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[Study of phylogenetic relations of hantaviruses by using the mutual information method. Tula genotype viruses].

Phylogenetic relations were studied in the group of Tula viruses (Hantavirus genus, Bunyaviridae family) of Eurasia. The similarity in the nucleotide sequences of segments was estimated by the value of mutual information. The application of this method confirmed that recombinant events might occur in some Tula-like viruses of Eurasia, as previously presumed by the results of bootscanning and analysis of amino acid sequences. It was found that might be recombination between distinct phylogenetic Tula sublineages; concepts of the microevolution of the group as a whole are specified.

Databases, Factual↗
PubMed2006

PhenoGO: assigning phenotypic context to gene ontology annotations with natural language processing.

Natural language processing (NLP) is a high throughput technology because it can process vast quantities of text within a reasonable time period. It has the potential to substantially facilitate biomedical research by extracting, linking, and organizing massive amounts of information that occur in biomedical journal articles as well as in textual fields of biological databases. Until recently, much of the work in biological NLP and text mining has revolved around recognizing the occurrence of biomolecular entities in articles, and in extracting particular relationships among the entities. Now, researchers have recognized a need to link the extracted information to ontologies or knowledge bases, which is a more difficult task. One such knowledge base is Gene Ontology annotations (GOA), which significantly increases semantic computations over the function, cellular components and processes of genes. For multicellular organisms, these annotations can be refined with phenotypic context, such as the cell type, tissue, and organ because establishing phenotypic contexts in which a gene is expressed is a crucial step for understanding the development and the molecular underpinning of the pathophysiology of diseases. In this paper, we propose a system, PhenoGO, which automatically augments annotations in GOA with additional context. PhenoGO utilizes an existing NLP system, called BioMedLEE, an existing knowledge-based phenotype organizer system (PhenOS) in conjunction with MeSH indexing and established biomedical ontologies. More specifically, PhenoGO adds phenotypic contextual information to existing associations between gene products and GO terms as specified in GOA. The system also maps the context to identifiers that are associated with different biomedical ontologies, including the UMLS, Cell Ontology, Mouse Anatomy, NCBI taxonomy, GO, and Mammalian Phenotype Ontology. In addition, PhenoGO was evaluated for coding of anatomical and cellular information and assigning the coded phenotypes to the correct GOA; results obtained show that PhenoGO has a precision of 91% and recall of 92%, demonstrating that the PhenoGO NLP system can accurately encode a large number of anatomical and cellular ontologies to GO annotations. The PhenoGO Database may be accessed at the following URL: http://www.phenoGO.org

Computational Biology↗
PubMed2006

Event ontology: a pathway-centric ontology for biological processes.

Event ontology is a new biomedical ontology developed to annotate pathway components in a pathway database. It organizes the concepts and terms of sub-pathways, pathways, biological phenomena, experimental conditions, medications, and external stimuli appearing in biological pathways (e.g. signal transduction, disease-, metabolic-, molecular interaction-, genetic interaction pathways, etc.). Concepts in the Event ontology are extracted manually from scientific literature. Each term has links to external databases such as Gene Ontology, Reactome, KEGG, BioCyc, and PubMed.

Computational Biology↗
PubMed1989

Informatics in professional education.

The University of Maryland at Baltimore (UMAB) is a professional school campus, including schools of Dentistry, Law, Medicine, Nursing, Pharmacy, Graduate Studies, and Social Work and Community Planning. In late 1987, UMAB convened a Task Force on Informatics, intended to support the campus as it worked to become a Centre of Excellence for Informatics. The Task Force reviewed the current computing environment at UMAB and the individual schools. In assessing the state of the art in informatics, its work was supplemented by the formation of external advisory committees of national and international informaticians. Deliberations proceeded according to a methodology designed to develop factual databases and to generate consensus. The Task Force report, which is excerpted in the following paper, established a tiered taxonomy of competencies; defined the three levels; and set forth program models for the two higher levels. Special note was made of the programs in nursing and dental informatics newly established at UMAB. The report concluded with three recommendations, each with detailed action points identified.

Computers↗
PubMed1986

Future programs at the National Library of Medicine.

The future of the National Library of Medicine will be shaped by a number of scientific, technical, and social influences. Among these are the continuing rapid development of computer technology and storage systems. Artificial intelligence techniques, factual databases, the emergence of medical informatics as a formal discipline, and the development of Integrated Academic Information Management Systems (IAIMS) are also important influences on the direction of the library. Public policy issues will influence the future of NLM--among them, sharing of scientific information between nations and the role of federal agencies in dissemination of information domestically. The formal, long-range plan now being prepared for the library by panels of expert advisers will be a guide for future programs and goals.

