Search PubMedSearch

SEARCH · Search PubMed

Results for “reference databases”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 127 records · Page 7Linked to original sources

Electrocardiographic quantitation of ventricular repolarization.

Quantification of the electrocardiographic ventricular repolarization involving the T-U wave complex is usually performed with reference to the axis of the T wave and the QT interval duration. A novel quantitative approach to improve the description of ventricular repolarization was applied to the digitized electrocardiograms of 423 normal subjects. Six electrocardiographic repolarization characteristics were identified: duration, rate, area, symmetry, late phenomena, and interlead heterogeneity. A computer algorithm was designed to automatically interpret the electrocardiographic repolarization segment and measure 11 variables that quantified these repolarization characteristics. The application of redundancy-reduction techniques selected a final set of seven variables that were used in the statistical analysis. The QT interval, which was included in the initial group of variables, was replaced by the time interval between S wave offset and T wave maximum. All selected electrocardiographic variables were independent of age (r2 less than 0.11) and body surface area (r2 less than 0.03); all except the early duration variable were heart rate- and QT interval-independent (r2 less than 0.2, r2 less than 0.13, respectively; and most were uncorrelated to each other. A comparison of repolarization characteristics by gender revealed that repolarization duration was significantly more prolonged (p less than 0.0001) in women than in men. This multidimensional quantitative approach conveys a new and more complete description of the repolarization process and provides an electrocardiographic repolarization database in normal subjects as a reference standard for identifying patients with disordered repolarization.

Adult

Experimental identification of technical and database factors that can affect the success of clinical computer systems.

The entry of clinical data into computer systems is an extremely demanding form of transaction processing. High speed is important, especially if the collection involves real-time data. Clinicians must feel that they intuitively understand a system and that it is responsive. Medical data must be easily accommodated without sacrificing accuracy or completeness. Most systems cannot do this. Clinical systems that involve on-line storage of data from patients should employ data-base technology. Systems that lack any of the following capabilities will not succeed: manual data entry, a data dictionary, a file system, utility functions, ad hoc query, and a statistical report generator. These general capabilities must satisfy a number of specific functional requirements if the entire system is to be a success. A group of such requirements have been experimentally validated. These will be discussed and a more comprehensive list presented.

Computer Systems

Artificial Intelligence in Diagnosing Depression Through Behavioural Cues: A Diagnostic Accuracy Systematic Review and Meta-Analysis.

AIM: To synthesise existing evidence concerning the application of AI methods in detecting depression through behavioural cues among adults in healthcare and community settings. DESIGN: This is a diagnostic accuracy systematic review. METHODS: This review included studies examining different AI methods in detecting depression among adults. Two independent reviewers screened, appraised and extracted data. Data were analysed by meta-analysis, narrative synthesis and subgroup analysis. DATA SOURCES: Published studies and grey literature were sought in 11 electronic databases. Hand search was conducted on reference lists and two journals. RESULTS: In total, 30 studies were included in this review. Twenty of which demonstrated that AI models had the potential to detect depression. Speech and facial expression showed better sensitivity, reflecting the ability to detect people with depression. Text and movement had better specificity, indicating the ability to rule out non-depressed individuals. Heterogeneity was initially high. Less heterogeneity was observed within each modality subgroup. CONCLUSIONS: This is the first systematic review examining AI models in detecting depression using all four behavioural cues: speech, texts, movement and facial expressions. IMPLICATIONS: A collaborative effort among healthcare professionals can be initiated to develop an AI-assisted depression detection system in general healthcare or community settings. IMPACT: It is challenging for general healthcare professionals to detect depressive symptoms among people in non-psychiatric settings. Our findings suggested the need for objective screening tools, such as an AI-assisted system, for screening depression. Therefore, people could receive accurate diagnosis and proper treatments for depression. REPORTING METHOD: This review followed the PRISMA checklist. PATIENTS OR PUBLIC CONTRIBUTION: No patients or public contribution.

Humans

A database of genetically determined neurological conditions for clinicians.

Progress is reported in the establishment of a database of genetically determined neurological conditions. There are now 1,300 conditions and 3,400 references store on the hard disk of a microcomputer. The database is searched, and a differential diagnosis obtained, by choosing a small number of signs and symptoms from a comprehensive list of cardinal features.

Diagnosis, Computer-Assisted

Exploring the use of machine and deep learning in genome-wide association studies: a comprehensive review.

