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Process development chemists can search for information on reactions from a variety of reaction databases. Niche databases are often available locally, whereas comprehensive databases are available online. This review surveys the current state of electronic reaction databases and their use by process chemists.
This article describes a generic model for access to samples and information in human genetic databases. The model utilises a "GeneTrustee", a third-party intermediary independent of the subjects and of the investigators or database custodians. The GeneTrustee model has been implemented successfully in various community genetics screening programs and has facilitated research access to genetic databases while protecting the privacy and confidentiality of research subjects. The GeneTrustee model could also be applied to various types of non-conventional genetic databases, including neonatal screening Guthrie card collections, and to forensic DNA samples.
Two important databases are often used in HIV genetic research, the HIV Sequence Database in Los Alamos, which collects all sequences and focuses on annotation and data analysis, and the HIV RT/Protease Sequence Database in Stanford, which collects sequences associated with the development of viral resistance against anti-retroviral drugs and focuses on analysis of those sequences. The types of data and services these two databases offer, the tools they provide, and the way they are set up and operated are described in detail.
AIM: To establish the whole rDNA ITS region sequence database of various Dendrobium species of "Fengdou" and to authenticate exactly the inspected species of "Fengdou". METHODS: The rDNA ITS regions of various Dendrobium species of "Fengdou" were amplified and sequenced. The database of their rDNA ITS regions was established in order to authenticate the inspected species by means of the softwares of CLUSTRAL and MEGA which were used to analyze the rDNA ITS region. RESULTS: A database of the rDNA ITS sequences of 21 species of Dendrobium has been established. The notable and stable differences of the interspecies of the rDNA ITS regions have been demonstrated. The numbers of transitions and transversions among 21 species are 11-122. The variable sites are 341 while the informative sites are 195. The ITS sequence differences between the outgroup species (Pholidota yunnanensis) and species of "Fengdou" are obvious. The numbers of transitions and transversions are 131-161. The population differences of the rDNA ITS region of various species of "Fengdou" are very small (0-6). CONCLUSION: On the basis of the database of various Dendrobium species of "Fengdou" and two genetics software, the botanical origin of the inspected species of "Fengdou" has been authenticated successfully by sequencing the rDNA ITS regions.
PURPOSE: We analyzed the frequency and content of journal reports on medical accidents over the past 15 years, and compared these findings with related articles in daily newspapers as a means of assessing medical professionals' awareness of current public opinion reflected in daily newspaper coverage. METHODS: A search of medical accident reports was conducted using CD-ROM versions of the medical literature database Japana Centra Revuo Medicina (1987-2001), with the key words "medical accident" and "medical error." The numbers of medical accident articles in newspapers and medical lawsuits were taken as indicators of public opinion. Relationships were investigated using correlation and time series analyses. RESULTS: 1) The total number of reports on medical accidents (including medical errors; hereinafter, medical accident reports) in the database was 2,858, equaling 0.78 medical accident reports for each 1,000 reports in the CD-ROM database. 2) The number of medical accident reports was 174 in 1987, gradually increasing to 333 in 2000 and 618 in 2001. 3) The proportion of the reports from the nursing field increased from 8.9% (1989) to 31.7% (1999). In contrast, the proportion concerning the medical field decreased from 68.8% to 50.2%. 4) The number of medical accident articles in two newspapers was investigated. The yearly trends were similar in both of these newspapers, showing an increase in 1999 and a peak in 2000. 5) A review of Supreme Court records revealed that the number of medical lawsuits each year increased gradually from 352 in 1990 to 805 in 2001. 6) There were significant correlations between the number of medical accident reports and the numbers of newspaper articles or medical lawsuits. A time series analysis of these trends showed that the trend in number of medical accident reports was closely linked with those for numbers of newspaper articles and medical lawsuits, with a time lag. CONCLUSION: Research trends in papers on medical accidents from a database of scientific papers were found to correspond with trend curves for medical lawsuits and articles on medical accidents in daily newspapers. It was thus demonstrated that awareness of medical accidents among medical professionals reflects social emphasis.
