Complexity measures to track the evolution of a SNOMED hierarchy.

PubMed

Wei, Duo; Wang, Yue; Perl, Yehoshua; Xu, Junchuan; Halper, Michael; Spackman, Kent A; Spackman, Kent

2008-11-06

SNOMED CT is an extensive terminology with an attendant amount of complexity. Two measures are proposed for quantifying that complexity. Both are based on abstraction networks, called the area taxonomy and the partial-area taxonomy, that provide, for example, distributions of the relationships within a SNOMED hierarchy. The complexity measures are employed specifically to track the complexity of versions of the Specimen hierarchy of SNOMED before and after it is put through an auditing process. The pre-audit and post-audit versions are compared. The results show that the auditing process indeed leads to a simplification of the terminology's structure.

Future of phytonematode taxonomy

USDA-ARS?s Scientific Manuscript database

The future of nematode taxonomy will be characterized by rapid accumulation of new and revised taxa examined in light of a refined understanding of phenotypic plasticity and cryptic speciation, multiple molecular markers and appropriate phylogenetic analyses. The inevitable result will be improved t...

Bacteriophage Taxonomy: An Evolving Discipline.

PubMed

Tolstoy, Igor; Kropinski, Andrew M; Brister, J Rodney

2018-01-01

While taxonomy is an often-unappreciated branch of science it serves very important roles. Bacteriophage taxonomy has evolved from a mainly morphology-based discipline, characterized by the work of David Bradley and Hans-Wolfgang Ackermann, to the holistic approach that is taken today. The Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) takes a comprehensive approach to classifying prokaryote viruses measuring overall DNA and protein identity and phylogeny before making decisions about the taxonomic position of a new virus. The huge number of complete genomes being deposited with NCBI and other public databases has resulted in a reassessment of the taxonomy of many viruses, and the future will see the introduction of new viral families and higher orders.

A Descriptive Content Analysis of the Extent of Bloom's Taxonomy in the Reading Comprehension Questions of the Course Book Q: Skills for Success 4 Reading and Writing

ERIC Educational Resources Information Center

Ulum, Ömer Gökhan

2016-01-01

Bloom's taxonomy is probably the most commonly used one among the cognitive process models. It is a classification system that emphasizes the procedures starting from remembering the knowledge to more complex cognitive levels like evaluating the knowledge. Firstly, the aim of this study has been to find out to what extent Bloom's taxonomy is…

Defining viral species: making taxonomy useful.

PubMed

Peterson, A Townsend

2014-07-23

Virus taxonomy at present is best characterized as a categorization of convenience, without a firm basis in the principles of evolutionary biology. Specifically, virus species definitions appear to depend more on tradition and popular opinion among virologists than on firm, quantitative biological evidence. I suggest a series of changes to underlying species concepts that would shift the field from one that simply files viruses away in taxonomic boxes to one that can learn important biological lessons from its taxonomy.

Application of a Taxonomy to Characterize the Public Health Workforce.

PubMed

Beck, Angela J; Meit, Michael; Heffernan, Megan; Boulton, Matthew L

2015-01-01

A public health workforce taxonomy was published in 2014 to provide a standardized mechanism for describing public health worker characteristics. The Public Health Workforce Interests and Needs Survey (PH WINS) used 7 of the taxonomy's 12 axes as a basis for its survey response choices, 3 of which are the focus of this analysis. The purpose of this study was to determine the relative utility, reliability, and accuracy of the public health workforce taxonomy in categorizing local and state public health workers using a survey tool. This specifically included the goal of reducing the number of responses classified as "other" occupation, certification, or program area by recoding responses into taxonomy categories and determining potential missing categories for recommendation to the advisory committee that developed the taxonomy. Survey questions associated with the occupation, certification, and program area taxonomy axes yielded qualitative data from respondents who selected "other." The "other" responses were coded by 2 separate research teams at the University of Michigan Center of Excellence in Public Health Workforce Studies and NORC at the University of Chicago. Researchers assigned taxonomy categories to all analyzable qualitative responses and assessed the percentage of PH WINS responses that could be successfully mapped to taxonomy categories. Between respondent self-selection and research team recoding, the public health workforce taxonomy successfully categorized 95% of occupation responses, 75% of credential responses, and 83% of program area responses. Occupational categories that may be considered for inclusion in the taxonomy in the future include disease intervention specialists and occupations associated with regulation, certification, and licensing. The public health workforce taxonomy performed remarkably well in categorizing worker characteristics in its first use in a national survey. The analysis provides some recommendations for future taxonomy refinement.

An Empirical Taxonomy of Social-Psychological Risk Indicators in Youth Suicide

ERIC Educational Resources Information Center

Hyde, Toni; Kirkland, John; Bimler, David; Pechtel, Pia

2005-01-01

The current study integrates descriptive (though primarily social-psychological) statements about youth suicide into a coherent, empirically supported taxonomy. Drawing from relevant literature, a set of 107 items characterizing these contributions about youth suicide was created. Seventy-two participants sorted these statements according to their…

A taxonomy of inductive problems.

PubMed

Kemp, Charles; Jern, Alan

2014-02-01

Inductive inferences about objects, features, categories, and relations have been studied for many years, but there are few attempts to chart the range of inductive problems that humans are able to solve. We present a taxonomy of inductive problems that helps to clarify the relationships between familiar inductive problems such as generalization, categorization, and identification, and that introduces new inductive problems for psychological investigation. Our taxonomy is founded on the idea that semantic knowledge is organized into systems of objects, features, categories, and relations, and we attempt to characterize all of the inductive problems that can arise when these systems are partially observed. Recent studies have begun to address some of the new problems in our taxonomy, and future work should aim to develop unified theories of inductive reasoning that explain how people solve all of the problems in the taxonomy.

Towards a Model of School-Based Curriculum Development and Assessment Using the SOLO Taxonomy.

ERIC Educational Resources Information Center

Biggs, John

1989-01-01

One factor preventing the wider acceptance of school-based curriculum development and assessment is the problem of comparing performances of different students, in different schools. The SOLO taxonomy is used to describe the complexity of learning outcomes in a language that is generally applicable across the curriculum. (Author/MLW)

Calibrating the Difficulty of an Assessment Tool: The Blooming of a Statistics Examination

ERIC Educational Resources Information Center

Dunham, Bruce; Yapa, Gaitri; Yu, Eugenia

2015-01-01

Bloom's taxonomy is proposed as a tool by which to assess the level of complexity of assessment tasks in statistics. Guidelines are provided for how to locate tasks at each level of the taxonomy, along with descriptions and examples of suggested test questions. Through the "Blooming" of an examination--that is, locating its constituent…

Tumor taxonomy for the developmental lineage classification of neoplasms

PubMed Central

Berman, Jules J

2004-01-01

Background The new "Developmental lineage classification of neoplasms" was described in a prior publication. The classification is simple (the entire hierarchy is described with just 39 classifiers), comprehensive (providing a place for every tumor of man), and consistent with recent attempts to characterize tumors by cytogenetic and molecular features. A taxonomy is a list of the instances that populate a classification. The taxonomy of neoplasia attempts to list every known term for every known tumor of man. Methods The taxonomy provides each concept with a unique code and groups synonymous terms under the same concept. A Perl script validated successive drafts of the taxonomy ensuring that: 1) each term occurs only once in the taxonomy; 2) each term occurs in only one tumor class; 3) each concept code occurs in one and only one hierarchical position in the classification; and 4) the file containing the classification and taxonomy is a well-formed XML (eXtensible Markup Language) document. Results The taxonomy currently contains 122,632 different terms encompassing 5,376 neoplasm concepts. Each concept has, on average, 23 synonyms. The taxonomy populates "The developmental lineage classification of neoplasms," and is available as an XML file, currently 9+ Megabytes in length. A representation of the classification/taxonomy listing each term followed by its code, followed by its full ancestry, is available as a flat-file, 19+ Megabytes in length. The taxonomy is the largest nomenclature of neoplasms, with more than twice the number of neoplasm names found in other medical nomenclatures, including the 2004 version of the Unified Medical Language System, the Systematized Nomenclature of Medicine Clinical Terminology, the National Cancer Institute's Thesaurus, and the International Classification of Diseases Oncolology version. Conclusions This manuscript describes a comprehensive taxonomy of neoplasia that collects synonymous terms under a unique code number and assigns each tumor to a single class within the tumor hierarchy. The entire classification and taxonomy are available as open access files (in XML and flat-file formats) with this article. PMID:15571625

The Security of Machine Learning

DTIC Science & Technology

2008-04-24

Machine learning has become a fundamental tool for computer security, since it can rapidly evolve to changing and complex situations. That...adaptability is also a vulnerability: attackers can exploit machine learning systems. We present a taxonomy identifying and analyzing attacks against machine ...We use our framework to survey and analyze the literature of attacks against machine learning systems. We also illustrate our taxonomy by showing

Childhood vaccination communication outcomes unpacked and organized in a taxonomy to facilitate core outcome establishment.

PubMed

Kaufman, Jessica; Ryan, Rebecca; Glenton, Claire; Lewin, Simon; Bosch-Capblanch, Xavier; Cartier, Yuri; Cliff, Julie; Oyo-Ita, Angela; Ames, Heather; Muloliwa, Artur Manuel; Oku, Afiong; Rada, Gabriel; Hill, Sophie

2017-04-01

We present a comprehensive taxonomy of outcomes for childhood vaccination communication interventions. Adding to our earlier map of trial outcomes, we aimed to (1) identify relevant outcomes not measured in trials, (2) identify outcomes from stakeholder focus groups, and (3) organize outcomes into a taxonomy. We identified additional outcomes from nonvaccination health communication literature and through parent and health care professional focus groups. We organized outcomes into the taxonomy through iterative discussion and informed by organizational principles established by leaders in core outcome research. The taxonomy includes three overarching core areas, divided into eight domains and then into outcomes. Core area one is psychosocial impact, including the domains "knowledge or understanding," "attitudes or beliefs," and "decision-making." Core area two is health impact, covering "vaccination status and behaviors" and "health status and well-being." Core area three is community, social, or health system impact, containing "intervention design and implementation," "community participation," and "resource use." To our knowledge, this taxonomy is the first attempt to conceptualize the range of potential outcomes for vaccination communication. It can be used by researchers selecting outcomes for complex communication interventions. We will also present the taxonomy to stakeholders to establish core outcome domains. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

A review of the taxonomy of chondrichthyan fishes: a modern perspective.

