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PubMed2003

Introduction to the integrated model: medical, surgical and psychological therapies for the couple.

The integrated model is the interplay of behavioural, cognitive, medical, and surgical approach to sexual problems. Research demonstrates that prognosis and outcome of patients with sexual diseases dramatically improve when medical solutions are proposed along with the evaluation of the therapies' sexual impact on the couple's dynamics. Current classification of treatments for erectile dysfunction (here used as a paradigm of sexual disorder therapies) distinguishes between central and peripheral "initiators" and "conditioners" of erection. However, such a taxonomy does not take into account the impact on the couple, the final recipient of the treatment. For this reason, we propose here a new, couple-based sexological taxonomy which divides therapies into "harmonious" and "inharmonious". Pilot data are also presented on the use of a carnitine analogue as a model of an etiological, harmonious therapy for impotence. The integrated model suggests a strict collaboration between sexologists of different areas. Considering the growing complexity of therapies for sexual symptoms and diseases, there seems to be a need for the new professional figure of the medical sexologist.

Couples Therapy↗

PubMed1993

Taxonomy of subjective phenomena: a neuropsychological basis of functional assessment of ischemic or traumatic brain lesions.

A proper evaluation of functional competence after central lesions has to be based on a classification of functions that one can agree upon. It is a sad fact in neuropsychology that such a classification is not available. An attempt will be made to discuss such a classification (or taxonomy) that might be useful. The basic idea is that elementary psychological functions are evolutionary products whose availability is dependent on the functional integrity of neuronal modules. Such modules are embedded neuronal mechanisms that are linked to localized structures or distributed neuronal algorithms. Constancy of interindividual loss of psychological functions associated with lesions of modules can be used to define a catalogue of functions. Using this principle one can differentiate four areas of psychological functions that are represented in a modular fashion. These areas are stimulus representations ("perception"), processing of information ("learning and memory"), evaluation of information (for instance by emotions), and finally action or reaction. Functional competence is, however, not only described by the potential availability of elementary psychological functions, but also by formal aspects, i.e. how functions are made available. Such formal aspects refer to activation and in particular to temporal problems of neuronal processing. A particular "time machine" will be discussed which is essential for functional competence. Central lesions may either effect the what of functions or the how of functions. A differentiation between these material and formal aspects of functional competence are essential with respect to recovery or restitution of function.

Algorithms↗

PubMed1999

An integration system to rapidly identify aquatic bacteria.

An identification system for aquatic bacteria which would be useful for aspects ranging from pollution monitoring to health care, is described. It contains relevant information concerning the nature, taxonomy and activity of aquatic bacteria and allows to identify fresh isolates by means of their chemotaxonomic profiles. The system is simple and user friendly, so that it can be used by people not familiar with computers and has a modular interface that allows an easy interaction with laboratory instruments. The system is also connected with artificial neural network based programs to identify strains starting from the considered chemotaxonomic features.

Bacteria↗

PubMed2026

FANTASIA suite: a reproducible and configurable framework for embedding-based functional annotation of proteins.

Embedding-based annotation transfer is increasingly used for protein function inference due to protein language models capture sequence, structural, and functional signals that may extend beyond conventional pairwise similarity. However, systematic application of these approaches requires control over model choice, reference composition, lookup parameters, evidence traceability, and output formats. We developed the FANTASIA suite, a configurable framework for embedding-based functional annotation of proteins. The suite combines a database-backed implementation for reproducible and extensible analyses with a portable flat-file implementation for rapid local annotation and pipeline integration. Using non-model and model-organism proteomes, we show that larger neighbourhood sizes remain practical for proteome-scale analyses and that taxonomy and sequence-identity filtering support leakage-aware benchmarking. We also compare the supported models with baseline methods through external CAFA5 evaluation and provide practical guidance based on empirical evidence variables. FANTASIA provides a controlled, scalable, and reproducible framework for extending functional annotation across the rapidly expanding diversity of sequenced organisms.