In the computer vision domain, content-based access methods to all forms of multimedia data are a hot research topic. A large number of tools have been developed to find documents in multimedia repositories and to manage the (visual) information that has been created, for example by the Internet. Although no general breakthrough has been achieved with respect to searching diverse databases with automatically extracted features, the techniques have gained acceptance in a few well-defined domains such as image agencies (Corbis) and trademark research. In the medical domain, the number of digital images produced and used for teaching, diagnostics and therapy is rising in a similar way as in other domains. Still, there are only a few image retrieval systems that use automatically extracted visual features for content-based access to medical image databases. This article describes the use of an open source image retrieval system (GIFT) that has been adapted for the use with medical images using the image case database CasImage that has been developed and maintained by the University Hospital of Geneva and that is in routine use. The first results show the potential of this technique to retrieve similar cases from a case database. This is an important task for teaching and might also become important for diagnostics using case-based reasoning, for example. For the use as a diagnostic tool, it is foreseen to specialize the visual features for the domain of lung image retrieval, using high resolution computed tomography (HRCT) images.
Development and evaluation of Intensive Care Unit (ICU) decision-support systems would be greatly facilitated by the availability of a large-scale ICU patient database. Following our previous efforts with the MIMIC (Multi-parameter Intelligent Monitoring for Intensive Care) Database, we have leveraged advances in networking and storage technologies to develop a far more massive temporal database, MIMIC II. MIMIC II is an ongoing effort: data is continuously and prospectively archived from all ICU patients in our hospital. MIMIC II now consists of over 800 ICU patient records including over 120 gigabytes of data and is growing. A customized archiving system was used to store continuously up to four waveforms and 30 different parameters from ICU patient monitors. An integrated user-friendly relational database was developed for browsing of patients' clinical information (lab results, fluid balance, medications, nurses' progress notes). Based upon its unprecedented size and scope, MIMIC II will prove to be an important resource for intelligent patient monitoring research, and will support efforts in medical data mining and knowledge-discovery.
Early in their study it was recognized that the genes encoding the HLA molecules were highly polymorphic and that there was a need for a systematic nomenclature. The result was the WHO Nomenclature Committee for Factors of the HLA System, which first met in 1968, and laid down the criteria for successive meetings. This committee meets regularly to discuss issues of nomenclature and has published 16 major reports documenting firstly the HLA antigens and more recently the genes and alleles. The standardization of HLA antigenic specificities has been controlled by the exchange of typing reagents and cells in the International Histocompatibility Workshops. Since 1989 when a large number of HLA allele sequences were first analysed and named, the job of curating and maintaining a database of sequences has been of prime importance. In 1998 the IMGT/HLA database became the official repository for HLA sequences. In addition to the nucleotide and protein sequences the database contains information of the cell from which the sequence was obtained. The database which provides tools for sequence analysis and the submission of new data, is updated quarterly and now contains over 1500 HLA allele sequences.
One of the more difficult tasks of informatics is allowing for the navigation of complex databases. At Partners Healthcare Inc. we have developed an analytical database to allow for searching clinical data to obtain cohorts of patients for research studies. The characteristics of the patients within the cohorts must often comply with complex inclusion and exclusion criteria. The users of the database are research clinicians, often with no prior database experience. To assist these clinicians in finding their patient cohorts, we constructed a Querytool that they use directly to find their desired populations. In order to understand if the Querytool could indeed be used successfully by novice users, we analyzed the first 10 queries of 219 users. This analysis was able show that novice users are able to achieve excellent success using the Querytool
BACKGROUND/AIMS: The purpose of this study was to extend previous publications and examine the Vaccine Adverse Events Reporting System (VAERS) database for the incidence of gastrointestinal reactions reported following tetra-valent rhesus-human reassortant rotavirus vaccine (RRV-TV). METHODOLOGY: The VAERS database was analyzed for adverse reactions reported for the entire year of 1999 following RRV-TV using Microsoft Access. In this study, the incidence rates of adverse reactions reported to VAERS following acellular diphtheria, pertussis and tetanus (DTaP) vaccine, whole-cell DTP vaccine, live polio (OPV) vaccine and pediatric hepatitis B vaccine were used as control vaccine groups. RESULTS: The results of a chi-square analysis showed that rotavirus vaccine was statistically significantly over represented by serious gastrointestinal reactions in comparison to vaccine control groups. CONCLUSIONS: This analysis demonstrated that the VAERS database provides a way to detect whether RRV-TV elevates the risk of adverse reactions compared to control vaccines given to similar age groups when appropriate denominators (number of annual doses given) are employed. Because of its massive size and the availability of numerous vaccine control groups, the VAERS database provides data on adverse reactions following vaccination that is available nowhere else.
