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PubMedDate not supplied

Genetic variation and relationships at six VNTR loci in two distinct sample populations in Brazil.

BACKGROUND: The Brazilian population has been the focus of intensive genetic study due to admixture characteristics whereas there are few reports on the variability of VNTR loci in Brazil. PRIMARY OBJECTIVE: The aim of this study was to analyse genetic parameters in sample populations from two geographically distant regions: São Luis City, in Maranhão State and Campinas City, in São Paulo State. We investigated if distinct colonization influences could produce detectable differences in genetic background. SUBJECT AND METHODS: DNA samples from peripheral drained blood were obtained from unrelated individuals who underwent paternity testing. Allelic variation in six VNTR loci (D2S44, D4S139, D5S110, D8S358, DI0S28 and D17S79) was evaluated. The results were compared to reference databases available for general Latin-derived European and African-American populations as well as for other Brazilian groups. RESULTS: This study reveals that forensic population parameters did not show differences among regions, although we detected admixture values varying between the south-east and north-east of Brazil. CONCLUSIONS: Differences between the two samples are probably due to different admixture proportions of European- and African-derived alleles in each region: both populations are in Hardy Weinberg equilibrium. In addition, the allelic frequency for all loci, in both populations, can be used as database for forensic purposes.

Alleles↗

PubMed2004

Intracranial presentation of systemic Hodgkin's disease.

Intracranial involvement by Hodgkin's disease is rare. We report a patient with Hodgkin's disease who had intracranial disease at presentation. We also review the literature pertaining to intracranial Hodgkin's disease. Using the key words "Hodgkin's disease" and "central nervous system (CNS) disease", we searched the Pubmed and Cancerlit databases. References were systematically reviewed and data regarding the following variables was extracted: age, gender, signs and symptoms at presentation, histology of Hodgkin's disease, cerebrospinal fluid analysis, stage and treatment. Only 36 cases of intracranial Hodgkin's disease were identified in the literature. Intracranial Hodgkin's disease at presentation is even more uncommon with only 8 reported cases. Most cases of intracranial involvement by Hodgkin's disease occur at the time of relapse. The most common presenting feature of intracranial Hodgkin's disease is a cranial nerve palsy with brain parenchyma being the most common intracranial site of involvement. Mixed cellularity histology is the most frequent subtype of Hodgkin's disease among these patients and the median survival following intracranial presentation is 46 months. Treatment has varied extensively but includes whole brain radiation with or without combination chemotherapy. Our literature review suggests that the prognosis is not dismal with appropriate treatment.

Adult↗

PubMedDate not supplied

Nasal lavage fluid and proteomics as means to identify the effects of the irritating epoxy chemical dimethylbenzylamine.

The aims of this study were to describe the changes in the nasal lavage fluid (NLF) protein pattern after exposure to the irritating epoxy chemical dimethylbenzylamine (DMBA) and to identify the affected proteins using a proteomic approach. The protein patterns of NLF from six healthy subjects and eight epoxy workers with airway irritation were analysed using two-dimensional gel electrophoresis (2-DE) before and after exposure to 100 microg m(-3) DMBA for 2 h in an exposure chamber. NLF proteins were identified by (i) comparison with a 2-DE NLF reference database; (ii) N-terminal amino acid sequencing; and (iii) mass spectrometry. In NLF from healthy subjects, the levels of immunoglobulin A increased and the levels of Clara cell protein 16 (CC16) decreased after chamber exposure, while in NLF from epoxy workers, alpha(2)-macroglobulin and caeruloplasmin increased. Two previously unidentified proteins decreased in NLF from epoxy workers after exposure; these were identified as statherin and calgranulin B. In addition, the subjects who developed high counts of eosinophils in their nasal mucosa after chamber exposure had significantly lower levels of immunoglobulin-binding factor (IgBF) before exposure than subjects with low eosinophil infiltration. These results show that short-term exposure to DMBA causes distinct changes in NLF proteins. Moreover, three proteins that have previously not been associated with upper airway irritation were identified: statherin, calgranulin B and IgBF. Further studies are needed to investigate whether these proteins may be used as biomarkers of airway irritation and to give new insight into the ways in which occupational exposure to irritants causes inflammation of the airways.

9,10-Dimethyl-1,2-benzanthracene↗

PubMed2006

Religion, spirituality and the well-being of informal caregivers: a review, critique, and research prospectus.