PubMed

White, W T; Last, P R

2012-04-01

Taxonomic clarity is a fundamental requirement as it forms the foundation of all other life sciences. In the last decade, chondrichthyan taxonomy has undergone a scientific renaissance with >180 new species formally described. This effort encompasses c. 15% of the global chondrichthyan fauna, which consists of 1185 currently recognized species. The important role of chondrichthyan taxonomy for conservation management has been highlighted in recent years with new species descriptions or taxonomic resolution of a number of threatened species. These include Australian gulper (genus Centrophorus) and speartooth sharks (genus Glyphis) in coastal waters of Australia and Borneo. Closer examination of other wide-ranging species, for which the taxonomy was thought to be stable, has shown that they consist of species complexes, e.g. manta rays (Manta spp.) and spotted eagle rays (the Aetobatus narinari complex), and highlights the need for critical re-examination of other wide-ranging species. Molecular methods have provided another useful tool to taxonomists and they have proven to assist greatly with identifying cryptic species and species complexes. The limitations of particular molecular methods being used need, however, to be carefully considered and there are some concerns about how these are being integrated with classical taxonomy. The fundamental importance of taxonomic nomenclature to life sciences is often poorly understood but striving for nomenclatural stability is a critical component of taxonomy. Similarly, biological collections are an extremely vital asset to both taxonomists and the broader scientific community. These collections are becoming increasingly important due in part to molecular species identification initiatives such as the Barcode of Life which has resulted in a large number of voucher specimens linked to tissue samples being deposited. Biological collections are also proving to be imperative in biodiversity studies as they contain a 'gold mine' of historical collection information important for assessing changes in faunal assemblages. Resources are typically limited for taxonomic research and the ageing taxonomic community is another issue of concern for the future of taxonomy on this important group. Succession planning and better resource allocation will be essential to ensure that this fundamental discipline is maintained into the future. © 2012 The Authors. Journal of Fish Biology © 2012 The Fisheries Society of the British Isles.

Proposal of an Extended Taxonomy of Serious Games for Health Rehabilitation.

PubMed

Rego, Paula Alexandra; Moreira, Pedro Miguel; Reis, Luís Paulo

2018-06-29

Serious Games is a field of research that has evolved substantially with valuable contributions to many application domains and areas. Patients often consider traditional rehabilitation approaches to be repetitive and boring, making it difficult for them to maintain their ongoing interest and assure the completion of the treatment program. Since the publication of our first taxonomy of Serious Games for Health Rehabilitation (SGHR), many studies have been published with game prototypes in this area. Based on literature review, our goal is to propose an updated taxonomy taking into account the works, updates, and innovations in game criteria that have been researched since our first publication in 2010. In addition, we aim to present the validation mechanism used for the proposed extended taxonomy. Based on a literature review in the area and on the analysis of the contributions made by other researchers, we propose an extended taxonomy for SGHR. For validating the taxonomy proposal, a questionnaire was designed to use on a survey among experts in the area. An extended taxonomy for SGHR was proposed. As we have identified that, in general, and besides the mechanisms associated with the adoption of a given taxonomy, there were no reported validation mechanisms for the proposals, we designed a mechanism to validate our proposal. The mechanism uses a questionnaire addressed to a sample of researchers and professionals with experience and expertise in domains of knowledge interrelated with SGHR, such as Computer Graphics, Game Design, Interaction Design, Computer Programming, and Health Rehabilitation. The extended taxonomy proposal for health rehabilitation serious games provides the research community with a tool to fully characterize serious games. The mechanism designed for validating the taxonomy proposal is another contribution of this work.

The brain injury case management taxonomy (BICM-T); a classification of community-based case management interventions for a common language.

PubMed

Lukersmith, Sue; Fernandez, Ana; Millington, Michael; Salvador-Carulla, Luis

2016-04-01

Case management is a complex intervention. Complexity arises from the interaction of different components: the model (theoretical basis), implementation context (service), population and health condition, focus for the intervention (client and/or their family), case manager's actions (interventions) and the target of case management (integrated care and support, client's community participation). There is a lack of understanding and a common language. To our knowledge there is no classification (taxonomy) for community-based case management. To develop a community-based case management in brain injury taxonomy (BICM-T), as a common language and understanding of case management for use in quality analysis, policy, planning and practice. The mixed qualitative methods used multiple sources of knowledge including scoping, framing and a nominal group technique to iteratively develop the Beta version (draft) of the taxonomy. A two part developmental evaluation involving case studies and mapping to international frameworks assessed the applicability and acceptability (feasibility) before finalization of the BICM-T. The BICM-T includes a definition of community-based case management, taxonomy trees, tables and a glossary. The interventions domain tree has 9 main actions (parent category): engagement, holistic assessment, planning, education, training and skills development, emotional and motivational support, advising, coordination, monitoring; 17 linked actions (children category); 8 related actions; 63 relevant terms defined in the glossary. The BICM-T provides a knowledge map with the definitions and relationships between the core actions (interventions domain). Use of the taxonomy as a common language will benefit practice, quality analysis, evaluation, policy, planning and resource allocation. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Diagnosis - the limiting focus of taxonomy.

PubMed

Sturmberg, Joachim P; Martin, Carmel M

2016-02-01

The focus on the diagnosis is a pivotal aspect of medical practice since antiquity. Diagnostic taxonomy helped to categorize ailments to improve medical care, and in its social sense resulted in validation of the sick role for some, but marginalization or stigmatization for others. In the medical industrial complex, diagnostic taxonomy structured health care financing, management and practitioner remuneration. However, with increasing demands from multiple agencies, there are increasing unintended and unwarranted consequences of our current taxonomies and diagnostic processes resulting from the conglomeration of underpinning concepts, theories, information and motivations. We argue that the increasing focus on the diagnosis resulted in excessive compartmentalization - 'partialism' - of medical practice, diminishing medical care and being naively simplistic in light of the emerging understanding of the interconnected nature of the diseasome. The human is a complex organic system of interconnecting dynamics and feedback loops responding to internal and external forces including genetic, epigenetic and environmental attractors, rather than the sum of multiple discrete organs which can develop isolated diseases or multiple morbidities. Solutions to these unintended consequences of many contemporary health system processes involve revisiting the nature of diagnostic taxonomies and the processes of their construction. A dynamic taxonomic framework would shift to more relevant attractors at personal, clinical and health system levels recognizing the non-linear nature of health and disease. Human health at an individual, group and population level is the ability to adapt to internal and external stressors with resilience throughout the life course, yet diagnostic taxonomies are increasingly constructed around fixed anchors. Understanding diagnosis as dissecting, pigeonholing or bean counting (learning by dividing) is no longer useful, the challenge for the future is to understand the big picture (learning by connecting). Diagnostic categorization needs to embrace a meta-learning approach open to human variability. © 2014 John Wiley & Sons, Ltd.

Developing an instrument to measure heart failure disease management program intensity and complexity.

PubMed

Riegel, Barbara; Lee, Christopher S; Sochalski, Julie

2010-05-01

Comparing disease management programs and their effects is difficult because of wide variability in program intensity and complexity. The purpose of this effort was to develop an instrument that can be used to describe the intensity and complexity of heart failure (HF) disease management programs. Specific composition criteria were taken from the American Heart Association (AHA) taxonomy of disease management and hierarchically scored to allow users to describe the intensity and complexity of the domains and subdomains of HF disease management programs. The HF Disease Management Scoring Instrument (HF-DMSI) incorporates 6 of the 8 domains from the taxonomy: recipient, intervention content, delivery personnel, method of communication, intensity/complexity, and environment. The 3 intervention content subdomains (education/counseling, medication management, and peer support) are described separately. In this first test of the HF-DMSI, overall intensity (measured as duration) and complexity were rated using an ordinal scoring system. Possible scores reflect a clinical rationale and differ by category, with zero given only if the element could potentially be missing (eg, surveillance by remote monitoring). Content validity was evident as the instrument matches the existing AHA taxonomy. After revision and refinement, 2 authors obtained an inter-rater reliability intraclass correlation coefficient score of 0.918 (confidence interval, 0.880 to 0.944, P<0.001) in their rating of 12 studies. The areas with most variability among programs were delivery personnel and method of communication. The HF-DMSI is useful for describing the intensity and complexity of HF disease management programs.

Crisamicin A, a new antibiotic from Micromonospora. I. Taxonomy of the producing strain, fermentation, isolation, physico-chemical characterization and antimicrobial properties.

PubMed

Nelson, R A; Pope, J A; Luedemann, G M; McDaniel, L E; Schaffner, C P

1986-03-01

A microorganism, designated as RV-79-9-101 and now identified as Micromonospora purpureochromogenes subsp. halotolerans, isolated from a mud sample in the Philippines, has been shown to produce a complex of antibiotics called crisamicins. Thin-layer chromatography and bioautography, employing solvent extracts of whole fermentation broths, revealed a minimum of five antimicrobial components. The major biologically-active component of the antibiotic complex, crisamicin A, was obtained in pure form after preparative silica gel column chromatography followed by crystallization. Based on physico-chemical data crisamicin A has been identified as a novel member of the isochromanequinone group of antibiotics. It exhibits excellent in vitro activity against Gram-positive bacteria but little or no activity towards Gram-negative bacteria or fungi.

A taxonomy for user-healthcare robot interaction.

PubMed

Bzura, Conrad; Im, Hosung; Liu, Tammy; Malehorn, Kevin; Padir, Taskin; Tulu, Bengisu

2012-01-01

This paper evaluates existing taxonomies aimed at characterizing the interaction between robots and their users and modifies them for health care applications. The modifications are based on existing robot technologies and user acceptance of robotics. Characterization of the user, or in this case the patient, is a primary focus of the paper, as they present a unique new role as robot users. While therapeutic and monitoring-related applications for robots are still relatively uncommon, we believe they will begin to grow and thus it is important that the spurring relationship between robot and patient is well understood.

50 years of the International Committee on Taxonomy of Viruses: progress and prospects.

PubMed

Adams, Michael J; Lefkowitz, Elliot J; King, Andrew M Q; Harrach, Balázs; Harrison, Robert L; Knowles, Nick J; Kropinski, Andrew M; Krupovic, Mart; Kuhn, Jens H; Mushegian, Arcady R; Nibert, Max L; Sabanadzovic, Sead; Sanfaçon, Hélène; Siddell, Stuart G; Simmonds, Peter; Varsani, Arvind; Zerbini, Francisco Murilo; Orton, Richard J; Smith, Donald B; Gorbalenya, Alexander E; Davison, Andrew J

2017-05-01

We mark the 50th anniversary of the International Committee on Taxonomy of Viruses (ICTV) by presenting a brief history of the organization since its foundation, showing how it has adapted to advancements in our knowledge of virus diversity and the methods used to characterize it. We also outline recent developments, supported by a grant from the Wellcome Trust (UK), that are facilitating substantial changes in the operations of the ICTV and promoting dialogue with the virology community. These developments will generate improved online resources, including a freely available and regularly updated ICTV Virus Taxonomy Report. They also include a series of meetings between the ICTV and the broader community focused on some of the major challenges facing virus taxonomy, with the outcomes helping to inform the future policy and practice of the ICTV.

A concept taxonomy and an instrument hierarchy: tools for establishing and evaluating the conceptual framework of a patient-reported outcome (PRO) instrument as applied to product labeling claims.

PubMed

Erickson, Pennifer; Willke, Richard; Burke, Laurie

2009-01-01

To facilitate development and evaluation of a PRO instrument conceptual framework, we propose two tools--a PRO concept taxonomy and a PRO instrument hierarchy. FDA's draft guidance on patient reported outcome (PRO) measures states that a clear description of the conceptual framework of an instrument is useful for evaluating its adequacy to support a treatment benefit claim for use in product labeling the draft guidance, however does not propose tools for establishing or evaluating a PRO instrument's conceptual framework. We draw from our review of PRO concepts and instruments that appear in prescription drug labeling approved in the United States from 1997 to 2007. We propose taxonomy terms that define relationships between PRO concepts, including "family,"compound concept," and "singular concept." Based on the range of complexity represented by the concepts, as defined by the taxonomy, we propose nine instrument orders for PRO measurement. The nine orders range from individual event counts to multi-item, multiscale instruments. This analysis of PRO concepts and instruments illustrates that the taxonomy and hierarchy are applicable to PRO concepts across a wide range of therapeutic areas and provide a basis for defining the instrument conceptual framework complexity. Although the utility of these tools in the drug development, review, and approval processes has not yet been demonstrated, these tools could be useful to improve communication and enhance efficiency in the instrument development and review process.

