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PubMedDate not supplied

Design of a diagnostic encyclopaedia using AIDA.

Diagnostic Encyclopaedia Workstation (DEW) is the name of a digital encyclopaedia constructed to contain reference knowledge with respect to the pathology of the ovary. Comparing DEW with the common sources of reference knowledge (i.e. books) leads to the following advantages of DEW: it contains more verbal knowledge, pictures and case histories, and it offers information adjusted to the needs of the user. Based on an analysis of the structure of this reference knowledge we have chosen AIDA to develop a relational database and we use a video-disc player to contain the pictorial part of the database. The system consists of a database input version and a read-only run version. The design of the database input version is discussed. Reference knowledge for ovary pathology requires 1-3 Mbytes of memory. At present 15% of this amount is available. The design of the run version is based on an analysis of which information must necessarily be specified to the system by the user to access a desired item of information. Finally, the use of AIDA in constructing DEW is evaluated.

Computer Systems↗
PubMed1996

An evaluation of the TransFER model for sharing clinical decision-support applications.

TransFER is a formal model designed to facilitate the sharing of decision-support applications across institutions with heterogeneous clinical databases. The TransFER model provides a mechanism to automatically customize database queries based on a reference schema of clinical data and an encoded set of database mappings. In this paper, we describe the elements of the TransFER model and we present the results of a formal evaluation we conducted to assess the utility and generality of the model. The results suggest that the TransFER has significant potential for automating query translation and facilitating application sharing, but that further work on the representation of temporal semantics, on the modeling of missing data, and on the optimization of complex queries is required.

Decision Making, Computer-Assisted↗
PubMed1997

Development of computerized storage facilities for twin data: a relational database system for a twin register.

Many twin registers hold information on flat file systems such as those provided by statistical packages or spreadsheets. Demographic details may be maintained separately from data collected in multiple different studies, leading to considerable problems with data consistency, redundancy, and integration. Ad hoc requests may be difficult. Implementation of a relational database system permits storage and maintenance of all records, simple data entry and validation procedures, linking of information from different projects with security of access, and the flexibility to provide rapid answers to ad hoc enquiries using standard Structured Query Language (SQL). Twin data provide a challenge for relational database design which rests on the technique of normalization and the use of unique identifiers to access associated groups of variables; for twins, "uniqueness" must preserve identification of both the pair and the individual twin subjects in the data structure to enable flexible access to and analysis of the data. An application on the Institute of Psychiatry Volunteer Twin Register (IOPVTR) database is described, through reference to one study of a sample of the twins, with simulated data. We show how a balance of adherence to database design principles and attention to ongoing clerical and research procedures has been used to produce an integrated, flexible, and open-ended system.

Data Collection↗
PubMed1993

ENB--resource and careers department.

The English National Board for Nursing, Midwifery and Health Visiting is aware that, in the current climate of change, a range of information is required by nurses, midwives and health visitors to enable them to update their professional knowledge and plan their careers. In response to this need the Board offers a comprehensive range of services through the Resource and Careers Department based in Sheffield. I will describe in detail the services provided by the Resource Section and then give a brief overview of the role and functions of the other sections, i.e. Publications, Careers Service and Projects. The Resource Section comprises three separate but interactive parts. These are the Health Care Database, Open Learning Resource and Reference Room and ENB Campus.

Databases, Factual↗
PubMed1995

Estimation of reference change limits using patient data.

Two approaches for deriving reference change limits from patient data are described. In the direct method, hospital database information is used for the selection of appropriate reference groups. If database information is not sufficient or reliable enough, but still most of the source data can be considered as health-related, an indirect method can be applied in the calculation of rough estimates for reference change limits. A computer program developed by us, GraphROC for Windows, includes both methods for the estimation of change limits from patient data. Time between specimen collections should be included as one classifying factor in the selection of source data. When only one previous result is available for comparison, change limits based on the reference sample group form the only available guide for clinical interpretation. However, when several previous results are available and the within-subject variances for the considered analyte are known to be heterogeneous between individuals, the clinical interpretation should rather be based on application of time series analysis.

Data Interpretation, Statistical↗
PubMed1989

ERIC: a resource for researchers in nursing education.

This chapter provides information on the ERIC system of bibliographic information covering the field of education. Information on topics related to nursing and specifically to research in nursing education is presented. The number of references in these areas and in the ERIC database and the content of these references is described.

Bibliographies as Topic↗
PubMed2026

Long-read Sequences Mapped to a Complete Reference Genome Uncover Uncaptured Structural Variants across the Beta-globin Cluster in Africans with Sickle Cell Disease.