The advent of high-throughput sequencing technologies has generated increasingly large and complex genomic datasets, necessitating analytical approaches capable of capturing high-dimensional and potentially nonlinear genetic interactions. This situation has significantly impacted the entire field of Genome-Wide Association Study (GWAS), whose primary goal is the identification of genomic traits and variants that are statistically associated with the risk of a disease. However, traditional GWAS methods may show reduced performance when applied to highly polygenic and nonlinear genetic architectures. Computational strategies from Artificial Intelligence (AI) and, in particular, from machine- and deep-learning may provide a powerful tool to overcome such limitations, especially by capturing nonlinear interactions and complex hidden regularities in large-scale data, which traditional GWAS approaches might overlook. To date, only a few approaches have been introduced and systematically assessed. In this review, we describe the main characteristics and limitations of standard statistical approaches for GWAS, the main uses of AI methods in computational genomics, and recent attempts to leverage AI strategies in GWAS. Particular attention will be devoted to key issues, such as the interpretability of methods and results, and the curse of dimensionality. More specifically, the review presents 30 methods designed to leverage AI in GWAS, as well as presenting a comprehensive set of evaluation metrics for their performance, also providing references to the most frequently used databases, and biobanks. Overall, this work may serve as a starting point for both dry- and wet-lab researchers, aiming to extract deeper insights from genomic data by moving beyond traditional linear additive assumptions, and leveraging large-scale datasets through AI-driven approaches.

Artificial intelligence

A technique to evaluate the performance of computerized ECG analysis systems.

No objective method to test computerized ECG systems has been available. Until now, tests have been conducted separately for instrumentation and algorithms. Hence, to facilitate objective verification and testing of modern computerized ECG equipment, a dedicated high resolution, low noise instrument (an "electronic test patient") has been developed. The purpose of this communication is to describe this new instrument and its electrocardiographic database. The instrument is designed not to cause any disturbances to the original ECG signals in the frequency range from 0 to 1 kHz. The input channels accommodating standard 12-lead and 3-lead Frank systems are sampled simultaneously at 10 kHz each with 90 dB dynamic range. The overall RMS noise figure of the instrument is 1 microV. The integral part of the instrument is a high resolution, high bandwidth minidatabase consisting of selected A-type and B-type verified electrocardiograms such as infarctions, ventricular hypertrophies, atrial fibrillations, etc. The minidatabase was collected with the aid of a computerized ECG system, which has a program for searching for specific electrocardiographic diagnosis. Each database record consists of simultaneous electrocardiographic signals of all standard leads and Frank leads, and a validated diagnostic report. A system under test is typically connected via its patient cable to the analog output of the instrument. The testing is performed with reference to the validated ECG from the database. In that way, our minidatabase is compatible with any electrocardiographic system. The only similar database assembled for testing purposes is that of the CSE group.(ABSTRACT TRUNCATED AT 250 WORDS)

Computer Systems

The Johns Hopkins Swallowing Center database.

A special database has been constructed for faculty working in the Swallowing Center of The Johns Hopkins University School of Medicine. The database supports the clinical, research, and publication needs of the Center. This database on swallowing disorders includes over 6000 references to the literature dating from the mid-1960s. The system operates on microcomputer technology and uses relatively inexpensive and intuitive software programs. Monthly updates keep members informed of the latest developments in a multidisciplinary literature.

Databases, Factual

Biomedical database inter-connectivity: an experiment linking MIM, GENBANK, and META-1 via MEDLINE.

The linkage of disparate biomedical databases is an important goal of the Unified Medical Language (UMLS) Project. We conducted an experiment to investigate the feasibility of using UMLS resources to link databases in clinical genetics and molecular biology. References from MIM ("Mendelian Inheritance in Man") were lexically mapped to the equivalent citations in MEDLINE. The MeSH major subject headings by which the citations in a particular MIM entry had been indexed were used to develop a "genetic-disorder-centered view of the world" in Meta-1 (the first official version of the UMLS Metathesaurus). Our hypothesis was that these MeSH subject headings could provide access to a "semantic neighborhood" in Meta-1 that would be relevant to a particular genetic disorder. By browsing in this "semantic neighborhood," a user could select various combinations of terms with which to search MEDLINE through an interface between Meta-1 and Grateful Med. Such searches might retrieve citations that were more recent than those in MIM or that provided useful supplementary information. Since some MEDLINE records contain pointers to entries in GENBANK, information about genetic sequences related to a particular clinical genetic disorder could also be retrieved. This scenario was implemented for a small number of MIM entries, providing a concrete demonstration that linking disparate electronic databases in an important subdomain of biomedicine is relatively straightforward.