PURPOSE: To summarize the basic requirement of cephalometric analysis and database product concluded from practice, and apply related products to improve the levels of medical treatment, teaching and scientific research. METHODS: By the use of digital X ray machine, digital camera, oral endoscope,scanner to import the image into system database, to edit, measure, make diagram, analyze and store the images, to catalog diagnosis according to the different need of patient to make convenient for retrieving by group, to design multi-page electronic case report including oral general diagram, the result of diagnosis cataloging, the result diagram of analysis, picture and text report, all of the above mentioned constitute a complete patient database system. RESULTS: About 400 medical case were accumulated, and these improved evidently the effect to present the production of medical treatment to potential patients, were convenient to the professional communication between doctors and conformation of treatment plan, provided a solid foundation to multimedia teaching, and promoted the development of the task of graduate student and the task of scientific research. CONCLUSION: Using related product with perfect functions to develop standardized cephalometric analysis and build standardized patient's database including image information, when such information is accumulated to certain extent, will become the invaluable treasure of relevant medical institution, will bring the obvious effect to improve the level of medical treatment, teaching and scientific research.
OBJECTIVE: Our aim was to identify the level of knowledge of surgical health-area specialists in Cancún, Quintana Roo, Mexico, from the personal productivity database. MATERIAL AND METHODS: We carried out an investigation of 37 surgical specialists: 24 belonged to the Mexican Social Security Institute (IMSS), while 13 belonged to the Mexican Health Secretariat (SSA). RESULTS: In our research, we found that 61% of surgical health-area specialist physicians were familiar with some aspects of the institutional surgical registry, including the following: 54% knew of the existence of a personal registry of surgeries carried out, and 43% keep a record of their personal activities. From the latter percentage, 69% of surgical health-area specialist physicians mentioned keeping their records manually, while 44% used the computer. Results of the research suggest that these physicians would like to have some kind of record of the surgeries carried out by each. CONCLUSIONS: An important percentage of these specialists do not keep a personal record on a database; due to this lack of knowledge, we obtain incorrect information in institutional records of the reality of what is actually done. We consider it important to inform surgical specialists concerning the existence of personal institutional records in database form or even of record done manually, as well as correct terminology for the International Codification (CIE-9 & 10). We inform here of the need to encourage a culture in records and databases in the formative stage of surgeon specialists.
We present the knowledge organisation of a database, which aims to collect information for the project "Plants in European Masterpieces". This project is financed by the European Union within the Culture 2000 program. The project is aimed to link art with plants within the frame of a common European history and to make it accessible to a wide public. The informatics aspect of this project is focused on the creation of a data base which collects detailed information on selected plants and masterpieces in which these plants are presented. The main efforts in the design phase have been devoted to knowledge organisation in order to retain the taxonomic structure of the botanical knowledge, and to minimise data structure redundancies by linking some features which can be applied to the plants at different levels of their taxonomy to the correct level without repeating it. At present the database is installed in the Pc of all the experts that in the 5 involved countries collaborate to collect data for this project. This data is weekly merged in a central database, using a specific automatic procedure that avoids possible duplications of data inserted and checks for possible inconsistencies among data inserted in different temporal databases. The multi-language and easy to use features of this data base make it an interesting prototype for the spreading of scientific information to common public
To assist the interpretation of STR DNA typing results from forensic casework samples containing mixtures, the range of heterozygous allele peak height and peak area ratios (HR) and stutter percentages (stutter %) for the loci comprised in the AmpFlSTR Profiler Plus (PP) kit were assessed on 468 database and 275 casework single source samples. Stutter % medians were similar for database and casework samples, ranging from 2% to 7%. The upper limit of the stutter value range was 16%, calculated as median +3 SD, although lower locus-specific values could be used. HR medians were 93 +/- 6.5% for database samples, 88 +/- 12% for casework samples. For casework samples, the maximum signal imbalance noted was 52%, calculated as median -3 SD. No significant difference was observed between peak height and peak area calculated values. This study shows the importance of selecting the proper reference database for the establishment of HR threshold values.