African genomes are marked by extensive complexity in the number and distribution of variants, yet remain under-represented in genetic databases and the human reference genome. This gap in representation limits the broad application of genomic medicine. Sickle cell disease (SCD) - one of the most common monogenic diseases - has its highest prevalence in Africa, and variation in disease severity has consistently been linked to the beta-globin locus, including levels of fetal hemoglobin (HbF). Modulation of HbF is central to current SCD gene therapies; however, the inherent complexity and variation at the locus in African genomes presents a challenge to translating these advances to Africa. Here, we align long-read single molecule sequences (LRS) targeted to the beta-globin region to the hg38 and T2T-CHM13v2 genome references in 40 individuals with SCD, predominantly recruited from three African countries. We demonstrate that the expanded T2T-CHM13v2 reference sequence at this locus reduces Structural Variant (SV) calls by 70% and uncovers uncaptured single nucleotide variants (SNVs). Across the cluster we report 343 SVs and 196 SNVs that have not been previously reported, including in LRS data from the All of Us project. By including African populations from ethnolinguistic groups that have not been previously surveyed we improve variant resolution and bolster evidence for observed variation. Finally, we identify a common ∼4kb insertion locus overlapping the HBB promoter among individuals with high HbF. These results demonstrate the utility of combining a comprehensive reference genome with LRS in African populations to uncover genomic variation at disease-associated loci.

SNV↗
PubMed2025

Characterization of microbial dark matter at scale with MetaSBT and taxonomy-aware Sequence Bloom Trees.

Metagenomics has become a powerful tool for studying microbial communities, allowing researchers to investigate microbial diversity within complex environmental samples. Recent advances in sequencing technology have enabled the recovery of near-complete microbial genomes directly from metagenomic samples, also known as metagenome-assembled genomes (MAGs). However, accurately characterizing these genomes remains a significant challenge due to the presence of sequencing errors, incomplete assembly, and contamination. Here we present MetaSBT, a new tool for organizing, indexing, and characterizing microbial reference genomes and MAGs. It is able to identify clusters of genomes at all seven taxonomic levels, from the kingdom all the way down to the species level, using the Sequence Bloom Tree (SBT) data structure that relies on Bloom Filters (BFs) to index massive amounts of genomes based on their k-mers composition. We have built an initial set of databases composed of over 190 thousand viral genomes from NCBI GenBank and public sources grouped into sequence consistent clusters at different taxonomic levels, making it the first software solution for the classification of viruses at different ranks, including still unknown ones. This results in the definition of over 40 thousand species clusters where ~80% do not match with any known viral species in reference databases to date. Furthermore, we show how our databases can be used as a new basis for existing quantitative metagenomic profilers to unlock the detection of unknown microbes and the estimation of their abundance in metagenomic samples. Finally, the framework is released open-source and, along with its public databases, is fully integrated into the Galaxy Platform enabling broad accessibility.

metagenome-assembled genomes↗
PubMed1992

'References'.

Explore the source record for details and available documents.

Databases, Bibliographic↗
PubMed1994

Dose-response assessment for developmental toxicity. I. Characterization of database and determination of no observed adverse effect levels.

Developmental toxicity risk assessment currently relies on the estimation of reference doses (RfDDTs) or reference concentrations (RfCDTS) based on the use of no observed adverse effect levels (NOAELs) and uncertainty factors. The benchmark dose (BMD) has been proposed as an alternative basis for reference value calculations. A large database of 246 developmental toxicity experiments (Segment II-type studies) representing 1825 data subsets for various endpoints was compiled for use in comparing NOAEL and BMD approaches to developmental toxicity risk assessment. This paper describes the characteristics of the database used and the estimation of NOAELs using several approaches. For each endpoint evaluated, two NOAELs were calculated using the NOSTASOT procedure (Tukey et al., 1985). The first NOAEL calculation, the QNOAEL, was based on a quantal response where a litter was defined as "affected" if one or more fetuses or implants in the litter had the endpoint of interest. The second NOAEL calculation, the CNOAEL, was based on the proportion of fetuses or implants affected within each litter and was treated as a continuous response variable. Fifty-seven percent of the 246 experiments had at least one endpoint that showed a significant trend with dose. A total of 386 data sets were significant with respect to both the quantal and continuous test of trend. An additional 44 data sets were identified with significant trend only by the quantal approach whereas 177 additional data sets were identified with significant trend tests only by the continuous approach. Thus, the continuous approach appeared to be more powerful in detecting dose-related toxicity, but the patterns detected by the two approaches differed.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMedDate not supplied

The frequency of chromosomal abnormalities in patients referred for fragile X analysis.