Software↗

PubMed2002

Shape recovery algorithms using level sets in 2-D/3-D medical imagery: a state-of-the-art review.

The class of geometric deformable models, also known as level sets, has brought tremendous impact to medical imagery due to its capability of topology preservation and fast shape recovery. In an effort to facilitate a clear and full understanding of these powerful state-of-the-art applied mathematical tools, this paper is an attempt to explore these geometric methods, their implementations and integration of regularizers to improve the robustness of these topologically independent propagating curves/surfaces. This paper first presents the origination of level sets, followed by the taxonomy of level sets. We then derive the fundamental equation of curve/surface evolution and zero-level curves/surfaces. The paper then focuses on the first core class of level sets, known as "level sets without regularizers." This class presents five prototypes: gradient, edge, area-minimization, curvature-dependent and application driven. The next section is devoted to second core class of level sets, known as "level sets with regularizers." In this class, we present four kinds: clustering-based, Bayesian bidirectional classifier-based, shape-based and coupled constrained-based. An entire section is dedicated to optimization and quantification techniques for shape recovery when used in the level set framework. Finally, the paper concludes with 22 general merits and four demerits on level sets and the future of level sets in medical image segmentation. We present applications of level sets to complex shapes like the human cortex acquired via MRI for neurological image analysis.

Algorithms↗

PubMedDate not supplied

Caring as an imperative for nursing education.

Caring is a universal need that is an important component in the delivery of nursing care. Nurse educators face the challenge of teaching the value of caring as a necessary part of nursing. Watson's theoretical framework, which focuses on interpersonal and transpersonal processes in human care, presents an effective model in understanding the concept of caring (1). Krathwohl, Bloom, and Masia's model of affective domain provides a taxonomy of affective competencies that guides the process of value development (2). Both models enhance our understanding of caring and provide the theoretical foundation for integrating caring into nursing education. This article describes an associate degree program's effort to thread the concept of caring across its curriculum. It includes an overview of the steps used for integrating caring in individual clinical courses and emphasizes teaching/learning and assessment strategies used in the educational process.

Affect↗

PubMed2004

Metabolite profiling of fungi and yeast: from phenotype to metabolome by MS and informatics.

Filamentous fungi and yeast from the genera Saccharomyces, Penicillium, Aspergillus, and Fusarium are well known for their impact on our life as pathogens, involved in food spoilage by degradation or toxin contamination, and also for their wide use in biotechnology for the production of beverages, chemicals, pharmaceuticals, and enzymes. The genomes of these eukaryotic micro-organisms range from about 6000 genes in yeasts (S. cerevisiae) to more than 10,000 genes in filamentous fungi (Aspergillus sp.). Yeast and filamentous fungi are expected to share much of their primary metabolism; therefore much understanding of the central metabolism and regulation in less-studied filamentous fungi can be learned from comparative metabolite profiling and metabolomics of yeast and filamentous fungi. Filamentous fungi also have a very active and diverse secondary metabolism in which many of the additional genes present in fungi, compared with yeast, are likely to be involved. Although the 'blueprint' of a given organism is represented by the genome, its behaviour is expressed as its phenotype, i.e. growth characteristics, cell differentiation, response to the environment, the production of secondary metabolites and enzymes. Therefore the profile of (secondary) metabolites--fungal chemodiversity--is important for functional genomics and in the search for new compounds that may serve as biotechnology products. Fungal chemodiversity is, however, equally efficient for identification and classification of fungi, and hence a powerful tool in fungal taxonomy. In this paper, the use of metabolite profiling is discussed for the identification and classification of yeasts and filamentous fungi, functional analysis or discovery by integration of high performance analytical methodology, efficient data handling techniques and core concepts of species, and intelligent screening. One very efficient approach is direct infusion Mass Spectrometry (diMS) integrated with automated data handling, but a full metabolic picture requires the combination of several different analytical techniques.