The purpose of this article is to review and critique the published literature examining the relationships between religion/spirituality and caregiver well-being and to provide directions for future research. A systematic search was conducted using bibliographic databases, reference sections of articles, and by contacting experts in the field. Articles were reviewed for measurement, theoretical, and design limitations. Eighty-three studies were retrieved. Research on religion/spirituality and caregiver well-being is a burgeoning area of investigation; 37% of the articles were published in the last five years. Evidence for the effects of religion/spirituality were unclear; the preponderance (n = 71, 86%) of studies found no or a mixed association (i.e., a combination of positive, negative, or non-significant results) between religion/spirituality and well-being. These ambiguous results are a reflection of the multidimensionality of religion/spirituality and the diversity of well-being outcomes examined. They also partially reflect the frequent use of unrefined measures of religion/spirituality and of atheoretical approaches to studying this topic. Investigators have a fairly large number of studies on religion/spirituality and caregiver well-being on which to build. Future studies should be theory driven and utilize psychometrically sound measures of religion/spirituality. Suggestions are provided to help guide future work.

Caregivers↗

PubMed2003

Sickness certification practices of physicians: a review of the literature.

BACKGROUND: In most Western countries the responsibilities of physicians include assessing work ability and issuing certificates for sickness absence and disability pension. These tasks often have a substantial impact on the lives of patients and constitute a financial burden on employers, insurance companies, and communities. AIM: The aim was to review scientific studies on sickness certification practices of physicians published in English, Danish, Norwegian, or Swedish. METHOD: Analyses were carried out of studies searched for through literature databases, reference lists, and personal contacts. RESULTS: Twenty-six publications fulfilled the inclusion criteria. Most of these were published in the last decade. The studies focused on physicians, and occasionally on physicians and patients, but never on interaction between them. Data had generally been collected using questionnaires, some including case vignettes. There was a large variation in how long different physicians sickness-certified similar patients. Three comprehensive categories of studies were identified dealing with the following: (1). how physicians certify sickness; (2). factors that might affect the certification process; (i.e. elements related to the patient, to the physician, or to restrictions in insurance legislation); and (3). studies concerning attitudes. No studies were found that took into account the work conditions of the hospital or health-care organization in which the physician works. CONCLUSIONS: The research problems were seldom medical in nature but were instead carried out within the realm of behavioural science and should preferably be conducted using theories from behavioural, social, and public health scientific theories. Furthermore, factors such as gender, ethnicity, and power should be taken into consideration in studies on this complex phenomenon.

Disability Evaluation↗

PubMed2004

Does the architecture of hospital facilities influence nosocomial infection rates? A systematic review.

OBJECTIVE: To review the evidence regarding the effects of interventions to improve hospital design and construction on the occurrence of nosocomial infections. METHODS: Systematic review of experimental and non-experimental, architectural intervention studies in intensive care units (ICUs), surgical departments, isolation units, and hospitals in general. The studies dated from 1975, and were in English, French, German, Italian, and Spanish. Regardless of format, the studies were identified through seven medical databases, reference lists, and expert consultation. RESULTS: One hundred seventy-eight scientific articles were identified; however, none of these described a meta-analysis, systematic review, or randomized, controlled trial. Most of the articles were categorized at the lowest level of evidence (expert judgment or consensus statements). Only 17 described completed concurrent or historical cohort studies matching the inclusion criteria (ICUs, 9; surgical departments, 4; isolation units, 2; hospitals in general, 2). The interventions generally included a move to other premises or renovation. However, in many studies, the staff-to-patient ratio was also improved. Some studies showed lower infection rates after intervention, but this finding cannot be generalized because of confounding and frequently small study populations. CONCLUSIONS: The lack of stringent evidence linking hospital design and construction with the prevention of nosocomial infection is partly attributable to the multifactorial nature of these infections, and some improvement will be seen if basic conditions such as the availability of sufficient space, isolation capacity, and facilities for handwashing are met. However, to our knowledge, other factors, especially the improper hand hygiene of medical staff, have greater impact.

Architecture↗

PubMed1995

Exploring homeopathic resources on the Internet: HOMEOWEB.

Electronic mail and other forms of communication on the Internet are especially important for complementary medicine disciplines, like homeopathy, which lack an efficient academic network for research purposes. The main advantages of using the Internet for homeopathy are outlined in this article. The first step to developing an electronic communications network was to create a Homeopathic Internet Resources List, which is available on-line now, and is being updated constantly. This references the great homeopathic libraries and reference databases. Most of these have been made accessible electronically through the Internet or by e-mail, although many homeopathic physicians are still unaware of the power of Internet communication. Since the summer of 1995 the HOMEOWEB webserver has tried to bring together scientific information on all aspects of homeopathic therapy on the Internet. This service will be enlarged in the near future, and the aim is to promote the Internet as the primary means of worldwide communication among the homeopathic community, ensuring that homeopathy survives into the next century.