The present paper summarizes our existing database on chromosomal abnormalities found in patients referred because of a question of the Fragile X Syndrome during the period from January 1, 1990 to June 30, 1995. Cytogenetic results were derived from testing performed at the cytogenetics laboratory at Rhode Island Hospital. All positive fragile X individuals detected among our sample population represent index patients from separate kindreds. Of a total of 327 cases referred for fragile X testing, 10 (3.06 percent) were found to be positive for fragile X by either cytogenetics alone or by both cytogenetics and DNA testing, 12 (3.60 percent) were found to be positive for either a numerical or structural chromosomal abnormality, while 10 (3.06 percent) were found to exhibit a heteromorphism. Positive chromosomal findings included numerical chromosomal abnormalities of the sex chromosomes and autosomes, deletions, and translocations. Heteromorphism mostly involved an increase in the length of heterochromatic regions of certain chromosomes as well as a pericentric inversion of a chromosome 9, usually considered normal variants. It is concluded that chromosomal abnormalities other than fragile X are found with equal and, in some cases, higher frequency than the frequency of fragile X positivity in patients referred for a question of the Fragile X Syndrome. Our figures, consistent with those reported in the literature, underscore the value of routine karyotyping in this population of patients. Except under special circumstances, it is important that GTG-banding analysis be performed so that the entire human genome be examined in addition to scoring for the fragile X mutation on Xq27.3. Especially in view of the recent finding of the relative rarity of this condition, the exclusive use of DNA analysis is not advised.

Chromosome Aberrations↗
PubMed1996

Cytomegalovirus prophylaxis and treatment following bone marrow transplantation.

OBJECTIVE: To provide an overview of the role of cytomegalovirus (CMV) in the bone marrow transplant (BMT) population and update the current methods of prevention and treatment of CMV infection and disease, with emphasis on CMV interstitial pneumonia (CMV-IP). DATA SOURCES: The current medical literature, including abstracts presented at recent national and international meetings, is reviewed. References were identified by searching the MEDLINE database from January 1988 through June 1994. The reference lists of the published studies and reviews obtained from the initial literature search were reviewed as well. STUDY SELECTION: Data regarding the epidemiology of CMV, the risk factor associated with CMV infection and disease, as well as data on the prevention and the treatment of CMV infection and disease in the BMT population are cited. Specific attention was focused on randomized, placebo-controlled studies pertaining to the prevention of CMV infection and disease in CMV-immunoglobulin G positive recipients undergoing allogeneic BMT. Information from nonrandomized, placebo-controlled studies was included in the absence of stronger data. DATA EXTRACTION: Information contributing to CMV in the BMT population was reviewed. Data supporting and disputing specific preventive and treatment modalities are presented. DATA SYNTHESIS: The incidence of CMV seropositivity in the general population is high and while BMT becomes a widely accepted treatment modality, CMV reactivation and subsequent disease, especially CMV-IP, becomes a significant prognostic factor of morbidity and mortality. Even though antiviral agents such as ganciclovir and foscarnet can inhibit the viral replication in vivo, they have not been able to treat CMV-IP effectively. It has been suggested that CMV-IP is an immunopathologic process that can cause irreversible damage, hence, the low efficacy of antiviral therapy and the associated high mortality. Immunomodulating agents such as intravenous immune globulin and cytomegalovirus hyperimmune globulin can increase the efficacy of antivirals in the treatment of CMV-IP. This further supports the postulated immunopathologic process of this disease. The lack of understanding of the pathophysiology of the disease compromised the efforts of treatment and led to the development of preventive interventions with antiviral and immunomodulatory regimens that resulted in a significantly lower incidence of infection and disease. As a result of current data, the Eastern Cooperative Oncology Group has published guidelines for the prevention and treatment of CMV infection and disease. CONCLUSIONS: The prognosis of CMV disease in the BMT recipients has improved as a result of a wide variety of modifications in the management of BMT recipients. These include an increased understanding of the risk factors associated with CMV infection, routine screening for CMV replication and excretion, and more effective prophylactic regimens. Still, more than half of the patients who develop pneumonia will die, indicating that more studies are needed to increase the understanding of the pathophysiology and refine the preventive and therapeutic regimens against CMV.

Antiviral Agents↗
PubMedDate not supplied

Computerized Dysmorphology Database Mackay (CDDM): preliminary report.

A computerized dysmorphology database is useful for the pediatrician and geneticist in the task of diagnosing multiple malformation syndromes in children. We set up a new dysmorphology database "Computerized Dysmorphology Database Mackay (CDDM)" managed by the Clipper program. At present 278 disease entities with their clinical features and references are stored in the database. In this article, we report a practice analysis of ten dysmorphic patients by CDDM. A specific syndrome was accurately and rapidly diagnosed with the aid of CDDM in all ten cases. They serve as examples on how CDDM can be efficiently applied to obtain a short list of syndromes for differential diagnosis.