Artificial Intelligence↗
PubMed1995

Forensic DNA data banking by state crime laboratories.

This article reports the results of a survey of the responsible crime laboratories in the first 19 states with legislation establishing forensic DNA data banks. The survey inquired into the labs' policies and procedures regarding the collection, storage, and analysis of samples; the retention of samples and data; search protocols; access to samples and data by third parties; and related matters. The research suggests that (1) the number of samples collected from convicted offenders for DNA data banking has far surpassed the number that have been analyzed; (2) data banks have already been used in a small but growing number of cases, to locate suspects and to identify associations between unresolved cases; (3) crime labs currently plan to retain indefinitely the samples collected for their data banks; and (4) the nature and extent of security safeguards that crime labs have implemented for their data banks vary among states. The recently enacted DNA Identification Act (1994) will provide $40 million in federal matching grants to states for DNA analysis activities, so long as states comply with specified quality-assurance standards, submit to external proficiency testing, and limit access to DNA information. Although these additional funds should help to ease some sample backlogs, it remains unclear how labs will allocate the funds, as between analyzing samples for their data banks and testing evidence samples in cases without suspects. The DNA Identification Act provides penalties for the disclosure or obtaining of DNA data held by data banks that participate in CODIS, the FBI's evolving national network of DNA data banks, but individual crime labs must also develop stringent internal safeguards to prevent breaches of data-bank security.

Civil Rights↗
PubMed1994

A review of state legislation on DNA forensic data banking.

Recent advances in DNA identification technology are making their way into the criminal law. States across the country are enacting legislation to create repositories for the storage both of DNA samples collected from convicted offenders and of the DNA profiles derived from them. These data banks will be used to assist in the resolution of future crimes. This study surveys existing state statues, pending legislation, and administrative regulations that govern these DNA forensic data banks. We critically analyzed these laws with respect to their treatment of the collection, storage, analysis, retrieval, and use of DNA and DNA data. We found much variation among data-banking laws and conclude that, while DNA forensic data banking carries tremendous potential for law enforcement, many states, in their rush to create data banks, have paid little attention to issues of quality control, quality assurance, and privacy. In addition, the sweep of some laws is unnecessarily broad. Legislative modifications are needed in many states to better safeguard civil liberties and individual privacy.

Advisory Committees↗
PubMed1993

Privacy rules for DNA databanks. Protecting coded 'future diaries'.

In privacy terms, genetic information is like medical information. But the information contained in the DNA molecule itself is more sensitive because it contains an individual's probabilistic "future diary," is written in a code that has only partially been broken, and contains information about an individual's parents, siblings, and children. Current rules for protecting the privacy of medical information cannot protect either genetic information or identifiable DNA samples stored in DNA databanks. A review of the legal and public policy rationales for protecting genetic privacy suggests that specific enforceable privacy rules for DNA databanks are needed. Four preliminary rules are proposed to govern the creation of DNA databanks, the collection of DNA samples for storage, limits on the use of information derived from the samples, and continuing obligations to those whose DNA samples are in the databanks.

Civil Rights↗
PubMed1995

The Visible Human data set: an image resource for anatomical visualization.

The National Library of Medicine (NLM) has long been a world leader in the archiving and distribution of the print-based images of biology and medicine. NLM has also been a pioneer in the use of computer systems to encode and distribute textual knowledge of the life sciences. NLM's Long Range Planning effort of 1985-86 foresaw a coming era where NLM's bibliographic and factual database services would be complemented by libraries of digital images, distributed over high speed computer networks and by high capacity physical media. The NLM Planning Panel on Electronic Imaging recommended that NLM should undertake the building of a digital image library consisting of computer-assisted tomography (CAT), magnetic resonance interferometry (MRI), and cryosection images of a representative, carefully selected and prepared male and female cadaver--the "Visible Human Project." The male Visible Human data set is now being made available through a license agreement with the NLM. A wide range of educational, diagnostic, treatment planning, and commercial uses is predicted. The Visible Human data set and its associated identification maps will serve as a "Boston Teapot" for medical imaging, a common public domain data set against which all medical imaging algorithms can be tested, and a cornerstone for future sets of related image libraries.