Databases, Factual

[A computerized database for problem patients in pediatric anesthesia].

A computerized database for use in pediatric anesthesia and in the perioperative care of patients with malformation syndromes and rare diseases is presented. A total of 2200 syndromes are listed, and the database contains helpful data, experience, guidelines and literature references relevant to about 500 rare diseases. The access to the databank, its structure and the probable benefits of the system are explained and discussed.

Anesthesiology

Long-term hormone therapy for perimenopausal and postmenopausal women.

BACKGROUND: Hormone therapy is widely provided to control menopausal symptoms and has been used for the management and prevention of cardiovascular disease, osteoporosis and dementia in older women. This is an updated version of a Cochrane review first published in 2005. OBJECTIVES: To assess the long-term effects of prolonged use (at least one year) of hormone therapy on mortality, cardiovascular outcomes, cancer, gallbladder disease, fractures and cognition in perimenopausal and postmenopausal women. SEARCH METHODS: We used the Cochrane Gynaecology and Fertility Group Specialised Register, CENTRAL, MEDLINE, three other databases and two trial registers, together with reference checking, citation searching and contact with study authors to identify the studies included in the review. The latest search date was 26 September 2024. SELECTION CRITERIA: We included randomised, double-blind trials in which peri- or postmenopausal women took hormone therapy or placebo for at least one year. We included various oestrogen formulations, with or without progestogens. We focused on studies assessing hormone therapy's effects on long-term clinical outcomes, including death, coronary events and cancer. Hormone therapy's efficacy in managing menopausal symptoms was beyond the scope of this review, and is assessed in other Cochrane reviews. DATA COLLECTION AND ANALYSIS: Two review authors independently selected studies, assessed risk of bias and extracted data. We calculated risk ratios (RRs) for dichotomous data and mean differences (MDs) for continuous data, along with 95% confidence intervals (CIs). We assessed the certainty of the evidence using GRADE. MAIN RESULTS: We included 24 studies - with two newly added in this update - involving 45,660 participants. We derived nearly 70% of the data from two well-conducted studies: the Heart and Estrogen/progestin Replacement Study (HERS 1998) and the large, multi-component Women's Health Initiative research programme, which included two hormone therapy arms (WHI 1998). Across all the studies, most participants were postmenopausal American women with one or more comorbidities. The mean participant age in most studies was over 60 years. Only one included study focused on perimenopausal women. We present full results for all included studies with available data in the main review. The results presented below are drawn from WHI 1998, in which the combined hormone therapy arm and the oestrogen-only arm were run concurrently, with women assigned to the appropriate trial based on their uterus status. One study with 16,608 postmenopausal women with an intact uterus compared combined continuous hormone therapy (conjugated equine oestrogen and medroxyprogesterone acetate) to placebo, and measured outcomes at an average of 5.6 years of follow-up. Based on this study, combined continuous hormone therapy probably makes little to no difference to the risk of a coronary event (RR 1.17, 95% CI 0.95 to 1.44; moderate-certainty evidence). It may increase the risk of stroke (RR 1.39, 95% CI 1.09 to 2.09; low-certainty evidence) and venous thromboembolism (RR 2.03, 95% CI 1.55 to 6.64; low-certainty evidence). Compared to placebo, combined continuous hormone therapy probably increases the risk of breast cancer (RR 1.27, 95% CI 1.03 to 1.56; moderate-certainty evidence) and probably makes little to no difference to the risk of lung cancer (RR 1.06, 95% CI 0.77 to 1.46; moderate-certainty evidence). It may increase gallbladder disease requiring surgery (RR 1.64, 95% CI 1.30 to 2.06; 14,203 participants; low-certainty evidence), and probably reduces the risk of all clinical fractures (RR 0.78, 95% CI 0.71 to 0.86; moderate-certainty evidence). One study including 10,739 postmenopausal women who had undergone a hysterectomy compared oestrogen-only (conjugated equine oestrogen) hormone therapy to placebo, and measured outcomes at an average of seven years' follow-up. Based on this study, oestrogen-only hormone therapy probably makes little to no difference to the risk of coronary events (RR 0.94, 95% CI 0.78 to 1.13), venous thromboembolism (RR 1.32, 95% CI 1.00 to 1.74) and breast cancer (RR 0.79, 95% CI 0.61 to 1.01), all with moderate-certainty evidence. It may make little to no difference to the risk of lung cancer (RR 1.04, 95% CI 0.73 to 1.48; low-certainty evidence). Oestrogen-only hormone therapy probably increases the risk of stroke (RR 1.33, 95% CI 1.06 to 1.67) and gallbladder disease requiring surgery (RR 1.78, 95% CI 1.42 to 2.24), and probably reduces the risk of all clinical fractures (RR 0.73, 95% CI 0.65 to 0.80), all with moderate-certainty evidence. We judged most included studies to have a low risk of bias for most domains. The overall certainty of evidence for the main comparisons was moderate. The main limitation was that only about 30% of women were 50 to 59 years old at baseline, the age group most likely to consider hormone therapy for vasomotor symptoms. AUTHORS' CONCLUSIONS: Long-term follow-up of women using hormone therapy suggests that the risk profiles vary between combined hormone therapy and oestrogen-only therapy. Oestrogen-only hormone therapy probably makes little to no difference to coronary events, and probably increases the risk of stroke and gallbladder disease. It probably makes little to no difference in the risk of breast cancer, and probably reduces the risk of all fractures. Combined hormone therapy may increase the risk of thromboembolism and probably increases the risk of breast cancer. These results should be interpreted with caution as they are based on one study using oral hormone therapy, which may not represent the risks of the hormone therapy currently used in clinical practice.

