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Results for “Integrative taxonomy”

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At least 109 records · Page 6Linked to original sources

PubMed1994

Cognitive-behavioral classifications of chronic pain: replication and extension of empirically derived patient profiles.

Many attempts have been made to classify patients with chronic pain in order to make sense of a very complex problem and to direct patients towards appropriate treatments for their condition. Unfortunately, these efforts have not been empirically based and have demonstrated limited clinical use. Predominant emphasis has been placed on either biomedical or psychopathological elements of the chronic pain experience with little integration of cognitive-behavioral factors. Turk and Rudy (1988) introduced an empirically derived pain patient taxonomy based on analyses of the Multidimensional Pain Inventory (MPI). The primary purpose of the present study was to replicate this classification system by using different measures for similar constructs in different groups of chronic pain patients. Items designed to measure 4 constructs (activity interference, emotional distress, pain intensity, and perceived support) were collected from 1594 pain patients evaluated at two separate pain treatment facilities. Confirmatory factor analytic results indicated high reliability of the items in measuring these 4 constructs. Replicated clustering techniques demonstrated the robustness of 3 patient profiles across the patient samples. The 3 clusters corresponded remarkably well to the groups initially labeled by Turk and Rudy (1988) as Dysfunctional, Interpersonally Distressed and Adaptive Copers. External validation of the classification system supported replication of the 3 groups and offered further interpretational clarity to the patient profiles. Strong evidence was found for a taxonomy of 3 chronic pain patient groups. Implication for predicting treatment outcome and for future research are discussed.

Adult↗

PubMed2005

HAGR: the Human Ageing Genomic Resources.

The Human Ageing Genomic Resources (HAGR) is a collection of online resources for studying the biology of human ageing. HAGR features two main databases: GenAge and AnAge. GenAge is a curated database of genes related to human ageing. Entries were primarily selected based on genetic perturbations in animal models and human diseases as well as an extensive literature review. Each entry includes a variety of automated and manually curated information, including, where available, protein-protein interactions, the relevant literature, and a description of the gene and how it relates to human ageing. The goal of GenAge is to provide the most complete and comprehensive database of genes related to human ageing on the Internet as well as render an overview of the genetics of human ageing. AnAge is an integrative database describing the ageing process in several organisms and featuring, if available, maximum life span, taxonomy, developmental schedules and metabolic rate, making AnAge a unique resource for the comparative biology of ageing. Associated with the databases are data-mining tools and software designed to investigate the role of genes and proteins in the human ageing process as well as analyse ageing across different taxa. HAGR is freely available to the academic community at http://genomics.senescence.info.

Aging↗

PubMed2026

Mutual Information-based Prognostic Biomarker Discovery in Cancer Genomics: Conceptual Framework and Representative Applications of MI-POG.

Mutual information (MI)-based approaches have increasingly been applied to cancer genomics; however, their use for genome-wide prognostic biomarker discovery remains relatively underexplored. The present article summarizes the conceptual workflow of Mutual Information-based Prognostic Omics Gene (MI-POG) based on previously published applications in breast cancer, lower-grade glioma, and other cancer datasets. The framework consists of clinical endpoint discretization, genome-wide MI-based screening, candidate ranking, and downstream validation using conventional survival-analysis approaches. Previous MI-POG applications identified solute carrier family 20 member 1 (SLC20A1) as a prognostic biomarker in hormone receptor-positive breast cancer. Elevated SLC20A1 expression was associated with unfavorable survival outcomes and was independently validated in the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) cohort. Methodological analyses demonstrated how survival endpoints can be integrated into an information-theoretic framework through fixed-time outcome discretization, enabling model-independent assessment of molecular-clinical dependencies. Applications across multiple cancer datasets suggested the potential applicability of the framework across biologically distinct tumor types, although further validation will be required to establish its robustness and generalizability. In conclusion, MI-POG can be formalized as an information-theoretic framework for genome-wide identification of prognostic biomarkers by quantifying molecular-clinical dependencies using mutual information. Representative applications from previously published studies suggest that MI-POG may complement conventional survival-analysis approaches and provide a useful strategy for biomarker discovery, although additional benchmarking and prospective validation will be required.

Humans↗

PubMed2026

SimpleMicrobiome: An integrated web-based platform for streamlined microbiome data analysis and visualization.