Biochemistry↗

PubMed1992

On "genomenclature": a comprehensive (and respectful) taxonomy for pseudogenes and other "junk DNA".

Genomic nomenclature has not kept pace with the levels and depth of analyzing and understanding genomic structure, function, and evolution. We wish to propose a general terminology that might aid the integrated study of evolution and molecular biology. Here we designate as a "nuon" any stretch of nucleic acid sequence that may be identifiable by any criterion. We show how such a general term will facilitate contemplation of the structural and functional contributions of such elements to the genome in its past, current, or future state. We focus in this paper on pseudogenes and dispersed repetitive elements, since their current names reflect the prevalent view that they constitute dispensable genomic noise (trash), rather than a vast repertoire of sequences with the capacity to shape an organism during evolution. This potential to contribute sequences for future use is reflected in the suggested terms "potonuons" or "potogenes." If such a potonuon has been coopted into a variant or novel function, an evolutionary process termed "exaptation," we employ the term "xaptonuon." If a potonuon remains without function (nonaptive nuon), it is a "nonaptation" and we term it "naptonuon." A number of examples for potonuons and xaptonuons are given.

Animals↗

PubMedDate not supplied

Ethnographic analysis of everyday ethics in the care of nursing home residents with dementia: a taxonomy.

BACKGROUND: The concept of everyday ethics was used to emphasize the moral basis of ordinary issues of daily living affecting quality of life for nursing home residents with dementia. OBJECTIVES: To critically examine ethical issues of daily living affecting nursing home residents with dementia and to construct a descriptive taxonomy inductively derived from ethnographic fieldwork data. METHOD: Combined anthropological methods of participant observation and in-depth interviewing were used in the natural setting of a 147-bed, voluntary, not-for-profit nursing home. Experiences of 30 residents, their family members, and nursing home staff were explored. In addition, the records of 10 ethics committee cases involving residents with dementia further enlarged the database. RESULTS: The taxonomy of everyday ethical issues includes the following four domains: (a) learning the limits of intervention; (b) tempering the culture of surveillance and restraint; (c) preserving the integrity of the individual; and (d) defining community norms and values. Each is representative of constellations of concerns that are grounded in the cultural and moral environment of the nursing home. CONCLUSIONS: Results highlight the challenges of recognizing the ethical in the ordinary, and of resolving everyday issues in ways that enhance quality of life for residents with dementia and those (family and staff) who care for them.

Activities of Daily Living↗

PubMedDate not supplied

Using a comprehensive taxonomy of diagnoses to describe the practice of pediatric nurse practitioners: findings of a field study.

The goal of this study was to develop and field test a classification of diagnoses for use by pediatric nurse practitioners. A secondary goal was to describe the clinical practice of pediatric nurse practitioners in a way using a classification that integrates medical, nursing, and developmental diagnoses. Six pediatric nurse practitioners were oriented to the system, established interrater reliability, and then used the system to record their diagnoses for 240 consecutive patients each. The pediatric nurse practitioners used more than 3000 diagnoses with 1450 cases. Their scope of practice included 1% developmental problems, 72% pediatric diseases, which included 51% illnesses and 21% disease prevention and screening, and 27% daily living problems. Pediatric nurse practitioner coders evaluated the system in positive terms. Issues related to the use of a taxonomy such as this one for practicing clinicians were discussed.

Adolescent↗

PubMed2006

SSRPrimer and SSR Taxonomy Tree: Biome SSR discovery.