Adult↗
PubMed2002

Comparison of 35 electronic databases for environmental risk assessment.

The objective of this work is to classify and evaluate the major factual electronic databases that could be efficiently questioned for environmental risk assessment of various chemicals. A series of 35 databases available on commercial CD-ROMs and/or freely accessible on the Internet were listed and compared for the presence or absence of information for 27 environmental criteria. A factorial correspondence analysis indicated that most of the 35 databases are specialized in physicochemical, toxicological or ecotoxicological data but a few of them are nonspecialized databases able to answer simultaneously in various areas. We then evaluated these 35 databases by querying them for 14 selected test chemicals. It appeared that the percentage of chemicals being listed in the databases was very unequal and none of the 35 databases obtained 14 positive responses. The quality of the responses was determined by calculating the number of criteria being documented for the previously listed chemicals in each database. It suggested that HSDB, DOSE, TOMES, IPCS are the most efficient databases to be used for an urgent search of environmental data.

Databases, Factual↗
PubMed2025

Analysis of Variants' Dynamic Using the CLIMB Database in COVID-19 Patients Admitted to Hospitals of Barts Health NHS Trust.

The COVID-19 pandemic, caused by SARS-CoV-2, has led to significant global health challenges. This study analyzes the dynamics of SARS-CoV-2 variants among patients admitted to Barts Health National Health Service (NHS) Trust hospitals using data from the CLIMB-COVID decentralized digital infrastructure allowing precise identification of SARS-CoV-2 variants. A total of 423 patients admitted between October 2020 and March 2021 were included in the study and divided into two groups: the alpha lineage group, which comprised the B.1.1.7 variant, and the other lineages group, which included all other variants. Whole-genome sequencing of SARS-CoV-2 genomes was conducted using the COVID-CLIMB pipelines. Clinical outcomes, such as mortality rates and deterioration within 28 days, were analyzed. To ensure robust findings, analyzes were adjusted for confounding factors, including age and comorbidities. Our findings revealed a significant increase in mortality with age for the alpha lineage and other lineages. The study underscores the importance of age adjustment in clinical studies to accurately assess the impact of different variants. Consistent genomic sequencing and data completeness are crucial for obtaining reliable results and guiding public health responses. These insights are vital for improving patient outcomes and providing a truthful picture of the pandemic, informing both current and future healthcare strategies.

Humans↗
PubMed2025

Covid-19 Vaccination During Pregnancy in France: a Descriptive Study of Uptake Using the National Healthcare data System.

Pregnant women and their fetus are at increased risk of complications when infected by SARS-CoV-2. This study describes COVID-19 vaccine uptake during pregnancy in France (i) according to socio-demographic characteristics, and (ii) over calendar time and pregnancy stages. Using the hospital discharge records of the national healthcare database, we identified women ending pregnancy at hospital between Dec 27, 2020, i.e. beginning of Covid-19 vaccine availability, and Dec 31, 2022. Covid-19 vaccinations and SARS-CoV-2 infections were also available on two specific linked databases. Vaccine coverage was defined as uptake of at least one dose of vaccine during the 2-year study period, or more specifically during one of five phases of pregnancy (first, second and third trimesters, pre-conceptional and post-pregnancy periods). We also defined ineligibility as the six-month period following each Covid-19 infection. We calculated weekly rates of vaccination by pregnancy phase, accounting for ineligibility. About 75% of women received at least one dose of vaccine in 2021-2022 vs. 90% in the general population with a similar age structure. About 26% received at least one dose of vaccine while pregnant. The rate was lower among younger women, deprived women, and those living in the south-east of mainland France or in overseas territories. Weekly vaccination rates according to the phase of pregnancy showed that women mostly received vaccination outside the pregnancy trimesters (after or, to a less extent, before pregnancy). Vaccinations during pregnancy mostly occurred in the second trimester. When only elective terminations were considered, weekly rates of vaccination were almost identical, whatever the pregnancy phase (before, during or after pregnancy). Overall, our results show the positive impact of national recommendations on uptake dynamics. Vaccine coverage in pregnant women could be improved with targeted campaigns.

Humans↗
PubMed2026

Published Database Resources for Traditional, Complementary, and Integrative Medicine: Update of a Systematic Review.