Microbiome studies require multiple analytical steps after initial sequence processing. These steps commonly include data harmonization, preprocessing, taxonomic profiling, diversity analysis, differential abundance testing, predictive modeling, network inference, and preparation of publication-ready outputs. Although robust packages are available for many of these tasks, routine use often depends on command-line workflows, repeated data reformatting, and method-specific scripting. These requirements can limit accessibility for experimental researchers and complicate consistent analysis across interdisciplinary teams. We developed SimpleMicrobiome, a web-based R Shiny platform that integrates established microbiome analysis methods into a single interactive downstream workflow. The application accepts standard abundance, taxonomy, and metadata tables, supports interactive preprocessing and sample filtering, and provides modules for taxa profile visualization, alpha and beta diversity analysis, ANCOM-BC2 and MaAsLin2 differential abundance testing, Random Forest modeling with SHAP-based interpretation, microbial association network inference using SparCC and SPIEC-EASI through NetCoMi, correlation heatmaps, and dbRDA/CAP-style association biplots. The platform is implemented as a modular Shiny application so that preprocessing choices are propagated across downstream analyses, results can be exported as figures and tables, and the same application can be run through the public server, source-code installation, or a Docker image. SimpleMicrobiome consolidates major downstream microbiome analysis tasks in an accessible browser-based environment while retaining links to established analytical frameworks. The platform may reduce technical barriers for non-programming users, improve consistency across exploratory and reporting-oriented analyses, and support collaborative microbiome research. The public application is available at https://simplemicrobiome.mglab.org, the source code is available at https://github.com/yjcho2252/SimpleMicrobiome, and a Docker image for local deployment is available at https://hub.docker.com/r/mglab2252/simplemicrobiome.

differential abundance↗

PubMed2006

BioWarehouse: a bioinformatics database warehouse toolkit.

BACKGROUND: This article addresses the problem of interoperation of heterogeneous bioinformatics databases. RESULTS: We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL) but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research. CONCLUSION: BioWarehouse embodies significant progress on the database integration problem for bioinformatics.

Computational Biology↗

PubMed1998

Perspectives on the biodiversity of parasitic protozoa in Australia.

Biodiversity is a term applied to described the number, variety and variability of organisms. Its colloquial application is usually as a measure of species diversity of species richness. Thus, the concepts of "species" and "species boundaries" are integral to any discussion on biodiversity, and with them, the basal question of what constitutes meaningful variation. Protozoan taxonomy is an evolving mix of morphological and molecular characters, and is based largely on decisions made intuitively and arbitrarily using multiple characters. Where to draw species boundaries has become more difficult in the face of a bewildering level of variation uncovered in recent years, due largely to an increase in the resolution of our taxonomic techniques (e.g., ultrastructural and genetic studies). A major challenge for contemporary protozoan taxonomists is to update the existing systematic framework to incorporate our current level of knowledge and to decide on the relative importance of parasite morphology, genetics and biology to the concept of the protozoan "species". This task is compounded by the relative paucity of information on our endemic protozoan parasites. In Australia, even in vertebrate hosts, little is known of the biodiversity of parasitic protozoa. Not surprisingly, what knowledge we do have is linked to clinical disease, e.g., detailed knowledge of some species of coccidia and of some enteric ciliates, flagellates and amoebae of mammals. We have some knowledge of a few species of haemosporidia of reptiles and birds but, even here, molecular studies and experimental work are required to identify species boundaries. In view of these limitations, the best estimate of the biodiversity of Australia's parasitic protozoa in at least the vertebrate fauna of Australia, is that less than one third of the total species have been discovered to date.

Amphibians↗

PubMed2003

Characterization of Cryptosporidium spp.--recent developments and future needs.

Cryptosporidia, widely distributed protozoan parasites of vertebrates have recently attracted increasing interest due to several serious waterborne outbreaks, the life-threatening nature of infection in immunocompromised patients, and the realization of economic losses caused by these pathogens in livestock. Genetic polymorphism within Cryptosporidium spp. is being detected at a continuously growing rate, owing to the widespread use of modern molecular techniques. The aim of this paper is to review the current status of taxonomy, genotyping, molecular phylogeny, and characterization of cryptosporidia, and to highlight the need for polyphasic typing, i.e. an integrated approach comprising standardized morphologic, biologic, and molecular methods for describing Cryptosporidium species and isolates, and for establishing "virtual" reference strains.

Animals↗

PubMed1999

Approaching psychotherapy of the personality disorders from the Millon perspective.