Computer Communication Networks↗

PubMed2003

Experience assessment and management of pain in people with dementia.

Pain is an inherently subjective experience that is difficult to prove. In a cognitively impaired older person whose verbal fluency is declining, both the experience and expression of pain are altered. Assessment poses many difficulties. Consequently the older person with dementia and pain may be under-treated and poorly managed. This review addresses each of these issues and makes recommendations for more effective care in the future. The search strategy for this review was carried out using Medline (1990-2002), Embase (1989-2001) and ClinPSYCH (1990-2001) databases. References cited within these sources were also reviewed. Searches were limited to English language studies. The quality of relevant studies retrieved was assessed and information from relevant papers synthesised using narrative summary.

Aged↗

PubMed2000

Magnesium, zinc, and chromium nutriture and physical activity.

Magnesium, zinc, and chromium are mineral elements required in modest amounts to maintain health and optimal physiologic function. For physically active persons, adequate amounts of these micronutrients are needed in the diet to ensure the capacity for increased energy expenditure and work performance. Most physically active individuals consume diets that provide amounts of magnesium and zinc sufficient to meet population standards. Women tend to consume less of these minerals than is recommended, in part because they eat less food than men. Inadequate intakes of magnesium and zinc have been reported for participants in activities requiring restriction of body weight. Dietary chromium is difficult to estimate because of a lack of appropriate reference databases. Acute, intense activity results in short-term increases in both urine and sweat losses of minerals that apparently diminish during recovery in the days after exercise. Supplemental magnesium and zinc apparently improve strength and muscle metabolism. However, evidence is lacking as to whether these observations relate to impaired nutritional status or a pharmacologic effect. Chromium supplementation of young men and women does not promote muscle accretion, fat loss, or gains in strength. Physically active individuals with concerns about meeting guidelines for nutrient intake should be counseled to select and consume foods with high nutrient densities rather than to rely on nutritional supplements. The indiscriminate use of mineral supplements can adversely affect physiologic function and impair health.

Adult↗

PubMed2026

jsPCA: fast, scalable, and interpretable identification of spatial domains and variable genes across multi-slice and multi-sample spatial transcriptomics data.

MOTIVATION: Spatial transcriptomics technologies record genome-wide measurements of gene expression with high spatial resolution. These technologies generate large and high-dimensional datasets requiring efficient automated methods for their analysis. We introduce joint spatial PCA (jsPCA), a novel, fast, scalable and interpretable method for the automatic identification of spatial domains and variable genes in multi-slice and multi-sample spatial transcriptomics data. RESULTS: jsPCA relies on a simple mathematical formulation of a spatial covariance defined as the product of the gene expression covariance with the spatial autocorrelation. The principal components of this spatial covariance yield a biologically meaningful low-dimensional representation. From this representation, spatial domains are derived by simple clustering and spatially variable genes are identified directly from the principal component coefficients. A joint representation of multiple slices and samples without spatial alignment is obtained by computing common principal components via joint diagonalization. By leveraging data sparsity and non-convex manifold optimization, jsPCA leads to computing time in the order of seconds to minutes, substantially outperforming state-of-the-art approaches. We benchmarked jsPCA against 10 state-of-the-art methods on two reference databases. Our approach demonstrated excellent performance, comparable or better than state-of-the-art methods, while being much faster, interpretable, and scalable to very large datasets.

Journal Article↗

PubMed1995

A computer system for analysis and integrated description of regulation of the molecular-genetic system of interferon induction and action.

A new theoretical approach to elaboration of an information-analytical integrated knowledge base containing data on regulation and function of biological systems is presented. The knowledge base incorporates: (i) a reference database containing experimental data on the structural-functional organization of a biological system; (ii) a dynamic mathematical model for analysis of the evolution of the system over time; and (iii) an interpretation module of simulation results. Application of this approach to theoretical investigation of the interferon system in the case of viral infection is discussed. The approach is specific in that it uses mathematical modeling technology, which allows one to generate mathematical models of different degrees of complexity in the analysis of the diverse aspects of biological system behavior. This approach allows one not only to store and to treat available experimental data, but also to acquire new knowledge about the behavior of a biological system. The proposed approach is implemented as a computer system for the IBM PC and compatibles.