INTRODUCTION: The lack of comparability of evaluation results is one of the major obstacles of research and development in Medical Image Processing (MIP). The main reason for that is the usage of different image datasets with different quality, size and Gold standard. OBJECTIVES: Therefore, one of the goals of the Working Group on Medical Image Processing of the European Federation for Medical Informatics (EFMI WG MIP) is to develop first parts of a Reference Image Database. METHODS: Kernel of the concept is to identify highly relevant medical problems with significant potential for improvement by MIP, and then to provide respective reference datasets. The EFMI WG MIP has primarily the role of a specifying group and an information broker, while the provider user relationships are defined by bilateral co-operation or license agreements. RESULTS: An explorative database prototype has been implemented using the MySQL database software on the Web. Templates for provider user agreements have been worked out and already applied for own 'pre-RID-MIP' co-operations of the authors. DISCUSSION AND CONCLUSION: First steps towards a comprehensive reference image database have been done. Issues like funding, motivation, management, provision of Gold standards and evaluation guidelines are to be solved. Due to the interest from research groups and industry the efforts will be continued.
Molecular chaperones are a wide group of unrelated protein families whose role is to assist others proteins. Comparably, under environmental stress, stress proteins behave as biocatalysts of protein stabilization. Stress proteins include a large class of proteins that were originally termed heat shock proteins (HSPs) due to their initial discovery in tissues exposed to elevated temperatures. Many, but not all, stress proteins and HSPs are molecular chaperones. Moreover, not all HSPs are derivable from stress. HSPs are structurally diversified by the contribution of various domains having specific roles. HSPs have been grouped, mainly on the basis of their molecular masses, into specific families that include small HSPs (sHSPs)/alpha-crystallins, HSP10s, HSP40s, HSP60s, HSP70s, HSP90s, HSP100s and HSP110s. The names of these major families are historical artefacts with limited information content. Using the current databases, names and proteic domains of many molecular chaperones in different species were analyzed. Although traditional names of HSPs are trivial, it is unrealistic to suggest replacing them, because they are preferred and widely used. Here we suggest that these traditional names be chaperoned, in silico, by a systematic nomenclature. Thus, for example, with the same intent of use of [trioxygen: O3] for ozone, we propose here C7HSP70[Ehsa]ER-P11021 for GRP78 (78 kDa endoplasmic Human molecular chaperone in HSP70 superfamily with P11021 as its accession number in the database of the National Center for Biotechnology Information (NCBI)). The proposed systematic computer-oriented naming and classification method is designed for HSPs and also their partners based on the number of amino acids, domain structure, phylogenetic domain, localization in the cell and accession number as stated in the NCBI. Arabidopsis thaliana was analyzed as a model, because it contains a large number of various HSPs localized in several organelles. Overall, this naming system helps in building, optimizing and managing a novel online database entirely devoted to HSPs. The purported taxonomy, coupled with the newly constructed database, can contribute to studies involving large amounts of stored data on HSPs.
OBJECTIVES: Building a database with the estimates of the observed populations of the Italian Cancer Registries (CR), subdivided into sex, annual age classes and calendar year; making this population database available in the AIRT website; making available an Excel file that allows the input of a population by 5-year age classes in order to obtain an esteem of the annual classes. DESIGN: Employment of different interpolation methods, namely annual age classes starting from 5-year classes, an esteem of the final open class of 85 years and over. PARTICIPANTS: 17 CRs that take part to the incidence and mortality trend study promoted by AIRT in 2003. SETTING: AIRT. MAIN OUTCOME: A database of the estimated populations observed by the CRs by sex and annual age classes on 31 December of each incidence year. RESULTS: Only for 6 on 17 CRs taking part in the AIRT trend terpolation methods have been used. The performance of these methods, tested with an empirical measure of error called WMISE, have given good results, even if in the elderly classes the fit is poor and sometimes not sufficient. CONCLUSIONS: Different interpolation methods have been used to build and make available a database containing reliable data of population, in order to use them as denominators for the incidence and mortality trend analysis. It is also available an Excel file that allows the input of a population by 5-year age classes in order to obtain an esteem of the annual classes.
Librarians have used bibliometrics for many years to assess collections and to provide data for making selection and deselection decisions. With the advent of new technology--specifically, CD-ROM databases and reprint file database management programs--new cost-effective procedures can be developed. This paper describes a recent multidisciplinary study conducted by two library faculty members and one allied health faculty member to test a bibliometric method that used the MEDLINE and CINAHL databases on CD-ROM and the Papyrus database management program to produce a new collection development methodology.