been tested. Our software system is meant as a tool to implement and facilitate evaluation of the randomised database approach.

Data Collection↗
PubMed2000

A closed-loop model of the canine cardiovascular system that includes ventricular interaction.

A closed-loop model of cardiopulmonary circulation has been developed for the study of right-left ventricular interaction under physiologically normal and altered conditions. The core model provides insight into the effects of ventricular interaction and pericardial mechanics on hemodynamics. The complete model contains realistic descriptions of (a) the interacting ventricular free walls and septum, (b) the atria, (c) the pericardium, and (d) the systemic and pulmonary vascular loads. The current analysis extends previous work on ventricular interaction and pericardial influence under isolated heart conditions to loading conditions imposed by a closed-loop model of the circulation. A nonlinear least-squares parameter identification method (Levenberg-Marquardt algorithm) is used, together with parameter sensitivity analysis, to estimate the values of key parameters associated with the ventricular and circulation models. Pressure measurements taken at several anatomical locations in the circulation during open-chest experiments on dogs are used as data in the identification process. The complete circulatory model, including septal and pericardial coupling, serves as a virtual testbed for assessing the global affects of localized mechanical or hemodynamic alterations. Studies of both direct and series ventricular interaction, as well as the effect of the pericardium on cardiac performance, are accomplished with this model. Alterations in model parameter values are used to predict the impact of disease and/or clinical interventions on steady-state hemodynamic performance. Additionally, a software package titled CardioPV has been developed to integrate the complete model with data acquisition tools and a sophisticated graphical user interface. The complete software package enables users to collect experimental data, use the data to estimate model parameters, and view the model outputs in an online setting.

Animals↗