Algorithms↗

PubMed2025

mettannotator: a comprehensive and scalable Nextflow annotation pipeline for prokaryotic assemblies.

SUMMARY: In recent years, there has been a surge in prokaryotic genome assemblies, coming from both isolated organisms and environmental samples. These assemblies often include novel species that are poorly represented in reference databases creating a need for a tool that can annotate both well-described and novel taxa, and can run at scale. Here, we present mettannotator-a comprehensive, scalable Nextflow pipeline for prokaryotic genome annotation that identifies coding and noncoding regions, predicts protein functions, including antimicrobial resistance, and delineates gene clusters. The pipeline summarizes these results in a GFF (General Feature Format) file that can be easily utilized in downstream analysis or visualized using common genome browsers. Here, we show how it works on 200 genomes from 29 prokaryotic phyla, including isolate genomes and known and novel metagenome-assembled genomes, and present metrics on its performance in comparison to other tools. AVAILABILITY AND IMPLEMENTATION: The pipeline is written in Nextflow and Python and published under an open source Apache 2.0 licence. Instructions and source code can be accessed at https://github.com/EBI-Metagenomics/mettannotator. The pipeline is also available on WorkflowHub: https://workflowhub.eu/workflows/1069.

Software↗

PubMed2025

SKiM: accurately classifying metagenomic ONT reads in limited memory.

MOTIVATION: Oxford Nanopore Technologies' devices, such as MinION, permit affordable, real-time DNA sequencing, and come with targeted sequencing capabilities. Such capabilities create new challenges for metagenomic classifiers that must be computationally efficient yet robust enough to handle potentially erroneous DNA reads, while ideally inspecting only a few hundred bases of a read. Currently available DNA classifiers leave room for improvement with respect to classification accuracy, memory usage, and the ability to operate in targeted sequencing scenarios. RESULTS: We present SKiM: Short K-mers in Metagenomics, a new lightweight metagenomic classifier designed for ONT reads. Compared to state-of-the-art classifiers, SKiM requires only a fraction of memory to run, and can classify DNA reads with higher accuracy after inspecting only their first few hundred bases. To achieve this, SKiM introduces new data compression techniques to maintain a reference database built from short k-mers, and treats classification as a statistical testing problem. AVAILABILITY AND IMPLEMENTATION: SKiM source code, documentation, and test data are available from: https://gitlab.com/SCoRe-Group/skim.

Metagenomics↗

PubMed2025

HI-FEVER: a Nextflow pipeline for the high-throughput discovery and annotation of endogenous viral elements.

SUMMARY: Endogenous viral elements (EVEs) offer valuable insights into virus and host evolution, but their detection remains computationally and biologically challenging. We present HI-FEVER, a user-friendly Nextflow pipeline for the discovery of EVEs in eukaryotic host genomes. HI-FEVER is highly parallelizable and customizable, ensuring computational efficiency while allowing researchers to fine-tune parameters to their specific needs. Its output provides a comprehensive analysis of discovered EVEs, including detailed annotations which can provide evolutionary insights. HI-FEVER scales seamlessly to handle millions of viral protein queries across multiple host genomes on both laptops and high-performance computing nodes. AVAILABILITY AND IMPLEMENTATION: The HI-FEVER source code is available on GitHub at https://github.com/PaleovirologyLab/hi-fever. Minimal reference databases, test datasets and benchmarking results are hosted on the Open Science Framework at https://osf.io/y357r. A detailed wiki is available at https://github.com/PaleovirologyLab/hi-fever/wiki, including usage instructions, parameter descriptions, and guidance on interpreting outputs. The pipeline includes a Pixi environment compatible with Conda and Apptainer containerization, and Docker images. HI-FEVER has been tested on Linux, Windows (via WSL2), and macOS (Intel and ARM64).

Software↗

PubMed2026

MetagenomicKG: a knowledge graph for metagenomic applications.