Auditing complex concepts of SNOMED using a refined hierarchical abstraction network.

PubMed

Wang, Yue; Halper, Michael; Wei, Duo; Gu, Huanying; Perl, Yehoshua; Xu, Junchuan; Elhanan, Gai; Chen, Yan; Spackman, Kent A; Case, James T; Hripcsak, George

2012-02-01

Auditors of a large terminology, such as SNOMED CT, face a daunting challenge. To aid them in their efforts, it is essential to devise techniques that can automatically identify concepts warranting special attention. "Complex" concepts, which by their very nature are more difficult to model, fall neatly into this category. A special kind of grouping, called a partial-area, is utilized in the characterization of complex concepts. In particular, the complex concepts that are the focus of this work are those appearing in intersections of multiple partial-areas and are thus referred to as overlapping concepts. In a companion paper, an automatic methodology for identifying and partitioning the entire collection of overlapping concepts into disjoint, singly-rooted groups, that are more manageable to work with and comprehend, has been presented. The partitioning methodology formed the foundation for the development of an abstraction network for the overlapping concepts called a disjoint partial-area taxonomy. This new disjoint partial-area taxonomy offers a collection of semantically uniform partial-areas and is exploited herein as the basis for a novel auditing methodology. The review of the overlapping concepts is done in a top-down order within semantically uniform groups. These groups are themselves reviewed in a top-down order, which proceeds from the less complex to the more complex overlapping concepts. The results of applying the methodology to SNOMED's Specimen hierarchy are presented. Hypotheses regarding error ratios for overlapping concepts and between different kinds of overlapping concepts are formulated. Two phases of auditing the Specimen hierarchy for two releases of SNOMED are reported on. With the use of the double bootstrap and Fisher's exact test (two-tailed), the auditing of concepts and especially roots of overlapping partial-areas is shown to yield a statistically significant higher proportion of errors. Copyright © 2011 Elsevier Inc. All rights reserved.

Spumaretroviruses: Updated taxonomy and nomenclature.

PubMed

Khan, Arifa S; Bodem, Jochen; Buseyne, Florence; Gessain, Antoine; Johnson, Welkin; Kuhn, Jens H; Kuzmak, Jacek; Lindemann, Dirk; Linial, Maxine L; Löchelt, Martin; Materniak-Kornas, Magdalena; Soares, Marcelo A; Switzer, William M

2018-03-01

Spumaretroviruses, commonly referred to as foamy viruses, are complex retroviruses belonging to the subfamily Spumaretrovirinae, family Retroviridae, which naturally infect a variety of animals including nonhuman primates (NHPs). Additionally, cross-species transmissions of simian foamy viruses (SFVs) to humans have occurred following exposure to tissues of infected NHPs. Recent research has led to the identification of previously unknown exogenous foamy viruses, and to the discovery of endogenous spumaretrovirus sequences in a variety of host genomes. Here, we describe an updated spumaretrovirus taxonomy that has been recently accepted by the International Committee on Taxonomy of Viruses (ICTV) Executive Committee, and describe a virus nomenclature that is generally consistent with that used for other retroviruses, such as lentiviruses and deltaretroviruses. This taxonomy can be applied to distinguish different, but closely related, primate (e.g., human, ape, simian) foamy viruses as well as those from other hosts. This proposal accounts for host-virus co-speciation and cross-species transmission. Published by Elsevier Inc.

The variety of primary healthcare organisations in Australia: a taxonomy.

PubMed

Rodwell, John; Gulyas, Andre

2013-04-08

Healthcare policy appears to treat healthcare organisations as being homogenous, despite evidence that they vary considerably. This study develops a taxonomy of primary health care practices using characteristics associated with the job satisfaction of general medical practitioners (GPs) and the practices. The study used data from 3,662 survey respondents who were GPs in the 2009 wave of the MABEL survey. Cluster analyses were used to determine natural groups of medical practices based on multidimensional characteristics. Seven configurations of primary health care practices emerged from multivariate cluster analyses: optimised team, independent craft, reactive, winding down, classic, practitioner flexible, and scale efficiency. This taxonomy of configurations moves beyond simplistic categorisations such as geographic location and highlights the complexity of primary health care organisations in Australia. Health policy, workforce and procedure interventions informed by taxonomies can engage the diversity of primary health care practices.

Phase-Angle Dependence of Determinations of Diameter, Albedo, and Taxonomy: A Case Study of NEO 3691 Bede

NASA Technical Reports Server (NTRS)

Wooden, Diane H.; Lederer, Susan M.; Jehin, Emmanuel; Howell, Ellen S.; Fernandez, Yan; Harker, David E.; Ryan, Erin; Lovell, Amy; Woodward, Charles E.; Benner, Lance A.

2015-01-01

Parameters important for NEO risk assessment and mitigation include Near-Earth Object diameter and taxonomic classification, which translates to surface composition. Diameters of NEOs are derived from the thermal fluxes measured by WISE, NEOWISE, Spitzer Warm Mission and ground-based telescopes including the IRTF and UKIRT. Diameter and its coupled parameters Albedo and IR beaming parameter (a proxy for thermal inertia and/or surface roughness) are dependent upon the phase angle, which is the Sun-target-observer angle. Orbit geometries of NEOs, however, typically provide for observations at phase angles greater than 20 degrees. At higher phase angles, the observed thermal emission is sampling both the day and night sides of the NEO. We compare thermal models for NEOs that exclude (NEATM) and include (NESTM) night-side emission. We present a case study of NEO 3691 Bede, which is a higher albedo object, X (Ec) or Cgh taxonomy, to highlight the range of H magnitudes for this object (depending on the albedo and phase function slope parameter G), and to examine at different phase angles the taxonomy and thermal model fits for this NEO. Observations of 3691 Bede include our observations with IRTF+SpeX and with the 10 micrometer UKIRT+Michelle instrument, as well as WISE and Spitzer Warm mission data. By examining 3691 Bede as a case study, we highlight the interplay between the derivation of basic physical parameters and observing geometry, and we discuss the uncertainties in H magnitude, taxonomy assignment amongst the X-class (P, M, E), and diameter determinations. Systematic dependencies in the derivation of basic characterization parameters of H-magnitude, diameter, albedo and taxonomy with observing geometry are important to understand. These basic characterization parameters affect the statistical assessments of the NEO population, which in turn, affects the assignment of statistically-assessed basic parameters to discovered but yet-to-be-fully-characterized NEOs.

Implementation of a novel taxonomy based on cognitive work analysis in the assessment of safety performance.

PubMed

Niskanen, Toivo

2017-12-12

The aim of this study was to examine how the developed taxonomy of cognitive work analysis (CWA) can be applied in combination with statistical analysis regarding different sociotechnical categories. This study applied a combination of quantitative and qualitative methodologies. Workers (n = 120) and managers (n = 85) in the chemical industry were asked in a questionnaire how different occupational safety and health (OSH) measures were being implemented. The exploration of the qualitative CWA taxonomy consisted of an analysis of the following topics: (a) work domain; (b) control task; (c) strategies; (d) social organization and cooperation; (e) worker competencies. The following hypotheses were supported - activities of the management had positive impacts on the aggregated variables: near-accident investigation and instructions (H 1 ); OSH training (H 2 ); operations, technical processes and safe use of chemicals (H 3 ); use of personal protective equipment (H 4 ); measuring, follow-up and prevention of major accidents (H 5 ). The CWA taxonomy was applied in mixed methods when testing H 1 -H 5 . A special approach is to analyze the work demands of complex sociotechnical systems with the taxonomy of CWA. In problem-solving, the CWA taxonomy should seek to capitalize on the strengths and minimize the limitations of safety performance.

A taxonomy of explanations in a general practitioner clinic for patients with persistent "medically unexplained" physical symptoms.

PubMed

Morton, LaKrista; Elliott, Alison; Cleland, Jennifer; Deary, Vincent; Burton, Christopher

2017-02-01

To develop a taxonomy of explanations for patients with persistent physical symptoms. We analysed doctors' explanations from two studies of a moderately-intensive consultation intervention for patients with multiple, often "medically-unexplained," physical symptoms. We used a constant comparative method to develop a taxonomy which was then applied to all verbatim explanations. We analysed 138 explanations provided by five general practitioners to 38 patients. The taxonomy comprised explanation types and explanation components. Three explanation types described the overall structure of the explanations: Rational Adaptive, Automatic Adaptive, and Complex. These differed in terms of who or what was given agency within the explanation. Three explanation components described the content of the explanation: Facts - generic statements about normal or dysfunctional processes; Causes - person-specific statements about proximal or distal causes for symptoms; Mechanisms - processes by which symptoms arise or persist in the individual. Most explanations conformed to one type and contained several components. This novel taxonomy for classifying clinical explanations permits detailed classification of explanation types and content. Explanation types appear to carry different implications of agency. The taxonomy is suitable for examining explanations and developing prototype explanatory scripts in both training and research settings. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

An Analytical Overview of Spirituality in NANDA-I Taxonomies.

PubMed

Mesquita, Ana Cláudia; Caldeira, Sílvia; Chaves, Erika; Carvalho, Emilia Campos de

2017-03-01

To discuss the approach of spirituality in NANDA-I taxonomies, based on the elements that characterize this phenomenon. This study was based on concepts that are usually adopted in the literature for defining spirituality and on the analysis of the NANDA-I taxonomies from I to III. Spirituality is included in all taxonomies but all three are missing some attributes to guarantee the completeness of this dimension for nursing diagnosis. Taxonomy III makes different approaches to spirituality and some inconsistencies. Contribute to the development and review of the new proposal for taxonomy. Discutir a abordagem à espiritualidade nas taxonomias da NANDA-I, baseada nos elementos que caracterizam este fenômeno. MÉTODOS: Este estudo foi baseado em conceitos usualmente adotados na literatura de enfermagem para definir espiritualidade e na análise das taxonomias da NANDA-I, desde a I à III. A espiritualidade está incluída nas taxonomias, porém estas carecem de atributos do seu conceito. CONCLUSÕES: A taxonomia III faz diferentes abordagens à espiritualidade, porém com algumas inconsistências identificadas. IMPLICAÇÕES PARA A ENFERMAGEM: Esta análise pode contribuir para o desenvolvimento e revisão da taxonomia III. © 2017 NANDA International, Inc.

Is the Cognitive Complexity of Commitment-to-Change Statements Associated With Change in Clinical Practice? An Application of Bloom's Taxonomy.