Humans

Using OMIM (On-line Mendelian Inheritance in Man) as an expert system in medical genetics.

Expert systems have been used in Medicine for many years, but they are usually highly sophisticated and not well integrated into day-to-day practice. On the other hand, bibliographic databases such as Medline and others are easily accessible and are widely used. We report here the use of OMIM (On-line Mendelian Inheritance in Man), one of these bibliographic databases, as an expert system in Medical Genetics. The description of 93 syndromes was used as search-key and the diagnoses proposed by OMIM were analyzed to determine whether the correct diagnosis was among them. The proposed diagnoses were automatically ranked by OMIM from the most probable (weight = 100) to the least probable (weight = 1). OMIM suggested a total of 1538 +/- 692.2 diagnoses per search. In order to deal with a reasonable number of proposed diagnoses, we only considered the diagnoses with a weight of 50 or more. With this limit, OMIM proposed a mean of 37.0 +/- 24.6 diagnoses per case. The overall accuracy was 76%. A correct answer with a perfect weight of 100 was proposed in 29% of the case. The diagnostic accuracy of OMIM increased linearly when weights lower than 100 were considered. When the rank alone was analyzed, the accuracy of OMIM increased very rapidly from position 1 to 5 with a subsequent almost linear increase. If one only considered the first five proposed diagnoses, the accuracy of OMIM was just above 50%. This study shows that bibliographic databases are not only restricted to the provision of references but could also be used as expert systems and are therefore of great value to medical geneticists.

Databases, Bibliographic

Post-operative confusion in the elderly--a literature review.

The literature indicates that the elderly form a substantial proportion of surgical patients and that a disproportionate number of them suffer an abnormal temporary change in mental state which can have an adverse effect on their recovery. A computer search using 'Medline' and the 'Nursing and Allied Health Database' from 1966-1988 revealed very few references which related directly to post-operative confusion in the elderly. One study in 1984 located only "one prospective, cohort, analytical study of post-operative confusion" which was undertaken in 1979. Two further studies have since been published in 1985, but there is obviously a paucity of literature in this area.

Aged

Localization of visually evoked cortical activity using magnetic resonance imaging and computerized tomography.

Evoked scalp potentials, computerized tomography, and magnetic resonance imaging were used together to localize cortical activity evoked by visual stimuli in humans. The temporal resolution of evoked potential measurements is sufficient to track the flow of cortical activity which evolves in epochs of a few tens of msec. Spatial localization was enhanced by deconvolving scalp potential fields with a Laplacian operator. Markers glue to the scalp served to unify the three geometric reference frames into a single computer graphics database.

Brain Mapping

In Situ Hybridization and RT-PCR Detection of Nervous Necrosis Virus in Fourfinger Threadfin, Eleutheronema tetradactylum, in Taiwan.