Simple sequence repeat (SSR) molecular genetic markers have become important tools for a broad range of applications such as genome mapping and genetic diversity studies. SSRs are readily identified within DNA sequence data and PCR primers can be designed for their amplification. These PCR primers frequently cross amplify within related species. We report a web-based tool, SSR Primer, that integrates SPUTNIK, an SSR repeat finder, with Primer3, a primer design program, within one pipeline. On submission of multiple FASTA formatted sequences, the script screens each sequence for SSRs using SPUTNIK. Results are then parsed to Primer3 for locus specific primer design. We have applied this tool for the discovery of SSRs within the complete GenBank database, and have designed PCR amplification primers for over 13 million SSRs. The SSR Taxonomy Tree server provides web-based searching and browsing of species and taxa for the visualisation and download of these SSR amplification primers. These tools are available at http://bioinformatics.pbcbasc.latrobe.edu.au/ssrdiscovery.html.

Classification↗

PubMedDate not supplied

A nurse-staffing taxonomy for decision making in long-term care nursing facilities.

A nurse-staffing taxonomy is proposed to facilitate informed staffing decisions in long-term care nursing facilities and to set forth construct components for empirically related research. Recommendations from an expert workgroup were synthesized with current staffing research to define a staffing taxonomy. Refinements were made, incorporating on-site nursing home quality assessments and concepts founded on psychometric theory and Donabedian's model. A quality monitoring protocol, based on the staffing taxonomy, was used to assess quality improvement systems. Results from 48 US nursing facilities indicate that most long-term care facilities struggle with staffing allocation and the integration of staffing into a quality monitoring process.

Attitude of Health Personnel↗

PubMed2026

Evolutionary dynamics of the chloroplast genome in Abutilon (Malvoideae, Malvaceae).

The genus Abutilon Mill. (Malvaceae) comprises approximately 178 species distributed across tropical and subtropical regions, many of which hold significant ornamental, economic, and medicinal value; yet its taxonomic classification remains challenging. In this study, six species were sequenced from herbarium specimens, and the chloroplast (cp.) genomes of ten additional species were assembled de novo from publicly available raw data. Three previously reported cp. genomes were also incorporated to characterise cp. genome structure, identify polymorphic loci, and perform phylogenetic analyses. The cp. genomes ranged from 159,458 to 160,454 bp and exhibited the typical quadripartite structure, with each genome containing 112 unique genes (78 protein-coding, 30 tRNA, and 4 rRNA) that showed conserved content and organisation. These genomes exhibited high similarity in GC content, inverted repeat boundaries, relative synonymous codon usage, amino acid frequencies, and substitution patterns. However, notable variation was observed in the total number of simple sequence repeats, ranging from 70 to 97 per genome. Selection analyses indicated predominant purifying selection, with evidence of episodic positive selection detected in rpoC2, rbcL, and ycf1. Two codons in rbcL were clade-specific and provided phylogenetic signal distinguishing Australian and Old World pantropical species. Nucleotide diversity analysis identified six highly polymorphic intergenic spacers (trnH-psbA, rps19-rpl2, psbT-pbf1, psaC-ndhD, trnR-atpA, and ndhJ-ndhK) that may be suitable for taxonomic studies. The phylogeny from maximum likelihood (ML) and Bayesian inference (BI) resolved two major clades: one comprising an exclusively Australian lineage occurring predominantly in arid and semi-arid environments, and the other a pantropical lineage spanning multiple continents. Abutilon grandifolium was recovered as sister to the remaining sampled Abutilon taxa in both ML and BI analyses, although no biogeographic origin inference can be drawn from this placement pending broader taxon sampling and integration of nuclear genomic data. These findings provide insights into the evolutionary dynamics of the cp. genome in Abutilon and offer a foundational genomic framework for refining Abutilon taxonomy.

Genome, Chloroplast↗

PubMed2005

Point-of-care testing error: sources and amplifiers, taxonomy, prevention strategies, and detection monitors.