PubMed

Armson, Heather; Elmslie, Tom; Roder, Stefanie; Wakefield, Jacqueline

2015-01-01

This study categorizes 4 practice change options, including commitment-to-change (CTC) statements using Bloom's taxonomy to explore the relationship between a hierarchy of CTC statements and implementation of changes in practice. Our hypothesis was that deeper learning would be positively associated with implementation of planned practice changes. Thirty-five family physicians were recruited from existing practice-based small learning groups. They were asked to use their usual small-group process while exploring an educational module on peripheral neuropathy. Part of this process included the completion of a practice reflection tool (PRT) that incorporates CTC statements containing a broader set of practice change options-considering change, confirmation of practice, and not convinced a change is needed ("enhanced" CTC). The statements were categorized using Bloom's taxonomy and then compared to reported practice implementation after 3 months. Nearly all participants made a CTC statement and successful practice implementation at 3 months. By using the "enhanced" CTC options, additional components that contribute to practice change were captured. Unanticipated changes accounted for one-third of all successful changes. Categorizing statements on the PRT using Bloom's taxonomy highlighted the progression from knowledge/comprehension to application/analysis to synthesis/evaluation. All PRT statements were classified in the upper 2 levels of the taxonomy, and these higher-level (deep learning) statements were related to higher levels of practice implementation. The "enhanced" CTC options captured changes that would not otherwise be identified and may be worthy of further exploration in other CME activities. Using Bloom's taxonomy to code the PRT statements proved useful in highlighting the progression through increasing levels of cognitive complexity-reflecting deep learning. © 2015 The Alliance for Continuing Education in the Health Professions, the Society for Academic Continuing Medical Education, and the Council on Continuing Medical Education, Association for Hospital Medical Education.

Auditing Complex Concepts of SNOMED using a Refined Hierarchical Abstraction Network

PubMed Central

Wang, Yue; Halper, Michael; Wei, Duo; Gu, Huanying; Perl, Yehoshua; Xu, Junchuan; Elhanan, Gai; Chen, Yan; Spackman, Kent A.; Case, James T.; Hripcsak, George

2012-01-01

Auditors of a large terminology, such as SNOMED CT, face a daunting challenge. To aid them in their efforts, it is essential to devise techniques that can automatically identify concepts warranting special attention. “Complex” concepts, which by their very nature are more difficult to model, fall neatly into this category. A special kind of grouping, called a partial-area, is utilized in the characterization of complex concepts. In particular, the complex concepts that are the focus of this work are those appearing in intersections of multiple partial-areas and are thus referred to as overlapping concepts. In a companion paper, an automatic methodology for identifying and partitioning the entire collection of overlapping concepts into disjoint, singly-rooted groups, that are more manageable to work with and comprehend, has been presented. The partitioning methodology formed the foundation for the development of an abstraction network for the overlapping concepts called a disjoint partial-area taxonomy. This new disjoint partial-area taxonomy offers a collection of semantically uniform partial-areas and is exploited herein as the basis for a novel auditing methodology. The review of the overlapping concepts is done in a top-down order within semantically uniform groups. These groups are themselves reviewed in a top-down order, which proceeds from the less complex to the more complex overlapping concepts. The results of applying the methodology to SNOMED’s Specimen hierarchy are presented. Hypotheses regarding error ratios for overlapping concepts and between different kinds of overlapping concepts are formulated. Two phases of auditing the Specimen hierarchy for two releases of SNOMED are reported on. With the use of the double bootstrap and Fisher’s exact test (two-tailed), the auditing of concepts and especially roots of overlapping partial-areas is shown to yield a statistically significant higher proportion of errors. PMID:21907827

Lighten the Load: Scaffolding Visual Literacy in Biochemistry and Molecular Biology

PubMed Central

Offerdahl, Erika G.; Arneson, Jessie B.; Byrne, Nicholas

2017-01-01

The development of scientific visual literacy has been identified as critical to the training of tomorrow’s scientists and citizens alike. Within the context of the molecular life sciences in particular, visual representations frequently incorporate various components, such as discipline-specific graphical and diagrammatic features, varied levels of abstraction, and spatial arrangements of visual elements to convey information. Visual literacy is achieved when an individual understands the various ways in which a discipline uses these components to represent a particular way of knowing. Owing to the complex nature of visual representations, the activities through which visual literacy is developed have high cognitive load. Cognitive load can be reduced by first helping students to become fluent with the discrete components of visual representations before asking them to simultaneously integrate these components to extract the intended meaning of a representation. We present a taxonomy for characterizing one component of visual representations—the level of abstraction—as a first step in understanding the opportunities afforded students to develop fluency. Further, we demonstrate how our taxonomy can be used to analyze course assessments and spur discussions regarding the extent to which the development of visual literacy skills is supported by instruction within an undergraduate biochemistry curriculum. PMID:28130273

Dynamic taxonomies applied to a web-based relational database for geo-hydrological risk mitigation

NASA Astrophysics Data System (ADS)

Sacco, G. M.; Nigrelli, G.; Bosio, A.; Chiarle, M.; Luino, F.

2012-02-01

In its 40 years of activity, the Research Institute for Geo-hydrological Protection of the Italian National Research Council has amassed a vast and varied collection of historical documentation on landslides, muddy-debris flows, and floods in northern Italy from 1600 to the present. Since 2008, the archive resources have been maintained through a relational database management system. The database is used for routine study and research purposes as well as for providing support during geo-hydrological emergencies, when data need to be quickly and accurately retrieved. Retrieval speed and accuracy are the main objectives of an implementation based on a dynamic taxonomies model. Dynamic taxonomies are a general knowledge management model for configuring complex, heterogeneous information bases that support exploratory searching. At each stage of the process, the user can explore or browse the database in a guided yet unconstrained way by selecting the alternatives suggested for further refining the search. Dynamic taxonomies have been successfully applied to such diverse and apparently unrelated domains as e-commerce and medical diagnosis. Here, we describe the application of dynamic taxonomies to our database and compare it to traditional relational database query methods. The dynamic taxonomy interface, essentially a point-and-click interface, is considerably faster and less error-prone than traditional form-based query interfaces that require the user to remember and type in the "right" search keywords. Finally, dynamic taxonomy users have confirmed that one of the principal benefits of this approach is the confidence of having considered all the relevant information. Dynamic taxonomies and relational databases work in synergy to provide fast and precise searching: one of the most important factors in timely response to emergencies.

Assessing Complexity in Learning Outcomes--A Comparison between the SOLO Taxonomy and the Model of Hierarchical Complexity

ERIC Educational Resources Information Center

Stålne, Kristian; Kjellström, Sofia; Utriainen, Jukka

2016-01-01

An important aspect of higher education is to educate students who can manage complex relationships and solve complex problems. Teachers need to be able to evaluate course content with regard to complexity, as well as evaluate students' ability to assimilate complex content and express it in the form of a learning outcome. One model for evaluating…

Complex Problem Solving in a Workplace Setting.

ERIC Educational Resources Information Center

Middleton, Howard

2002-01-01

Studied complex problem solving in the hospitality industry through interviews with six office staff members and managers. Findings show it is possible to construct a taxonomy of problem types and that the most common approach can be termed "trial and error." (SLD)

Cracking complex taxonomy of Costa Rican moths: Anacrusis Zeller (Lepidoptera: Tortricidae)

USDA-ARS?s Scientific Manuscript database

Remarkably similar forewing patterns, striking sexual dimorphism, and rampant sympatry all combine to present a taxonomically and morphologically bewildering complex of five species of Anacrusis tortricid moths in Central America: Anacrusis turrialbae Razowski, Anacrusis piriferana (Zeller), Anacrus...

The ADL taxonomy for persons with mental disorders - adaptation and evaluation.

PubMed

Holmqvist, Kajsa Lidström; Holmefur, Marie

2018-05-03

There is a lack of occupation-focused instruments to assess Activities of Daily Living (ADL) that are intended for persons with mental disorders. The ADL Taxonomy is an instrument that is widely-used within clinical practice for persons with physical impairment. The aim of this study was to adapt the ADL Taxonomy for persons with mental disorders and evaluate its validity. An expert group of Occupational Therapists (OTs) from psychiatric care adapted the ADL Taxonomy to fit the client group, including creating three new items. OTs in psychiatric care collected client data and evaluated the instrument for usability. Rasch analysis was used to evaluate the contruct validity of 16 activities separately. The OTs collected 123 assessments from clients with various mental disorders. Ten activities had excellent, and four had acceptable, psychometric properties with regard to item and person fit and unidimensionality. The activity managing the day/time gave complex results and would benefit from further development. The OTs found the test version intelligible, relevant and easy to use. The ADL Taxonomy for persons with mental disorders has 16 activities with three to six actions each, and is now ready for clinical use.

Known unknowns: indirect energy effects of information and communication technology

DOE PAGES

Horner, Nathaniel C.; Shehabi, Arman; Azevedo, Ines L.

2016-10-05

There has been sustained and growing interest in characterizing the net energy impact of information and communication technology (ICT), which results from indirect effects offsetting (or amplifying) the energy directly consumed by ICT equipment. These indirect effects may be either positive or negative, and there is considerable disagreement as to the direction of this sign as well as the effect magnitude. Literature in this area ranges from studies focused on a single service (such as e-commerce versus traditional retail) to macroeconomic studies attempting to characterize the overall impact of ICT. Methods. We review the literature on the indirect energy effectmore » of ICT found via Google Scholar, our own research, and input from other researchers in the field. The various studies are linked to an effect taxonomy, which is synthesized from several different hierarchies present in the literature. References are further grouped according to ICT service (e.g., e-commerce, telework) and summarized by scope, method, and quantitative and qualitative findings. Review results. Uncertainty persists in understanding the net energy effects of ICT. Results of indirect energy effect studies are highly sensitive to scoping decisions and assumptions made by the analyst. Uncertainty increases as the impact scope broadens, due to complex and interconnected effects. However, there is general agreement that ICT has large energy savings potential, but that the realization of this potential is highly dependent on deployment details and user behavior. Discussion. While the overall net effect of ICT is likely to remain unknown, this review suggests several guidelines for improving research quality in this area, including increased data collection, enhancing traditional modeling studies with sensitivity analysis, greater care in scoping, less confidence in characterizing aggregate impacts, more effort on understanding user behavior, and more contextual integration across the different levels of the effect taxonomy.« less

Known unknowns: indirect energy effects of information and communication technology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Horner, Nathaniel C.; Shehabi, Arman; Azevedo, Ines L.

There has been sustained and growing interest in characterizing the net energy impact of information and communication technology (ICT), which results from indirect effects offsetting (or amplifying) the energy directly consumed by ICT equipment. These indirect effects may be either positive or negative, and there is considerable disagreement as to the direction of this sign as well as the effect magnitude. Literature in this area ranges from studies focused on a single service (such as e-commerce versus traditional retail) to macroeconomic studies attempting to characterize the overall impact of ICT. Methods. We review the literature on the indirect energy effectmore » of ICT found via Google Scholar, our own research, and input from other researchers in the field. The various studies are linked to an effect taxonomy, which is synthesized from several different hierarchies present in the literature. References are further grouped according to ICT service (e.g., e-commerce, telework) and summarized by scope, method, and quantitative and qualitative findings. Review results. Uncertainty persists in understanding the net energy effects of ICT. Results of indirect energy effect studies are highly sensitive to scoping decisions and assumptions made by the analyst. Uncertainty increases as the impact scope broadens, due to complex and interconnected effects. However, there is general agreement that ICT has large energy savings potential, but that the realization of this potential is highly dependent on deployment details and user behavior. Discussion. While the overall net effect of ICT is likely to remain unknown, this review suggests several guidelines for improving research quality in this area, including increased data collection, enhancing traditional modeling studies with sensitivity analysis, greater care in scoping, less confidence in characterizing aggregate impacts, more effort on understanding user behavior, and more contextual integration across the different levels of the effect taxonomy.« less

Known unknowns: indirect energy effects of information and communication technology

NASA Astrophysics Data System (ADS)

Horner, Nathaniel C.; Shehabi, Arman; Azevedo, Inês L.