MOTIVATION: The sheer volume and variety of genomic content within microbial communities makes metagenomics a field rich in biomedical knowledge. To traverse these complex communities and their vast unknowns, metagenomic studies often depend on distinct reference databases, such as the Genome Taxonomy Database (GTDB), the Kyoto Encyclopedia of Genes and Genomes (KEGG), and the Bacterial and Viral Bioinformatics Resource Center (BV-BRC), for various analytical purposes. These databases are crucial for the genetic and functional annotation of microbial communities. Nevertheless, the inconsistent nomenclature or identifiers of these databases present challenges for effective integration, representation, and utilization. Knowledge graphs (KGs) offer an appropriate solution by organizing biological entities from different databases to standardized identifiers, allowing their interrelations to be captured into a cohesive network regardless of the naming conventions used in each source. The graph structure not only facilitates the unveiling of hidden patterns but also enriches our biological understanding with deeper insights. Despite KGs having shown potential in various biomedical fields, their application in metagenomics remains underexplored. RESULTS: We present MetagenomicKG, a novel knowledge graph specifically tailored for metagenomic analysis. MetagenomicKG integrates taxonomic, functional, and pathogenesis-related information on the human microbiome sourced from various databases, and further connects these with existing biomedical KGs to expand the biological network. Through various case studies involving the human microbiome, we demonstrate its utility in enabling hypothesis generation regarding the relationships between microbes and diseases, generating sample-specific graph embeddings, and providing robust pathogen prediction. CODE AVAILABILITY: The source code and technical details for constructing the MetagenomicKG and reproducing all analyses are available on GitHub at https://github.com/KoslickiLab/MetagenomicKG. The data used in this manuscript, including the pre-built files and use case input data, are archived on Zenodo with DOI: 10.5281/zenodo.17546861.

Metagenomics↗

PubMed2004

galaxie--CGI scripts for sequence identification through automated phylogenetic analysis.

MOTIVATION: The prevalent use of similarity searches like BLAST to identify sequences and species implicitly assumes the reference database to be of extensive sequence sampling. This is often not the case, restraining the correctness of the outcome as a basis for sequence identification. Phylogenetic inference outperforms similarity searches in retrieving correct phylogenies and consequently sequence identities, and a project was initiated to design a freely available script package for sequence identification through automated Web-based phylogenetic analysis. RESULTS: Three CGI scripts were designed to facilitate qualified sequence identification from a Web interface. Query sequences are aligned to pre-made alignments or to alignments made by ClustalW with entries retrieved from a BLAST search. The subsequent phylogenetic analysis is based on the PHYLIP package for inferring neighbor-joining and parsimony trees. The scripts are highly configurable. AVAILABILITY: A service installation and a version for local use are found at http://andromeda.botany.gu.se/galaxiewelcome.html and http://galaxie.cgb.ki.se

Algorithms↗

PubMed2003

The effects of clean indoor air laws: what do we know and what do we need to know?

Our objective was to review the research on the effects of public clean air laws on smoking rates, compare these effects to those found in studies on the impact of private worksite restrictions and derive estimates of the potential reductions in smoking rates that might be expected from the implementation of the two types of policies. Data sources were computerized databases, references identified from pertinent peer-reviewed journal articles and books, and suggestions by experts on tobacco control policy. Comprehensive public clean air laws have the potential to reduce prevalence and consumption rates of the entire population (including non-working and non-indoor working smokers) by about 10%. Studies on private worksite regulations also suggest that strong worksite restrictions have the potential to reduce the prevalence rate of the entire population by about 6% over the long-term and the quantity smoked by continuing smokers by 28%, depending on the length of time after the ban. Further research is needed on the effects of the different types of public clean air policies on the entire smoking population and on different sociodemographic groups, how the effects of public clean indoor air laws depend on private restrictions already in place, and how the effect of private restrictions depend on whether or not they are supported by public clean air laws.

Adolescent↗

PubMedDate not supplied

Use of short, wide-bore capillary columns in GC toxicological screening.

The usefulness of wide-bore, thick film capillary columns for routine toxicological screening was assessed. Two such columns were examined: fused silica CPSil 5CB (i.d., 0.53 mm; length, 10 m; film thickness, 5.2 microns) and glass SPB-1 (i.d. 0.75 mm; length, 30 m; film thickness, 1.0 micron). A standard packed column filled with 3% OV-1 (i.d., 2 mm; length, 1.5 m) and a medium-bore fused silica column CPSil 5 (i.d., 0.32 mm; length, 25 m; film thickness, 0.4 micron) were examined for comparison. Mixtures of alkanes and drugs, as well as biological samples from routine casework, were analyzed. Both types of wide-bore columns proved to be very useful in routine toxicological practice, due to satisfactory efficiency, high capacity, and ease of installation. The retention index values of various drugs, examined on wide-bore columns, were in agreement with the reference database obtained from packed columns.

Autopsy↗