Millon's integrative model for a clinical science begins with a theory that is consistent with current knowledge, establishes a taxonomy for classification, develops a coordinated assessment system, and develops and implements interventions with the guidance of the preceding elements of the model. In recent years, work on the last step of the model, clinical interventions, has accelerated rapidly, and the model now permits the therapist to directly extrapolate specific treatment goals, objective, and techniques to the practice of therapy with the individual patient. This article summarizes how treatment planning and implementation flows logically from the Millon model.

Humans↗

PubMed2026

Genome-resolved analysis of colonization factor repertoires reveals ecological stratification in cervid gut microbiomes.

INTRODUCTION: Colonization factors (CFs) are important microbial traits associated with persistence and host adaptation in the gut, yet their large-scale organization in cervid gut microbiomes remains unclear. METHODS: A total of 3,311 non-redundant high-quality metagenome-assembled genomes (MAGs), derived from 688 cervid gut metagenomic samples across 15 publicly available projects and one in-house dataset, were analyzed. CF-associated genes were identified by comparison against the GHA CF database, and CF repertoires were characterized at genome, host-species, and gastrointestinal-segment levels. RESULTS: A total of 138,729 CF-associated genes spanning 71 CF families were identified. MAGs from Cervinae contained richer CF repertoires than those from Caprinae, and CF47 (Peptidase_C69), CF24_29 (QueH), and CF18 (Glycos_transf_2) were among the most prevalent families. CF repertoires were strongly structured by taxonomy, showed a moderate association with bacterial phylogenetic distance, and formed two recurrent genome-level configurations with distinct KEGG functional profiles. Integration of sample metadata further revealed differentiation of CF repertoires across host species and gastrointestinal segments, representing the major ecological dimensions examined in this study. Segment-associated CF variation was accompanied by redistribution of broader functional profiles, including enrichment of carbohydrate and lipid metabolism in the jejunum, membrane transport in the ileum, xenobiotics biodegradation in the cecum, and environmental adaptation in the rumen. DISCUSSION: These findings provide a genome-resolved view of CF repertoire organization in cervid gut microbiomes and demonstrate that colonization-associated functions are structured across microbial lineages and ecological contexts. This study highlights the importance of considering microbial taxonomy and host-associated environments when interpreting the distribution of CF repertoires in mammalian gut ecosystems.

Cervidae↗

PubMedDate not supplied

Trauma-related dissociation: conceptual clarity lost and found.

OBJECTIVE: Imprecise conceptualizations of dissociation hinder understanding of trauma-related dissociation. An heuristic resolution for research and clinical practice is proposed. METHOD: Current conceptualizations of dissociation are critically examined. They are compared with a new theory that incorporates classical views on dissociation with other contemporary theories related to traumatization, viewing dissociation as a lack of integration among psychobiological systems that constitute personality, that is, as a structural dissociation of the personality. RESULTS: Most current views of dissociation are overinclusive and underinclusive. They embrace non-dissociative phenomena--rigid alterations in the level and field of consciousness--prevalent in non-traumatized populations, and which do not require structural dissociation. These views also largely disregard somatoform and positive symptoms of dissociation and underestimate integrative deficiencies, while emphasizing the psychological defensive function of dissociation. They do not offer a common psychobiological pathway for the spectrum of trauma-related disorders. Structural dissociation of the personality likely involves divisions among at least two psychobiological systems, each including a more or less distinct apperceptive centre, that is, a dissociative part of the personality. Three prototypical levels of structural dissociation are postulated to correlate with particular trauma-related disorders. CONCLUSIONS: Limitation of the concept of dissociation to structural dividedness of the personality sets it apart from related but non-dissociative phenomena and provides a taxonomy of dissociative symptoms. It postulates a common psychobiological pathway for all trauma-related disorders. Trauma-related dissociation is maintained by integrative deficits and phobic avoidance. This conceptualization advances diagnosis, classification, treatment and research of trauma-related disorders.

Brain Injuries↗

PubMed2026

Stenotrophomonas maltophilia in the Antimicrobial Resistance Era: Species-Complex Taxonomy, Pathogenesis, Evolving Therapeutic Priorities, and Genomic Surveillance.