2016-10-01

Background. There has been sustained and growing interest in characterizing the net energy impact of information and communication technology (ICT), which results from indirect effects offsetting (or amplifying) the energy directly consumed by ICT equipment. These indirect effects may be either positive or negative, and there is considerable disagreement as to the direction of this sign as well as the effect magnitude. Literature in this area ranges from studies focused on a single service (such as e-commerce versus traditional retail) to macroeconomic studies attempting to characterize the overall impact of ICT. Methods. We review the literature on the indirect energy effect of ICT found via Google Scholar, our own research, and input from other researchers in the field. The various studies are linked to an effect taxonomy, which is synthesized from several different hierarchies present in the literature. References are further grouped according to ICT service (e.g., e-commerce, telework) and summarized by scope, method, and quantitative and qualitative findings. Review results. Uncertainty persists in understanding the net energy effects of ICT. Results of indirect energy effect studies are highly sensitive to scoping decisions and assumptions made by the analyst. Uncertainty increases as the impact scope broadens, due to complex and interconnected effects. However, there is general agreement that ICT has large energy savings potential, but that the realization of this potential is highly dependent on deployment details and user behavior. Discussion. While the overall net effect of ICT is likely to remain unknown, this review suggests several guidelines for improving research quality in this area, including increased data collection, enhancing traditional modeling studies with sensitivity analysis, greater care in scoping, less confidence in characterizing aggregate impacts, more effort on understanding user behavior, and more contextual integration across the different levels of the effect taxonomy.

The User Knows What to Call It: Incorporating Patient Voice Through User-Contributed Tags on a Participatory Platform About Health Management

PubMed Central

Carriere, Rachel M; Kaplan, Samantha Jan

2017-01-01

Background Body listening, described as the act of paying attention to the body’s signals and cues, can be an important component of long-term health management. Objective The aim of this study was to introduce and evaluate the Body Listening Project, an innovative effort to engage the public in the creation of a public resource—to leverage collective wisdom in the health domain. This project involved a website where people could contribute their experiences of and dialogue with others concerning body listening and self-management. This article presents an analysis of the tags contributed, with a focus on the value of these tags for knowledge organization and incorporation into consumer-friendly health information retrieval systems. Methods First, we performed content analysis of the tags contributed, identifying a set of categories and refining the relational structure of the categories to develop a preliminary classification scheme, the Body Listening and Self-Management Taxonomy. Second, we compared the concepts in the Body Listening and Self-Management Taxonomy with concepts that were automatically identified from an extant health knowledge resource, the Unified Medical Language System (UMLS), to better characterize the information that participants contributed. Third, we employed visualization techniques to explore the concept space of the tags. A correlation matrix, based on the extent to which categories tended to be assigned to the same tags, was used to study the interrelatedness of the taxonomy categories. Then a network visualization was used to investigate structural relationships among the categories in the taxonomy. Results First, we proposed a taxonomy called the Body Listening and Self-Management Taxonomy, with four meta-level categories: (1) health management strategies, (2) concepts and states, (3) influencers, and (4) health-related information behavior. This taxonomy could inform future efforts to organize knowledge and content of this subject matter. Second, we compared the categories from this taxonomy with the UMLS concepts that were identified. Though the UMLS offers benefits such as speed and breadth of coverage, the Body Listening and Self-Management Taxonomy is more consumer-centric. Third, the correlation matrix and network visualization demonstrated that there are natural areas of ambiguity and semantic relatedness in the meanings of the concepts in the Body Listening and Self-Management Taxonomy. Use of these visualizations can be helpful in practice settings, to help library and information science practitioners understand and resolve potential challenges in classification; in research, to characterize the structure of the conceptual space of health management; and in the development of consumer-centric health information retrieval systems. Conclusions A participatory platform can be employed to collect data concerning patient experiences of health management, which can in turn be used to develop new health knowledge resources or augment existing ones, as well as be incorporated into consumer-centric health information systems. PMID:28882809

The User Knows What to Call It: Incorporating Patient Voice Through User-Contributed Tags on a Participatory Platform About Health Management.

PubMed

Chen, Annie T; Carriere, Rachel M; Kaplan, Samantha Jan

2017-09-07

Body listening, described as the act of paying attention to the body's signals and cues, can be an important component of long-term health management. The aim of this study was to introduce and evaluate the Body Listening Project, an innovative effort to engage the public in the creation of a public resource-to leverage collective wisdom in the health domain. This project involved a website where people could contribute their experiences of and dialogue with others concerning body listening and self-management. This article presents an analysis of the tags contributed, with a focus on the value of these tags for knowledge organization and incorporation into consumer-friendly health information retrieval systems. First, we performed content analysis of the tags contributed, identifying a set of categories and refining the relational structure of the categories to develop a preliminary classification scheme, the Body Listening and Self-Management Taxonomy. Second, we compared the concepts in the Body Listening and Self-Management Taxonomy with concepts that were automatically identified from an extant health knowledge resource, the Unified Medical Language System (UMLS), to better characterize the information that participants contributed. Third, we employed visualization techniques to explore the concept space of the tags. A correlation matrix, based on the extent to which categories tended to be assigned to the same tags, was used to study the interrelatedness of the taxonomy categories. Then a network visualization was used to investigate structural relationships among the categories in the taxonomy. First, we proposed a taxonomy called the Body Listening and Self-Management Taxonomy, with four meta-level categories: (1) health management strategies, (2) concepts and states, (3) influencers, and (4) health-related information behavior. This taxonomy could inform future efforts to organize knowledge and content of this subject matter. Second, we compared the categories from this taxonomy with the UMLS concepts that were identified. Though the UMLS offers benefits such as speed and breadth of coverage, the Body Listening and Self-Management Taxonomy is more consumer-centric. Third, the correlation matrix and network visualization demonstrated that there are natural areas of ambiguity and semantic relatedness in the meanings of the concepts in the Body Listening and Self-Management Taxonomy. Use of these visualizations can be helpful in practice settings, to help library and information science practitioners understand and resolve potential challenges in classification; in research, to characterize the structure of the conceptual space of health management; and in the development of consumer-centric health information retrieval systems. A participatory platform can be employed to collect data concerning patient experiences of health management, which can in turn be used to develop new health knowledge resources or augment existing ones, as well as be incorporated into consumer-centric health information systems. ©Annie T Chen, Rachel M Carriere, Samantha Jan Kaplan. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 07.09.2017.

Botany, Taxonomy and Cytology of Crocus sativus series

PubMed Central

Saxena, R. B.

2010-01-01

Saffron is produced from the dried styles of Crocus sativus L. (Iridaceae) which is unknown as wild plant, representing a sterile triploid. These belong to subgenus Crocus series Crocus sativus – series are closely related species; and are difficult to be separated taxonomically and have a complex cytology. Botany of C. sativus – series, taxonomy of their species and their infraspecific taxa are presented, and their distribution, ecology and phenology; full description and chromosome counts are provided with key to their identification. PMID:22131743

Observer properties for understanding dynamical displays: Capacities, limitations, and defaults

NASA Technical Reports Server (NTRS)

Proffitt, Dennis R.; Kaiser, Mary K.

1991-01-01

People's ability to extract relevant information while viewing ongoing events is discussed in terms of human capabilities, limitations, and defaults. A taxonomy of event complexity is developed which predicts which dynamical events people can and cannot construe. This taxonomy is related to the distinction drawn in classical mechanics between particle and extended body motions. People's commonsense understandings of simple mechanical systems are impacted little by formal training, but rather reflect heuristical simplifications that focus on a single dimension of perceived dynamical relevance.

Taxonomy of the Rhizopogon vinicolor species complex based on analysis of ITS sequences and microsatellite loci.

Treesearch

Annette M. Kretzer; Daniel L. Luoma; Randy Molina; Joseph W. Spatafora

2003-01-01

We are re-addressing species concepts in the Rhizopogon vinicolor species complex (Boletales, Basidiomycota) using sequence data from the interna transcribed spacer (ITS) region of the nuclear ribosomal repeat, as well as genoLypic data from five microsatellite loci. The R. vinicolor species complex by our definition includes,...

Structure, Spatial and Temporal Distribution of the Culex pipiens Complex in Shanghai, China

PubMed Central

Gao, Qiang; Xiong, Chenglong; Su, Fei; Cao, Hui; Zhou, Jianjun; Jiang, Qingwu

2016-01-01

Background: Culex pipiens molestus was first reported in Shanghai in 2010. The population structures and seasonal distributions of Culex pipiens subspecies C. p. molestus, Culex pipiens pallens, and Culex pipiens quinquefasciatus are not well known. Methods: From late February to November 2013, we conducted daily field surveillance of mosquitoes at eight sites at two green lands and three residential areas in downtown Shanghai. Morphological comparison and DV/D ratios (DV/D is an indicator of mosquito taxonomy) were used to identify adult mosquitoes. Results: The distribution curves of the Culex pipiens complex members indicated seasonal fluctuations. The temperature range of 20–25 °C was the most suitable for adult activity. Micro-environmental factors may differentiate the complex population structures. Hybridization between C. p. pallens and C. p. quinquefasciatus was common and neither “DV/D = 0.40” nor “DV/D = 0.50” can distinguish these subspecies and their hybrids. Conclusion: the population structure of the Culex pipiens complex is complex and characterized by significant hybridization. Measures other than DV/D ratios are needed for the discrimination of subspecies. The C. p. molestus invasion might result in the transmission of novel vector-borne diseases in Shanghai. PMID:27869687

Improving Virus Taxonomy by Recontextualizing Sequence-Based Classification with Biologically Relevant Data: the Case of the Alphacoronavirus 1 Species

PubMed Central

André, Nicole M.

2018-01-01

ABSTRACT The difficulties related to virus taxonomy have been amplified by recent advances in next-generation sequencing and metagenomics, prompting the field to revisit the question of what constitutes a useful viral classification. Here, taking a challenging classification found in coronaviruses, we argue that consideration of biological properties in addition to sequence-based demarcations is critical for generating useful taxonomy that recapitulates complex evolutionary histories. Within the Alphacoronavirus genus, the Alphacoronavirus 1 species encompasses several biologically distinct viruses. We carried out functionally based phylogenetic analysis, centered on the spike gene, which encodes the main surface antigen and primary driver of tropism and pathogenesis. Within the Alphacoronavirus 1 species, we identify clade A (encompassing serotype I feline coronavirus [FCoV] and canine coronavirus [CCoV]) and clade B (grouping serotype II FCoV and CCoV and transmissible gastroenteritis virus [TGEV]-like viruses). We propose this clade designation, along with the newly proposed Alphacoronavirus 2 species, as an improved way to classify the Alphacoronavirus genus. IMPORTANCE Our work focuses on improving the classification of the Alphacoronavirus genus. The Alphacoronavirus 1 species groups viruses of veterinary importance that infect distinct mammalian hosts and includes canine and feline coronaviruses and transmissible gastroenteritis virus. It is the prototype species of the Alphacoronavirus genus; however, it encompasses biologically distinct viruses. To better characterize this prototypical species, we performed phylogenetic analyses based on the sequences of the spike protein, one of the main determinants of tropism and pathogenesis, and reveal the existence of two subgroups or clades that fit with previously established serotype demarcations. We propose a new clade designation to better classify Alphacoronavirus 1 members. PMID:29299531

Improving Virus Taxonomy by Recontextualizing Sequence-Based Classification with Biologically Relevant Data: the Case of the Alphacoronavirus 1 Species.