CONTEXT: In a survey performed 4 years ago, testing venues doing only point-of-care testing (POCT) made up 78% of sites for patient testing licensed under federal regulations. OBJECTIVES: To identify sources of POCT error, to present a classification of such errors, to suggest strategies to prevent errors, and to describe monitors that assess and reduce the frequency of errors. DESIGN: To identify sources of POCT error, large studies of error among US Federal Certificate of Waiver laboratories (CoWs) and practitioner-performed microscopy certificate holders were reviewed. To facilitate investigation and management of POCT error, a taxonomy of such errors (modified from a classification previously published by Gerald Kost) was used to identify 4 steps with error potential in each of the 3 phases (ie, preanalytic, analytic, and postanalytic) of the POCT process. To prevent observed POCT errors, 4 strategies are suggested: direct observation of instrument/method functionality, structured observation of method performance, proficiency testing/use of relevant test scenarios, and autonomation. To assess frequency of errors, a quartet of indices are introduced as detection monitors: order documentation, patient identification, specimen adequacy, and result integrity. RESULTS: Three sources of POCT error were identified: operator incompetence, nonadherence to test procedures, and use of uncontrolled reagents and equipment. Three other characteristics of many point-of-care tests amplify their risk of error: incoherent regulation, rapid availability of results, and the results' immediate therapeutic implications. Two members of the quartet of detection monitors, order documentation and specimen adequacy, are relatively difficult to measure and are controversial, but the other 2, patient identification and result integrity, are easier to assess and are relatively widely accepted. CONCLUSIONS: Point-of-care testing errors are relatively common, their frequency is amplified by incoherent regulation, and their likelihood of affecting patient care is amplified by the rapid availability of POCT results and the results' immediate therapeutic implications. The modified Kost taxonomy offers a reasonable approach to the identification of POCT errors. Direct observation of test functionality, structured observation of test performance, and testing the competence of POCT operators, as well as autonomation of devices, are strategies to prevent such errors. In this context, we suggest monitoring POCT order documentation, patient identification, specimen integrity, and result reporting to detect errors in this sort of testing.

Humans↗

PubMed2006

Guide to blackflies of the Simulium damnosum complex in eastern and southern Africa.

At least 26 members of the Simulium damnosum Theobald complex (Diptera: Simuliidae) are known from eastern Africa, most of which are assumed to be non-anthropophilic and some are restricted to small areas of endemicity. Their discovery was based on polytene chromosome inversion polymorphisms and since then they have been cited as cytological entities, but, in many cases, with inadequate descriptions (e.g. without illustrations of the chromosomes). The present distribution, taxonomy and vector identity have been re-evaluated during the last decade in conjunction with ongoing onchocerciasis control programmes. Here, a summary of the relevant data is presented, integrating results of cytotaxonomic, morphotaxonomic and molecular investigations into a guide that provides a comprehensive system of identification for the cytoforms 'Kagera', 'Kasyabone', 'Kibwezi', 'Kisiwani', 'Kisiwani E', 'Kulfo', 'Linthipe', 'Mombo', 'Mutonga', 'Njombe', 'Nkusi', 'Nkusi SA', 'Nkusi SW', 'Nyika', 'Pienaars', 'Sanje', 'Sebwe', 'Turiani', Simulium damnosum sensu stricto, Simulium kaffaense Hadis et al., Simulium kilibanum Gouteux, Simulium kipengere Krueger, Simulium latipollex (Enderlein), Simulium pandanophilum Krüger, Nurmi & Garms, Simulium plumbeum Krueger, Simulium thyolense Vajime et al. and for five newly recognized molecular forms of 'Nkusi' and S. kilibanum. All taxa except S. pandanophilum are assigned to one of five subcomplexes (damnosum, Ketaketa, Kibwezi, Sanje, squamosum) within the S. damnosum complex. The guide encompasses anthropophilic and non-anthropophilic segregates for the whole of eastern and southern Africa, and is not restricted to larval chromosome criteria; in many cases it also allows the typing of adult flies.

Africa, Eastern↗

PubMed2004

Robotic technology in surgery: past, present, and future.