Stenotrophomonas maltophilia is a globally distributed, aerobic, non-fermenting Gram-negative bacillus increasingly recognized as an opportunistic pathogen in hospitalized and immunocompromised patients. Clinical interpretation is challenging because respiratory and device-associated isolates may represent colonization, polymicrobial infection, or true invasive disease. Recent genomic studies further suggest that organisms historically identified as S. maltophilia comprise a genetically diverse species complex, with implications for epidemiology, virulence, resistance surveillance, and susceptibility testing. Treatment is difficult because of biofilm formation, persistence in water-associated healthcare reservoirs, and intrinsic or acquired resistance mediated by L1 and L2 β-lactamases, multidrug efflux pumps, reduced permeability, mobile resistance determinants, and biofilm-associated tolerance. Current IDSA guidance identifies cefiderocol monotherapy as the preferred treatment for invasive S. maltophilia infection, whereas aztreonam-avibactam and agents such as trimethoprim-sulfamethoxazole, levofloxacin, and minocycline occupy alternative or combination-based roles. Nevertheless, the therapeutic evidence base remains uneven, and clinical decisions should integrate infection severity, source control, susceptibility findings, pharmacokinetic/pharmacodynamic (PK/PD) exposure, toxicity, infection site, and host-related factors. This review summarizes advances in taxonomy, epidemiology, pathogenesis, diagnostics, resistance, treatment, infection prevention, and genomic surveillance, and highlights the need for standardized identification, validated breakpoints, prospective comparative-effectiveness studies, and pragmatic or adaptive trial designs.

L1 β-lactamase↗

PubMed2001

An evaluation of the utility of the CEN categorical structure for nursing diagnoses as a terminology model for integrating nursing diagnosis concepts into SNOMED.

We evaluated the utility of the CEN Categorical Structure for Nursing Diagnoses as a terminology model for integrating nursing diagnosis concepts into SNOMED. First, we dissected nursing diagnosis term phrases from two source terminologies (North American Nursing Diagnosis Association (NANDA) Taxonomy 1 and Omaha System) into the semantic categories of the CEN categorical structure. Second, we critically analyzed the similarities between the semantic links in the CEN model and the semantic links used to formally define diagnostic concepts in SNOMED RT and SNOMED CT. Our findings demonstrated that focus, bearer, and judgment were present in 100% of the NANDA and Omaha term phrases. The Omaha term phrases contained no additional descriptors beyond those considered mandatory in the CEN model. In contrast, at least 3% of NANDA diagnoses included a term in each semantic category of the categorical structure. The comparison among the semantic links showed that neither SNOMED RT and SNOMED CT currently contain all the semantic links needed to model the two source terminologies for integration. In conclusion, our findings support the potential utility of the CEN categorical structure as a terminology model for dissecting nursing diagnostic concepts for integration into SNOMED RT and SNOMED CT. However, in order to accomplish this task, appropriate semantic links must be added to SNOMED RT and SNOMED CT.

Nursing Diagnosis↗

PubMed2005

An integrated approach to fast and informative morphological vouchering of nematodes for applications in molecular barcoding.

Molecular surveys of meiofaunal diversity face some interesting methodological challenges when it comes to interstitial nematodes from soils and sediments. Morphology-based surveys are greatly limited in processing speed, while barcoding approaches for nematodes are hampered by difficulties of matching sequence data with traditional taxonomy. Intermediate technology is needed to bridge the gap between both approaches. An example of such technology is video capture and editing microscopy, which consists of the recording of taxonomically informative multifocal series of microscopy images as digital video clips. The integration of multifocal imaging with sequence analysis of the D2D3 region of large subunit (LSU) rDNA is illustrated here in the context of a combined morphological and barcode sequencing survey of marine nematodes from Baja California and California. The resulting video clips and sequence data are made available online in the database NemATOL (http://nematol.unh.edu/). Analyses of 37 barcoded nematodes suggest that these represent at least 32 species, none of which matches available D2D3 sequences in public databases. The recorded multifocal vouchers allowed us to identify most specimens to genus, and will be used to match specimens with subsequent species identifications and descriptions of preserved specimens. Like molecular barcodes, multifocal voucher archives are part of a wider effort at structuring and changing the process of biodiversity discovery. We argue that data-rich surveys and phylogenetic tools for analysis of barcode sequences are an essential component of the exploration of phyla with a high fraction of undiscovered species. Our methods are also directly applicable to other meiofauna such as for example gastrotrichs and tardigrades.

Animals↗

PubMed2001

Introduction of green fluorescent protein gene into phenol-degrading Alcaligenes faecalis cells and their monitoring in phenol-contaminated soil.