PubMed

Whittaker, Gary R; André, Nicole M; Millet, Jean Kaoru

2018-01-01

The difficulties related to virus taxonomy have been amplified by recent advances in next-generation sequencing and metagenomics, prompting the field to revisit the question of what constitutes a useful viral classification. Here, taking a challenging classification found in coronaviruses, we argue that consideration of biological properties in addition to sequence-based demarcations is critical for generating useful taxonomy that recapitulates complex evolutionary histories. Within the Alphacoronavirus genus, the Alphacoronavirus 1 species encompasses several biologically distinct viruses. We carried out functionally based phylogenetic analysis, centered on the spike gene, which encodes the main surface antigen and primary driver of tropism and pathogenesis. Within the Alphacoronavirus 1 species, we identify clade A (encompassing serotype I feline coronavirus [FCoV] and canine coronavirus [CCoV]) and clade B (grouping serotype II FCoV and CCoV and transmissible gastroenteritis virus [TGEV]-like viruses). We propose this clade designation, along with the newly proposed Alphacoronavirus 2 species, as an improved way to classify the Alphacoronavirus genus. IMPORTANCE Our work focuses on improving the classification of the Alphacoronavirus genus. The Alphacoronavirus 1 species groups viruses of veterinary importance that infect distinct mammalian hosts and includes canine and feline coronaviruses and transmissible gastroenteritis virus. It is the prototype species of the Alphacoronavirus genus; however, it encompasses biologically distinct viruses. To better characterize this prototypical species, we performed phylogenetic analyses based on the sequences of the spike protein, one of the main determinants of tropism and pathogenesis, and reveal the existence of two subgroups or clades that fit with previously established serotype demarcations. We propose a new clade designation to better classify Alphacoronavirus 1 members.

Time-dependent extinction rate and species abundance in a tangled-nature model of biological evolution.

PubMed

Hall, Matt; Christensen, Kim; di Collobiano, Simone A; Jensen, Henrik Jeldtoft

2002-07-01

We present a model of evolutionary ecology consisting of a web of interacting individuals, a tangle-nature model. The reproduction rate of individuals characterized by their genome depends on the composition of the population in genotype space. Ecological features such as the taxonomy and the macroevolutionary mode of the dynamics are emergent properties. The macrodynamics exhibit intermittent two-mode switching with a gradually decreasing extinction rate. The generated ecologies become gradually better adapted as well as more complex in a collective sense. The form of the species abundance curve compares well with observed functional forms. The model's error threshold can be understood in terms of the characteristics of the two dynamical modes of the system.

Unravelling the Phellinus pini s.l. complex in North America: a multilocus phylogeny and differentiation analysis of Porodaedalea

Treesearch

N.J. Brazee; D.L. Lindner

2013-01-01

Phellinus sensu lato (s.l.) is a complex of segregate genera that act as aggressive pathogens of woody plants. Nearly all of the genera in this complex have unresolved taxonomies, including Porodaedalea, which is one of the most important trunk rot pathogens of coniferous trees throughout the northern hemisphere. In an attempt...

Quantitative proteomic analysis reveals evolutionary divergence and species-specific peptides in the Alexandrium tamarense complex (Dinophyceae).

PubMed

Li, Cheng; Zhang, Yong; Xie, Zhang-Xian; He, Zhi-Ping; Lin, Lin; Wang, Da-Zhi

2013-06-28

The Alexandrium tamarense/catenella/fundyense complex is the major causative agent responsible for harmful algal blooms and paralytic shellfish poisoning around the world. However, taxonomy of the A. tamarense complex is contentious and the evolutionary relationships within the complex are unclear. This study compared protein profiles of the A. tamarense complex collected from different geographic regions using the two dimensional fluorescence difference gel electrophoresis (2-D DIGE) approach, and identified species-specific peptides using MALDI-TOF/TOF mass spectrometry. The results showed that three Alexandrium morphotypes presented significantly different protein expression patterns with about 30-40% shared proteins. However, ecotypes from different geographic regions within a species exhibited the same expression patterns, although a few proteins were altered in abundance. Several proteins, i.e. ribulose-1,5-bisphosphate carboxylase oxygenase form II, plastid protein NAP50, methionine S-adenosyltransferase, and peridinin-chlorophyll a-binding protein, were identified and presented different shift patterns in isoelectric point and/or molecular weight in the 2-D DIGE gels, indicating that amino acid mutation and/or posttranslational modification of these proteins had occurred. The species-specific peptide mass fingerprint and amino acid sequence of ribulose-1,5-bisphosphate carboxylase oxygenase were characterized in the A. tamarense complex, and amino acid substitution occurred among them. This study indicated that evolutionary divergence had occurred at the proteomic level in the A. tamarense complex, and that the species-specific peptides could be used as potential biomarkers to distinguish the three morphotypes. Scientific question: The Alexandrium tamarense/catenella/fundyense complex is the major causative agent responsible for harmful algal blooms and paralytic shellfish poisoning around the world. However, taxonomy of the A. tamarense complex is contentious and the evolutionary relationships within the complex are unclear, which has seriously impeded our understanding of Alexandrium-causing HABs and, consequently, the monitoring, mitigation and prevention. Technical significance: This study, for the first time, compared the global protein expression patterns of eight ecotypes from the A. tamarense complex and identified species-specific peptides using a quantitative proteomic approach combining 2-D DIGE and MALDI-TOF/TOF MS. This study demonstrated that the evolutionary divergence had occurred in the A. tamarense complex at the proteomic level, and the complex should be classified into three species, i.e. A. tamarense, A. catenella, and A. fundyense. Moreover, the species-specific peptide mass fingerprints could be used as potential biomarkers to distinguish the three morphotypes. Copyright © 2013 Elsevier B.V. All rights reserved.

Plant taxonomy: a historical perspective, current challenges, and perspectives.

PubMed

Rouhan, Germinal; Gaudeul, Myriam

2014-01-01

Taxonomy is the science that explores, describes, names, and classifies all organisms. In this introductory chapter, we highlight the major historical steps in the elaboration of this science that provides baseline data for all fields of biology and plays a vital role for society but is also an independent, complex, and sound hypothesis-driven scientific discipline.In a first part, we underline that plant taxonomy is one of the earliest scientific disciplines that emerged thousands of years ago, even before the important contributions of Greeks and Romans (e.g., Theophrastus, Pliny the Elder, and Dioscorides). In the fifteenth to sixteenth centuries, plant taxonomy benefited from the Great Navigations, the invention of the printing press, the creation of botanic gardens, and the use of the drying technique to preserve plant specimens. In parallel with the growing body of morpho-anatomical data, subsequent major steps in the history of plant taxonomy include the emergence of the concept of natural classification, the adoption of the binomial naming system (with the major role of Linnaeus) and other universal rules for the naming of plants, the formulation of the principle of subordination of characters, and the advent of the evolutionary thought. More recently, the cladistic theory (initiated by Hennig) and the rapid advances in DNA technologies allowed to infer phylogenies and to propose true natural, genealogy-based classifications.In a second part, we put the emphasis on the challenges that plant taxonomy faces nowadays. The still very incomplete taxonomic knowledge of the worldwide flora (the so-called taxonomic impediment) is seriously hampering conservation efforts that are especially crucial as biodiversity enters its sixth extinction crisis. It appears mainly due to insufficient funding, lack of taxonomic expertise, and lack of communication and coordination. We then review recent initiatives to overcome these limitations and to anticipate how taxonomy should and could evolve. In particular, the use of molecular data has been era-splitting for taxonomy and may allow an accelerated pace of species discovery. We examine both strengths and limitations of such techniques in comparison to morphology-based investigations, we give broad recommendations on the use of molecular tools for plant taxonomy, and we highlight the need for an integrative taxonomy based on evidence from multiple sources.

a Comparison of Morphological Taxonomy and Next Generation DNA Sequencing for the Assessment of Zooplankton Diversity

NASA Astrophysics Data System (ADS)

Harvey, J.; Fisher, J. L.; Johnson, S.; Morgan, S.; Peterson, W. T.; Satterthwaite, E. V.; Vrijenhoek, R. C.

2016-02-01

Our ability to accurately characterize the diversity of planktonic organisms is affected by both the methods we use to collect water samples and our approaches to assessing sample contents. Plankton nets collect organisms from high volumes of water, but integrate sample contents along the net's path. In contrast, plankton pumps collect water from discrete depths. Autonomous underwater vehicles (AUVs) can collect water samples with pinpoint accuracy from physical features such as upwelling fronts or biological features such as phytoplankton blooms, but sample volumes are necessarily much smaller than those possible with nets. Characterization of plankton diversity and abundances in water samples may also vary with the assessment method we apply. Morphological taxonomy provides visual identification and enumeration of organisms via microscopy, but is labor intensive. Next generation DNA sequencing (NGS) shows great promise for assessing plankton diversity in water samples but accurate assessment of relative abundances may not be possible in all cases. Comparison of morphological taxonomy to molecular approaches is necessary to identify areas of overlap and also areas of disagreement between these methods. We have compared morphological taxonomic assessments to mitochondrial COI and nuclear 28S ribosomal RNA NGS results for plankton net samples collected in Monterey bay, California. We have made a similar comparison for plankton pump samples, and have also applied our NGS methods to targeted, small volume water samples collected by an AUV. Our goal is to communicate current results and lessons learned regarding application of traditional taxonomy and novel molecular approaches to the study of plankton diversity in spatially and temporally variable, coastal marine environments.

Using mitogenomic and nuclear ribosomal sequence data to investigate the phylogeny of the Xiphinema americanum species complex

USDA-ARS?s Scientific Manuscript database

Nematodes within the Xiphinema americanum species complex are economically important because they vector nepoviruses which cause considerable damage to a variety of agricultural crops. The taxonomy of X. americanum is controversial, with the number of putative species being the subject of debate. Ac...

Taxonomy of the Loggerhead Kingbird (Tyrannus caudifasciatus) complex (Aves: Tyrannidae)

Treesearch

Orlando H. Garrido; James W. Wiley; George B. Reynard

2009-01-01

We examined the complex of populations of the Loggerhead Kingbird (Tyrannus caudifasciatus), a West Indian endemic. We separate populations in Puerto Rico and Isla Vieques (T. taylori), and Hispaniola (T. gabbii) as distinct species. Subspecific distinction is assigned to populations in Cuba, Isla de Pinos, and Cuban satellites (T. caudifasciatus caudifasciatus);...

78 FR 64357 - Endangered and Threatened Wildlife and Plants; Threatened Status for the Bi-State Distinct...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-10-28

..., including: (a) Habitat requirements for feeding, breeding, and sheltering; (b) Genetics and taxonomy; (c...-grouse breeding complex) counts, population trends, and land ownership information is available in the... local breeding complexes. The six PMUs include: Pine Nut, Desert Creek-Fales, Bodie, Mount Grant, South...