It has been nearly 20 years since the first appearance of robotics in the operating room. In that time, much progress has been made in integrating robotic technologies with surgical instrumentation, as evidenced by the many thousands of successful robot-assisted cases. However, to build on past success and to fully leverage the potential of surgical robotics in the future, it is essential to maximize a shared understanding and communication among surgeons, engineers, entrepreneurs, and healthcare administrators. This article provides an introduction to medical robotic technologies, develops a possible taxonomy, reviews the evolution of a surgical robot, and discusses future prospects for innovation. Robotic surgery has demonstrated some clear benefits. It remains to be seen where these benefits will outweigh the associated costs over the long term. In the future, surgical robots should be smaller, less expensive, easier to operate, and should seamlessly integrate emerging technologies from a number of different fields. Such advances will enable continued progress in surgical instrumentation and, ultimately, surgical care.

Equipment Design↗

PubMed1999

A taxonomy of health networks and systems: bringing order out of chaos.

OBJECTIVE: To use existing theory and data for empirical development of a taxonomy that identifies clusters of organizations sharing common strategic/structural features. DATA SOURCES: Data from the 1994 and 1995 American Hospital Association Annual Surveys, which provide extensive data on hospital involvement in hospital-led health networks and systems. STUDY DESIGN: Theories of organization behavior and industrial organization economics were used to identify three strategic/structural dimensions: differentiation, which refers to the number of different products/services along a healthcare continuum; integration, which refers to mechanisms used to achieve unity of effort across organizational components; and centralization, which relates to the extent to which activities take place at centralized versus dispersed locations. These dimensions were applied to three components of the health service/product continuum: hospital services, physician arrangements, and provider-based insurance activities. DATA EXTRACTION METHODS: We identified 295 health systems and 274 health networks across the United States in 1994, and 297 health systems and 306 health networks in 1995 using AHA data. Empirical measures aggregated individual hospital data to the health network and system level. PRINCIPAL FINDINGS: We identified a reliable, internally valid, and stable four-cluster solution for health networks and a five-cluster solution for health systems. We found that differentiation and centralization were particularly important in distinguishing unique clusters of organizations. High differentiation typically occurred with low centralization, which suggests that a broader scope of activity is more difficult to centrally coordinate. Integration was also important, but we found that health networks and systems typically engaged in both ownership-based and contractual-based integration or they were not integrated at all. CONCLUSIONS: Overall, we were able to classify approximately 70 percent of hospital-led health networks and 90 percent of hospital-led health systems into well-defined organizational clusters. Given the widespread perception that organizational change in healthcare has been chaotic, our research suggests that important and meaningful similarities exist across many evolving organizations. The resulting taxonomy provides a new lexicon for researchers, policymakers, and healthcare executives for characterizing key strategic and structural features of evolving organizations. The taxonomy also provides a framework for future inquiry about the relationships between organizational strategy, structure, and performance, and for assessing policy issues, such as Medicare Provider Sponsored Organizations, antitrust, and insurance regulation.

American Hospital Association↗

PubMedDate not supplied

Fuzzy measures on the Gene Ontology for gene product similarity.

One of the most important objects in bioinformatics is a gene product (protein or RNA). For many gene products, functional information is summarized in a set of Gene Ontology (GO) annotations. For these genes, it is reasonable to include similarity measures based on the terms found in the GO or other taxonomy. In this paper, we introduce several novel measures for computing the similarity of two gene products annotated with GO terms. The fuzzy measure similarity (FMS) has the advantage that it takes into consideration the context of both complete sets of annotation terms when computing the similarity between two gene products. When the two gene products are not annotated by common taxonomy terms, we propose a method that avoids a zero similarity result. To account for the variations in the annotation reliability, we propose a similarity measure based on the Choquet integral. These similarity measures provide extra tools for the biologist in search of functional information for gene products. The initial testing on a group of 194 sequences representing three proteins families shows a higher correlation of the FMS and Choquet similarities to the BLAST sequence similarities than the traditional similarity measures such as pairwise average or pairwise maximum.

Algorithms↗