Between April and July 2020, suspected outbreaks of nervous necrosis virus (NNV) infection were observed in fourfinger threadfin (Eleutheronema tetradactylum) fingerling hatcheries in Pingtung County, southern Taiwan. Affected fish exhibited spiral swimming behaviour and abdominal distension, resulting in mortality rates between 50% and 100%. Histopathological examination showed severe vacuolation in the brain and ocular tissues, with large oval and/or irregular basophilic cytoplasmic inclusion bodies in the brain. Phylogenetic analysis of the viral replicase (RNA1) and capsid protein (RNA2) genes revealed high nucleotide sequence identities among the isolates in this study, with sequence similarity rates of 96.9%-99% for RNA1 and 98.2%-99.0% for RNA2 compared to RGNNV reference strains available in the NCBI GenBank database. This is the first detection of betanodavirus in fourfinger threadfin in Taiwan, using RT-PCR and ISH. A positive correlation between elevated water temperatures and disease severity indicates the need for year-round surveillance and genomic analysis to clarify the epidemiology of FTNNV. The data suggest that infected eggs may facilitate the vertical transmission of Betanodavirus. Crucially, utilising virus-free broodstock, alongside routine health screening and environmental control, is essential for mitigating NNV risks in fourfinger threadfin aquaculture.

Animals

Pilea: profiling bacterial growth dynamics from metagenomes with sketching.

BACKGROUND: Quantifying bacteria's growth rates is essential for understanding their ecological roles and for building predictive models in environmental and clinical settings. Peak-to-trough ratios (PTRs) derived from shotgun metagenomes offer a culture-independent proxy for in situ growth rates of bacterial species, yet their reliable computation remains challenging. RESULTS: We introduce Pilea ( https://github.com/xinehc/pilea ), an alignment-free, sketching-based method that incorporates statistical models for robust PTR estimation. Pilea achieves speed improvements over existing methods while also enhancing accuracy, as demonstrated on both simulated and real datasets. CONCLUSIONS: By scaling efficiently to comprehensive reference collections such as the Genome Taxonomy Database (GTDB), Pilea enables large-scale analyses of bacterial growth dynamics across biomes, unlocking new insights for ecological research. Video Abstract.

Bacteria

Mass-to-surface area index in a large cohort.

Many biological and anthropological investigations have described the role between mass-to-surface area index (M/SA) and heat tolerance. No large M/SA database exists that can be used as a reference standard to interpret previous or future M/SA studies. This report presents the M/SA data of a large military cohort (1,170 males aged 17-54 years, 305 females aged 17-40 years). The effects of gender, ethnic group, and age on the distribution of M/SA, as well as the relationship between M/SA and other physical characteristics, were described. It was observed that the increases of M/SA with increasing age (over the 17-75 years category) were not significant. All descriptive characteristics (including M/SA) were different (P less than .001) between males and females. M/SA was not statistically different between ethnic groups among both males and females. These data may be utilized to compare the M/SA values of U.S. citizens to those of other ethnic groups and to identify those laborers or athletes who possess the greatest theoretical risk of heat intolerance.

Adolescent

Trust, but verify. The accuracy of references in four anesthesia journals.

To determine the accuracy of bibliographic citation in the anesthesia literature, we reviewed all 1988 volumes of ANESTHESIOLOGY, Anesthesia and Analgesia, British Journal of Anaesthesia, and Canadian Journal of Anaesthesia and sequentially numbered all references appearing in that year (n = 22,748). One hundred references from each of the four journals were randomly selected. After citations to nonjournal articles (i.e., books or book chapters) were excluded, the remaining 348 citations were analyzed in detail. Six standard bibliographic elements--authors' names, article title, journal title, volume number, page numbers, and year--were examined in each selected reference. Primary sources were reviewed, unless our institution did not own the source or could not obtain it through interlibrary loan, in which case standard indexes, abstracting services, and computerized databases were consulted. Each element was checked for accuracy, and references were classified as either correct or incorrect. A reference was correct if each element of the citation was identical to its source. Of the examined references, more than half (50.3%) contained an error in at least one element. The elements most likely to be inaccurate were, in descending order, article title, author, page numbers, journal title, volume number, and year. No significant differences (P = 0.283) existed in the error rates of the four journals; the percentage of citations containing at least one error ranged from 44% (Anesthesia and Analgesia) to 56% (British Journal of Anaesthesia). The citation error rate of anesthesia journals is similar to that reported in other specialties, where error rates ranging from 38% to 54% have been documented.

Anesthesiology