Taxonomy and phylogeny of Pluteus glaucotinctus sensu lato (Agaricales, Basidiomycota), a multicontinental species complex

Treesearch

Nelson Menolli; Alfredo Justo; Pedro Arrillaga; C.K. Pradeep; Andrew M. Minnis; Marina Capelari

2014-01-01

In order to better understand species delimitation in the Pluteus glaucotinctus species complex, we present a detailed study based on morphological and DNA sequence (nrITS + tef1) data. Pluteus glaucotinctus sensu stricto is known only from the type collection (Democratic Republic of the Congo), which is re-...

Characterization of the Musa spp. Taxonomic Reference Collection at the USDA-ARS, Tropical Agriculture Research Station.

USDA-ARS?s Scientific Manuscript database

Plant characterization descriptors enable an easy and quick way to discriminate between phenotypes. However, the best descriptors for taxonomy and germplasm rationalization purposes should be highly heritable (i.e., express equally in all environments) and easy to score to avoid bias due to differen...

Floral Volatiles in Parasitic Plants of the Orobanchaceae. Ecological and Taxonomic Implications.

PubMed

Tóth, Peter; Undas, Anna K; Verstappen, Francel; Bouwmeester, Harro

2016-01-01

The holoparasitic broomrapes, Orobanche spp. and Phelipanche spp. (Orobanchaceae), are root parasites that completely depend on a host plant for survival and reproduction. There is considerable controversy on the taxonomy of this biologically and agronomically important family. Flowers of over 25 parasitic Orobanchaceae and a number of close, parasitic and non-parasitic, relatives emitted a complex blend of volatile organic compounds (VOCs), consisting of over 130 VOCs per species. Floral VOC blend-based phylogeny supported the known taxonomy in internal taxonomic grouping of genus and eliminated the uncertainty in some taxonomical groups. Moreover, phylogenetic analysis suggested separation of the broomrapes into two main groups parasitizing annual and perennial hosts, and for the annual hosts, into weedy and non-weedy broomrapes. We conclude that floral VOCs are a significant tool in species identification and possibly even in defining new species and can help to improve controversial taxonomy in the Orobanchaceae.

Morphological, molecular and phylogenetic analyses of Diplotriaena bargusinica Skrjabin, 1917 (Nematoda: Diplotriaenidae).

PubMed

Dutra Vieira, Thainá; Pegoraro de Macedo, Marcia Raquel; Fedatto Bernardon, Fabiana; Müller, Gertrud

2017-10-01

The nematode Diplotriaena bargusinica is a bird air sac parasite, and its taxonomy is based mainly on morphological and morphometric characteristics. Increasing knowledge of genetic information variability has spurred the use of DNA markers in conjunction with morphological data for inferring phylogenetic relationships in different taxa. Considering the potential of molecular biology in taxonomy, this study presents the morphological and molecular characterization of D. bargusinica, and establishes the phylogenetic position of the nematode in Spirurina. Twenty partial sequences of the 18S region of D. bargusinica rDNA were generated. Phylogenetic trees were obtained through the Maximum Likelihood and Bayesian Inference methods where both had similar topology. The group Diplotriaenoidea is monophyletic and the topologies generated corroborate the phylogenetic studies based on traditional and previously performed molecular taxonomy. This study is the first to generate molecular data associated with the morphology of the species. Copyright © 2017 Elsevier B.V. All rights reserved.

Qualitative task analysis to enhance sports characterization: a surfing case study.

PubMed

Moreira, Miguel; Peixoto, César

2014-09-29

The aim of this study was to develop a Matrix of Analysis for Sports Tasks (MAST), regardless of the sports activity, based on practice classification and task analysis. Being this a qualitative research our main question was: in assessing sports' structure is it possible to make the characterization of any discipline through context and individuals' behaviours? The sample was within a surf discipline in a competition flowing having 5 of the top 16 Portuguese surfers training together. Based on a qualitative method, studying the surf as the main activity was an interpretative study case. The MAST was applied in four phases: taxonomy; tasks and context description; task analysis; teaching and performance strategies. Its application allowed the activities' characterization through the observation, surfer's opinions and bibliographical support. The triangulation of the data was used as an information data treatment. The elements were classified by the challenges proposed to the practitioners and the taxonomy was constituted by the sport activities, group, modality and discipline. Surf is a discipline of surfing which is a sliding sport modality, therefore, a nature sport. In the context description, we had the wave's components and constraints and the surfboards' qualities. Through task analysis we obtained a taxonomy of surf manoeuvres. The structural and functional analysis allowed finding solutions for learning of surf techniques with trampoline and skateboards because these fit in sliding sports. MAST makes possible the development of strategies that benefit teaching and performance intervention.

A taxonomy of adolescent health: development of the adolescent health profile-types.

PubMed

Riley, A W; Green, B F; Forrest, C B; Starfield, B; Kang, M; Ensminger, M E

1998-08-01

The aim of this study was to develop a taxonomy of health profile-types that describe adolescents' patterns of health as self-reported on a health status questionnaire. The intent was to be able to assign individuals to mutually exclusive and exhaustive groups that characterize the important aspects of their health and need for health services. Cluster analytic empirical methods and clinically based conceptual methods were used to identify patterns of health in samples of adolescents from schools and from clinics that serve adolescents with chronic conditions and acute illnesses. Individuals with similar patterns of scores across multiple domains were assigned to the same profile-type. Results from the empirical and conceptually based methods were integrated to produce a practical system for assigning youths to profile-types. Four domains of health (Satisfaction, Discomfort, Risks and Resilience) were used to group individuals into 13 distinct profile-types. The profile-types were characterized primarily by the number of domains in which health is poor, identifying the unique combinations of problems that characterize different subgroups of adolescents. This method of reporting the information available on health status surveys is potentially a more informative way of identifying and classifying the health needs of subgroups in the population than is available from global scores or multiple scale scores. The reliability and validity of this taxonomy of health profile-types for the purposes of planning and evaluating health services must be demonstrated. That is the purpose of the accompanying study.

Qualitative Task Analysis to Enhance Sports Characterization: A Surfing Case Study

PubMed Central

Moreira, Miguel; Peixoto, César

2014-01-01

The aim of this study was to develop a Matrix of Analysis for Sports Tasks (MAST), regardless of the sports activity, based on practice classification and task analysis. Being this a qualitative research our main question was: in assessing sports’ structure is it possible to make the characterization of any discipline through context and individuals’ behaviours? The sample was within a surf discipline in a competition flowing having 5 of the top 16 Portuguese surfers training together. Based on a qualitative method, studying the surf as the main activity was an interpretative study case. The MAST was applied in four phases: taxonomy; tasks and context description; task analysis; teaching and performance strategies. Its application allowed the activities’ characterization through the observation, surfer’s opinions and bibliographical support. The triangulation of the data was used as an information data treatment. The elements were classified by the challenges proposed to the practitioners and the taxonomy was constituted by the sport activities, group, modality and discipline. Surf is a discipline of surfing which is a sliding sport modality, therefore, a nature sport. In the context description, we had the wave’s components and constraints and the surfboards’ qualities. Through task analysis we obtained a taxonomy of surf manoeuvres. The structural and functional analysis allowed finding solutions for learning of surf techniques with trampoline and skateboards because these fit in sliding sports. MAST makes possible the development of strategies that benefit teaching and performance intervention. PMID:25414757

A taxonomy for disease management: a scientific statement from the American Heart Association Disease Management Taxonomy Writing Group.

PubMed

Krumholz, Harlan M; Currie, Peter M; Riegel, Barbara; Phillips, Christopher O; Peterson, Eric D; Smith, Renee; Yancy, Clyde W; Faxon, David P

2006-09-26

Disease management has shown great promise as a means of reorganizing chronic care and optimizing patient outcomes. Nevertheless, disease management programs are widely heterogeneous and lack a shared definition of disease management, which limits our ability to compare and evaluate different programs. To address this problem, the American Heart Association's Disease Management Taxonomy Writing Group developed a system of classification that can be used both to categorize and compare disease management programs and to inform efforts to identify specific factors associated with effectiveness. The AHA Writing Group began with a conceptual model of disease management and its components and subsequently validated this model over a wide range of disease management programs. A systematic MEDLINE search was performed on the terms heart failure, diabetes, and depression, together with disease management, case management, and care management. The search encompassed articles published in English between 1987 and 2005. We then selected studies that incorporated (1) interventions designed to improve outcomes and/or reduce medical resource utilization in patients with heart failure, diabetes, or depression and (2) clearly defined protocols with at least 2 prespecified components traditionally associated with disease management. We analyzed the study protocols and used qualitative research methods to develop a disease management taxonomy with our conceptual model as the organizing framework. The final taxonomy includes the following 8 domains: (1) Patient population is characterized by risk status, demographic profile, and level of comorbidity. (2) Intervention recipient describes the primary targets of disease management intervention and includes patients and caregivers, physicians and allied healthcare providers, and healthcare delivery systems. (3) Intervention content delineates individual components, such as patient education, medication management, peer support, or some form of postacute care, that are included in disease management. (4) Delivery personnel describes the network of healthcare providers involved in the delivery of disease management interventions, including nurses, case managers, physicians, pharmacists, case workers, dietitians, physical therapists, psychologists, and information systems specialists. (5) Method of communication identifies a broad range of disease management delivery systems that may include in-person visitation, audiovisual information packets, and some form of electronic or telecommunication technology. (6) Intensity and complexity distinguish between the frequency and duration of exposure, as well as the mix of program components, with respect to the target for disease management. (7) Environment defines the context in which disease management interventions are typically delivered and includes inpatient or hospital-affiliated outpatient programs, community or home-based programs, or some combination of these factors. (8) Clinical outcomes include traditional, frequently assessed primary and secondary outcomes, as well as patient-centered measures, such as adherence to medication, self-management, and caregiver burden. This statement presents a taxonomy for disease management that describes critical program attributes and allows for comparisons across interventions. Routine application of the taxonomy may facilitate better comparisons of structure, process, and outcome measures across a range of disease management programs and should promote uniformity in the design and conduct of studies that seek to validate disease management strategies.

Stability of an empirical psychosocial taxonomy across type of diabetes and treatment.

PubMed

Nouwen, A; Breton, M-C; Urquhart Law, G; Descôteaux, J

2007-01-01

The aims of the study were (i) to examine whether an empirical psychosocial taxonomy, based on key diabetes-related variables, is independent of type of diabetes and treatment, and (ii) to further establish the external validation of the taxonomy. In a cross-sectional study, 82 patients with Type 1 and 86 patients with Type 2 diabetes mellitus were assigned to one of three psychosocial patient profiles based on their Multidimensional Diabetes Questionnaire (MDQ) scores. General psychological and diabetes-specific measures were obtained through self-report and HbA(1c) was measured. Equal proportions of Type 1 and Type 2 patients, and of patients using insulin and oral medication/diet only were classified within each of the three psychosocial profiles. External validation confirmed the validity and distinctiveness of the patients' profiles. The patient profiles were independent of demographic variables, body mass index, duration of diabetes, complexity of treatment, number of complications, social desirability, and major stress levels. The Psychosocial Taxonomy for Patients with Diabetes provides a new way to categorize individuals who may have more in common than just their type of diabetes and/or its treatment and can help target interventions to individual patients' needs.

The 5As: A practical taxonomy for the determinants of vaccine uptake.