BACKGROUND: Traditional, Complementary, and Integrative Medicine (TCIM) has been established in the academic context of universities. In recent years, strategies have been developed worldwide to strengthen the role of TCIM in supporting the health of the population. Online databases are a common way for obtaining evidence-based information. This article is an update of a former systematic review from 2010 on published databases resources for TCIM. METHODS: The databases CINAHL, CAMbase, Web of Science, MEDLINE/PubMed, and Google Scholar search engine were searched for databases related to TCIM published in peer-reviewed journals between 2010 and November 2024. All included databases were visited online, and information on the origin, content, and scope of the database was extracted. RESULTS: A total of 6579 articles were identified through the literature search. After exclusion of irrelevant articles, full-text screening of 127 articles yielded 37 new databases. Together with 16 still available old databases, these mainly contained information on herbal therapies (n = 15) and Traditional Chinese Medicine (n = 11) from 18 different countries. Newly identified medicinal plant databases offer various scientific resources such as crude drugs, indigenous plants, and structures for natural and phytochemical components with molecular biological content. CONCLUSIONS: This literature review illustrates the dynamic development in the database landscape over the last 15 years. While the number of bibliographic databases is shrinking, databases in the field of medical plants/herbal therapy content are on the rise, which might be due to advances in plant genomics and molecular biology.

Humans↗
PubMed2006

Forty years of 90Sr in situ migration: importance of soil characterization in modeling transport phenomena.

In 1960 experiments were carried out on the transfer of (90)Sr between soil, grapes and wine. The experiments were conducted in situ on a piece of land limited by two control strips. The (90)Sr migration over the last 40 years was studied by performing radiological and physico-chemical characterizations of the soil on eight 70 cm deep cores. The vertical migration modeling of (90)Sr required the definition of a triple layer conceptual model integrating the rainwater infiltration at constant flux as the only external factor of influence. Afterwards the importance of a detailed soil characterization for modeling was discussed and satisfactory simulation of the (90)Sr vertical transport was obtained and showed a calculated migration rate of about 1.0 cm year(-1) in full agreement with the in situ measured values. The discussion was regarding some of the key parameters such as granulometry, organic matter content (in the Van Genuchten parameter determination), Kd and the efficient rainwater infiltration. Besides the experimental data, simplifying assumptions in modeling such as water-soil redistribution calculation and factual discontinuities in conceptual model were examined.

Biological Transport↗
PubMed1998

Melanoma resection margin recommendations, unconventionally based on available facts.

Precedent from early in the twentieth century led to the traditionally wide resection margins for primary melanoma, but at that time there was little relevant empirical evidence that substantiated the efficacy of the practice. Later, neither numerous retrospective analyses nor several prospective, randomized trials were able to demonstrate an adverse effect on outcome from melanoma with narrowing of margins to 1 cm. A slightly increased rate of local recurrence was observed in some nonrandomized analyses when margins were less than 1 cm, an effect that may be accentuated with thicker primary tumors. The factual record therefore does not support the use of resection margins greater than 1 cm for invasive melanoma of any thickness.

Databases, Factual↗
PubMed2004

Drug use among fathers around time of conception: two register based surveys from Denmark and The Netherlands.

STUDY OBJECTIVE: Despite the increasing attention for the role of paternal exposures around the period of conception, there is no factual information about drug utilisation of fathers. Therefore, the aim of this study was to describe the drugs dispensed to fathers around conception, using pharmacy dispensing data of community pharmacies in Denmark and The Netherlands. DESIGN AND SETTING: Using pharmacy dispensing data from the Pharmaco-epidemiological Prescription Database of North Jutland in Denmark and the InterAction database in The Netherlands, we examined the prescriptions reimbursed in the half year before conception of 56,735 Danish fathers from 1991 to 2000, and 5859 Dutch fathers from 1995 to 2000. MAIN RESULTS: One third of all fathers had taken up prescriptions for at least one drug in the half year before conception, both in Denmark and in The Netherlands. In the majority of fathers only one type of drug was dispensed, but in both countries at least 5% of all fathers had redeemed three or more types of drugs. The main drugs purchased by fathers in Denmark and The Netherlands were antibiotics (14.3 and 6.3% of all fathers, respectively), analgesics (6.1 and 7.6%), antihistamines (2.0 and 2.0%) and anti-ulcer drugs (1.6 and 2.5%). CONCLUSION: A large proportion of fathers used drugs around the time of conception. This finding emphasises the importance of safety information on therapeutic drugs with respect to potential paternal teratogenicity.

Abnormalities, Drug-Induced↗