Abnormalities, Multiple↗
PubMed1995

A study of intracranial volume in Apert syndrome.

The present study was undertaken to characterize the intracranial volume in patients with Apert syndrome. Radiographic and CT-based techniques for measuring intracranial volume were found to show close correlation when validated in dry normal adult skulls. A standard-deviation score of intracranial volume, determined from CT scans in 20 patients with Apert syndrome from birth to 30 years of age, was calculated with reference to a normative database of age- and sex-matched controls. Analysis of the data showed no significant difference in standard-deviation score between Apert patients with or without ventriculomegaly, before or after cranial vault surgery, or between male and female patients. The mean standard-deviation score among all Apert CT scans compared with normative data was 3.1, which was highly significant (p < 0.001). However, the growth curves showed no significant difference in intracranial volume between Apert and normal patients below 3.5 months of age. In summary, intracranial volume in Apert syndrome is within normal range at birth but increases to greater than 3 standard deviations above normal after 3.5 months of age, a finding independent of cranial vault surgery.

Acrocephalosyndactylia↗
PubMed1998

Proteins of rat serum: I. Establishing a reference two-dimensional electrophoresis map by immunodetection and microbore high performance liquid chromatography-electrospray mass spectrometry.

In the present investigation, we have identified 56 major spots, or spot rows, corresponding to 22 proteins, in the 2-DE pattern of adult male rats. This was done mainly by applying two complementary techniques, namely immunoblotting and high performance liquid chromatography-mass spectrometry (HPLC-MS) peptide mapping. Glycoproteins were characterized by affinity blotting with six lectins. We have also detailed how rat serum differs from human serum in two main respects: (i) relative abundance of individual proteins, which amounts in some cases to a complete absence in either sample, and (ii) varying molecular parameters for homologous proteins. It was thus possible to establish a first-generation reference map of rat serum proteins, which can be accessed through http://weber.u.washington.edu/ruedilab/aebersold++ +.html. We hope the present database will be a useful reference for the evaluation of changes in serum protein distribution in the course of pharmacological and toxicological studies. The recognition of species-specific proteins appears of special relevance in this respect.

Animals↗
PubMed1995

Review of dental materials citations: Part A, January to June 1995.

OBJECTIVE: Electronic databases are an excellent resource for identifying relevant references for research and education projects. However, these databases are not yet a substitute for direct inspection of the literature because: (a) there still is a lag of many months between journal issue publication and updates of the database, and (b) most databases selectively report a portion of the entire literature. The objective was to identify and categorize all the dental materials citations in biomedical journals that were published from January 1995 through June 1995. METHODS: Seventeen primary and 56 secondary dental journals were manually searched via their tables of contents to detect dental materials publications from January to June of 1995. Dental materials citations were categorized into 17 major sections and further divided into several subsections. The review excluded case reports and literature primarily related to dental implants or biomedical materials outside of dentistry. RESULTS: Three hundred-sixty-nine citations were identified. The greatest number of citations were associated with dentin bonding, composites, and glass ionomers. There was no significant increase in dental materials publications vs. the number reported for 1994. SIGNIFICANCE: This list provides a comprehensive source for review by academicians and researchers to bridge the gap between initial publication and electronic citation.

Dental Materials↗
PubMed1996

Acephalgic migraines of childhood.

Migraine aura without headache (acephalgic migraines) is a recognized subset of migrainous phenomena in the adult population. No reports of its prevalence or characteristics in a series of children exists. Using diagnostic criteria for migraine aura without headache established by the International Headache Society, a retrospective review of a computerized database of all patients referred over a 4-year period (July 1991 to June 1995 inclusive) to a single university-based pediatric neurologist was performed. Fourteen patients were identified, representing 2% of all patients with a primary diagnosis of migraine. Nine were females and 13 had a strong family history of migraines. Age of onset of symptoms ranged from 5 to 12 years with a mean of 8 years. Symptoms were episodic in all, varying in frequency from weekly to more typically monthly, lasting generally less than 10 min. In 9 patients the aura described was that of often colorful photopsias or scintillating scotomas. Two had micropsia, one had temporal distortion (time "speeded up"), one had hyperacusis, and the final patient had a vague sense of disconnection from her surroundings. Only 2 patients had a headache occasionally associated with the described aura. In addition to the acephalgic migraines, 9 patients had either common or classical migraines, the latter typically featuring aura distinct from those observed in these patients' acephalgic episodes. Neurologic examination, electrophysiologic investigation (EEG/evoked potentials), and neuroimaging were noncontributory in all instances. Migraine aura without headache is a recognizable benign migraine syndrome of late childhood.

Child↗