Alcaligenesfaecalis (CCT 7145) was isolated from an Amazonian soil sample after an enrichment process to select for phenol-degrading microorganisms. The isolate was labeled with the green fluorescent protein (gfp) gene. The gfp-transformed cells were easily detected using a hand-held UV transilluminator and their taxonomy was confirmed by 16S rRNA sequencing. Polymerase chain reaction (PCR) and Southern blot analyses confirmed that the gfp gene was integrated into the chromosome. The addition of the gfp marker did not affect phenol degradation ability compared with the wild-type. Both, wild-type and gfp-marked A. faecalis cells encapsulated in alginate, tolerated 1,700 microg ml(-1) phenol in liquid medium compared with 1,100 microg ml(-1) phenol for free cells. 14C-Phenol mineralization in soil microcosms was also enhanced by inoculation with encapsulated cells. Survival of gfp-marked cells in phenol-contaminated soil over 22 days was determined from plate counts using an epifluorescence microscope.

Alcaligenes↗

PubMed2002

An evaluation of the usefulness of two terminology models for integrating nursing diagnosis concepts into SNOMED Clinical Terms.

OBJECTIVES: We evaluated the usefulness of two models for integrating nursing diagnosis concepts into SNOMED Clinical Terms (CT). METHODS: First, we dissected nursing diagnosis term phrases from two source terminologies (North American Nursing Diagnosis Association Taxonomy 1 (NANDA) and Omaha System) into the semantic categories of the European Committee for Standardization (CEN) categorical structure and ISO reference terminology model (RTM). Second, we critically analyzed the similarities between the semantic links in the CEN and ISO models and the semantic links used to formally define diagnostic concepts in SNOMED CT. RESULTS: Our findings demonstrated that focus, bearer/subject of information, and judgment were present in 100% of the NANDA and Omaha term phrases. The Omaha term phrases contained no additional descriptors beyond those considered mandatory in the CEN and ISO models. The comparison among the semantic links showed that SNOMED CT currently contains all but one of the semantic links needed to model the two source terminologies for integration. In conclusion, our findings support the potential utility of the CEN and ISO models for integrating nursing diagnostic concepts into SNOMED CT.

Classification↗

PubMedDate not supplied

[Nursing diagnoses in cardiac surgery patients].

Exploratory and transversal research accomplished with postoperative patients outgoing coronary bypass. It was aimed at identifying nursing diagnoses according to Taxonomy II of NANDA and nursing interventions according to Nursing Interventions Classification, associating with the results of Nursing Outcomes Classification. The data were collected fom 22 patients using formularies and physical examination. The information made possible the identification of fifteen nursing diagnosis, according to Taxonomy II of NANDA. Among them, stand out: risk of infection; Risk of constipation; Deficit in self-care intimate hygiene and integrity of harmed skin. The study revealed being fundamental to develop studies about nursing diagnoses to direct analyses of problems that concern to the demanding patients of specific nursing actions, that contribute to the devepoment of the profession.

Adult↗

PubMed2003

Lessons from a quiet classic.

Parasitology has a rich tradition of studies linking taxonomy, ecology, and life cycles and development. This tradition has produced an enormous amount of empirical evidence demonstrating that parasites form highly integrated reproductive-developmental-ecological systems that are highly persistent through space and time. As well, phylogenetic studies of parasites, especially of parasitic platyhelminths, represent 1 of the most progressive areas of systematic biology. Consequently, parasitologists should be at the forefront of research in evolutionary developmental biology (evo-devo) and integrative biology, and parasite systems should be model systems of choice for those research programs. Species of the digenean, Alloglossidium, provide a superb exemplar for such studies because we know so much about their phylogeny, population biology, ecology, and life cycles. Equally important is the recognition that Alloglossidium spp. is such an outstanding model system because of more than 30 yr of effort by a number of people working with little funding at small institutions, beginning with a short unassuming species description by Gerald D. Schmidt. For dedicated and creative scientists, the size of the institution and the research budget need not be an impediment to producing high-quality research. These are the people who produce the quiet classics, and they need to be recognized for their invaluable contributions.

Animals↗

PubMed1981

A new pattern discriminant method for evoked potentials.

A statistical approach to evaluate evoked potentials (EPs), consisting of three stages in procedure, was proposed with an application to study on postictal changes of visually evoked potentials (VEPs). At the first step, time series data of EPs were reduced by the means of using an autoregressive (AR) model. In this way, EPs were described in terms of AR coefficient vectors. Then statistical distances which are well known as the Mahalanobis' distances were determined as a scale for dissimilarity between patterns of EPs. At the third stage, a retrospective classification through a numerical taxonomy based on similarity of patterns was demonstrated. This procedure will tell us some standards for future experiments as well as an integrative insight of results from present experiment. By the above method, it was suggested that there may be two different processes in postictal recovery of kindled cats.

Animals↗