PubMed

Thomson, Angus; Robinson, Karis; Vallée-Tourangeau, Gaëlle

2016-02-17

Suboptimal vaccine uptake in both childhood and adult immunisation programs limits their full potential impact on global health. A recent progress review of the Global Vaccine Action Plan stated that "countries should urgently identify barriers and bottlenecks and implement targeted approaches to increase and sustain coverage". However, vaccination coverage may be determined by a complex mix of demographic, structural, social and behavioral factors. To develop a practical taxonomy to organise the myriad possible root causes of a gap in vaccination coverage rates, we performed a narrative review of the literature and tested whether all non-socio-demographic determinants of coverage could be organised into 4 dimensions: Access, Affordability, Awareness and Acceptance. Forty-three studies were reviewed, from which we identified 23 primary determinants of vaccination uptake. We identified a fifth domain, Activation, which captured interventions such as SMS reminders which effectively nudge people towards getting vaccinated. The 5As taxonomy captured all identified determinants of vaccine uptake. This intuitive taxonomy has already facilitated mutual understanding of the primary determinants of suboptimal coverage within inter-sectorial working groups, a first step towards them developing targeted and effective solutions. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Cryptosporidium Taxonomy: Recent Advances and Implications for Public Health

PubMed Central

Xiao, Lihua; Fayer, Ronald; Ryan, Una; Upton, Steve J.

2004-01-01

There has been an explosion of descriptions of new species of Cryptosporidium during the last two decades. This has been accompanied by confusion regarding the criteria for species designation, largely because of the lack of distinct morphologic differences and strict host specificity among Cryptosporidium spp. A review of the biologic species concept, the International Code of Zoological Nomenclature (ICZN), and current practices for Cryptosporidium species designation calls for the establishment of guidelines for naming Cryptosporidium species. All reports of new Cryptosporidium species should include at least four basic components: oocyst morphology, natural host specificity, genetic characterizations, and compliance with the ICZN. Altogether, 13 Cryptosporidium spp. are currently recognized: C. muris, C. andersoni, C. parvum, C. hominis, C. wrairi, C. felis, and C. cannis in mammals; C. baïleyi, C. meleagridis, and C. galli in birds; C. serpentis and C. saurophilum in reptiles; and C. molnari in fish. With the establishment of a framework for naming Cryptosporidium species and the availability of new taxonomic tools, there should be less confusion associated with the taxonomy of the genus Cryptosporidium. The clarification of Cryptosporidium taxonomy is also useful for understanding the biology of Cryptosporidium spp., assessing the public health significance of Cryptosporidium spp. in animals and the environment, characterizing transmission dynamics, and tracking infection and contamination sources. PMID:14726456

Highway-rail intersection crash taxonomy for connected vehicle safety research

DOT National Transportation Integrated Search

2015-05-01

This report characterizes the frequency, severity, and costs of highway-rail intersection (HRI) collisions, and the estimated potential reductions in these metrics resulting from the implementation of Connected Vehicle HRI safety applications. Multip...

Complex within complex: integrative taxonomy reveals hidden diversity in Cicadetta brevipennis (Hemiptera: Cicadidae) and unexpected relationships with a song divergent relative

USDA-ARS?s Scientific Manuscript database

Multiple sources of data in combination are essential for species delimitation and classification of difficult taxonomic groups. Here we investigate a cicada taxon with unusual cryptic diversity and we attempt to resolve seemingly contradictory data sets. Cicada songs act as species-specific premati...

Player Types, Play Styles, and Play Complexity: Updating the Entertainment Grid

ERIC Educational Resources Information Center

Rademacher Mena, Ricardo Javier

2012-01-01

In a previous work the author created the Education and Entertainment Grid by combining various taxonomies from the fields of play and learning. In this paper, a section of this grid known as the Entertainment Grid will be extended by including previously unused elements of Richard Bartle's online player types and Robert Caillois' play complexity.…

An Empirically Derived Taxonomy of Factors Affecting Physicians' Willingness to Disclose Medical Errors

PubMed Central

Kaldjian, Lauris C; Jones, Elizabeth W; Rosenthal, Gary E; Tripp-Reimer, Toni; Hillis, Stephen L

2006-01-01

BACKGROUND Physician disclosure of medical errors to institutions, patients, and colleagues is important for patient safety, patient care, and professional education. However, the variables that may facilitate or impede disclosure are diverse and lack conceptual organization. OBJECTIVE To develop an empirically derived, comprehensive taxonomy of factors that affects voluntary disclosure of errors by physicians. DESIGN A mixed-methods study using qualitative data collection (structured literature search and exploratory focus groups), quantitative data transformation (sorting and hierarchical cluster analysis), and validation procedures (confirmatory focus groups and expert review). RESULTS Full-text review of 316 articles identified 91 impeding or facilitating factors affecting physicians' willingness to disclose errors. Exploratory focus groups identified an additional 27 factors. Sorting and hierarchical cluster analysis organized factors into 8 domains. Confirmatory focus groups and expert review relocated 6 factors, removed 2 factors, and modified 4 domain names. The final taxonomy contained 4 domains of facilitating factors (responsibility to patient, responsibility to self, responsibility to profession, responsibility to community), and 4 domains of impeding factors (attitudinal barriers, uncertainties, helplessness, fears and anxieties). CONCLUSIONS A taxonomy of facilitating and impeding factors provides a conceptual framework for a complex field of variables that affects physicians' willingness to disclose errors to institutions, patients, and colleagues. This taxonomy can be used to guide the design of studies to measure the impact of different factors on disclosure, to assist in the design of error-reporting systems, and to inform educational interventions to promote the disclosure of errors to patients. PMID:16918739

Taxonomy of Trauma Leadership Skills: A Framework for Leadership Training and Assessment.

PubMed

Leenstra, Nico F; Jung, Oliver C; Johnson, Addie; Wendt, Klaus W; Tulleken, Jaap E

2016-02-01

Good leadership is essential for optimal trauma team performance, and targeted training of leadership skills is necessary to achieve such leadership proficiency. To address the need for a taxonomy of leadership skills that specifies the skill components to be learned and the behaviors by which they can be assessed across the five phases of trauma care, the authors developed the Taxonomy of Trauma Leadership Skills (TTLS). Critical incident interviews were conducted with trauma team leaders and members from different specialties-emergency physicians, trauma surgeons, anesthesiologists, and emergency ward nurses-at three teaching hospitals in the Netherlands during January-June 2013. Data were iteratively analyzed for examples of excellent leadership skills at each phase of trauma care. Using the grounded theory approach, elements of excellent leadership skills were identified and classified. Elements and behavioral markers were sorted and categorized using multiple raters. In a two-round verification process in late 2013, the taxonomy was reviewed and rated by trauma team leaders and members from the multiple specialties for its coverage of essential items. Data were gathered from 28 interviews and 14 raters. The TTLS details 5 skill categories (information coordination, decision making, action coordination, communication management, and coaching and team development) and 37 skill elements. The skill elements are captured by 67 behavioral markers. The three-level taxonomy is presented according to five phases of trauma care. The TTLS provides a framework for teaching, learning, and assessing team leadership skills in trauma care and other complex, acute care situations.

New Abstraction Networks and a New Visualization Tool in Support of Auditing the SNOMED CT Content

PubMed Central

Geller, James; Ochs, Christopher; Perl, Yehoshua; Xu, Junchuan

2012-01-01

Medical terminologies are large and complex. Frequently, errors are hidden in this complexity. Our objective is to find such errors, which can be aided by deriving abstraction networks from a large terminology. Abstraction networks preserve important features but eliminate many minor details, which are often not useful for identifying errors. Providing visualizations for such abstraction networks aids auditors by allowing them to quickly focus on elements of interest within a terminology. Previously we introduced area taxonomies and partial area taxonomies for SNOMED CT. In this paper, two advanced, novel kinds of abstraction networks, the relationship-constrained partial area subtaxonomy and the root-constrained partial area subtaxonomy are defined and their benefits are demonstrated. We also describe BLUSNO, an innovative software tool for quickly generating and visualizing these SNOMED CT abstraction networks. BLUSNO is a dynamic, interactive system that provides quick access to well organized information about SNOMED CT. PMID:23304293

New abstraction networks and a new visualization tool in support of auditing the SNOMED CT content.

PubMed

Geller, James; Ochs, Christopher; Perl, Yehoshua; Xu, Junchuan

2012-01-01

Medical terminologies are large and complex. Frequently, errors are hidden in this complexity. Our objective is to find such errors, which can be aided by deriving abstraction networks from a large terminology. Abstraction networks preserve important features but eliminate many minor details, which are often not useful for identifying errors. Providing visualizations for such abstraction networks aids auditors by allowing them to quickly focus on elements of interest within a terminology. Previously we introduced area taxonomies and partial area taxonomies for SNOMED CT. In this paper, two advanced, novel kinds of abstraction networks, the relationship-constrained partial area subtaxonomy and the root-constrained partial area subtaxonomy are defined and their benefits are demonstrated. We also describe BLUSNO, an innovative software tool for quickly generating and visualizing these SNOMED CT abstraction networks. BLUSNO is a dynamic, interactive system that provides quick access to well organized information about SNOMED CT.

Conference on Complex Turbulent Flows: Comparison of Computation and Experiment, Stanford University, Stanford, CA, September 14-18, 1981, Proceedings. Volume 2 - Taxonomies, reporters' summaries, evaluation, and conclusions

NASA Technical Reports Server (NTRS)

Kline, S. J. (Editor); Cantwell, B. J. (Editor); Lilley, G. M.

1982-01-01

Computational techniques for simulating turbulent flows were explored, together with the results of experimental investigations. Particular attention was devoted to the possibility of defining a universal closure model, applicable for all turbulence situations; however, conclusions were drawn that zonal models, describing localized structures, were the most promising techniques to date. The taxonomy of turbulent flows was summarized, as were algebraic, differential, integral, and partial differential methods for numerical depiction of turbulent flows. Numerous comparisons of theoretically predicted and experimentally obtained data for wall pressure distributions, velocity profiles, turbulent kinetic energy profiles, Reynolds shear stress profiles, and flows around transonic airfoils were presented. Simplifying techniques for reducing the necessary computational time for modeling complex flowfields were surveyed, together with the industrial requirements and applications of computational fluid dynamics techniques.

Multiple Analogies for Complex Concepts: Antidotes for Analogy-Induced Misconception in Advanced Knowledge Acquisition. Technical Report No. 439.

ERIC Educational Resources Information Center

Spiro, Rand J.; And Others

This report argues that there exists a pervasive tendency for analogies to contribute to the development of entrenched misconceptions in the form of reducing complex new knowledge to the core of a source analogy. The report presents a taxonomy of ways that simple analogy induces conceptual error and an alternative approach involving integrated…

Improved resolution of major clades within Tuber and taxonomy of species within the Tuber gibbosum complex

Treesearch

Gregory M. Bonito; James M. Trappe; Pat Rawlinson; Rytas Vilgalys

2010-01-01

Tuber gibbosum Harkn., described from northern California, originally was thought to be a single, variable species that fruited from autumn through winter to spring. It has become popular as a culinary truffle in northwestern USA, where it is commercially harvested. Morphological studies suggested it might be a complex that includes at least two...

Decision models for capital investment and financing decisions in hospitals.

PubMed Central

Vraciu, R A

1980-01-01

The literature on capital investment and financing decisions for hospitals has suggested several approaches to analyzing sets of options. In this paper, I present a taxonomy of the different approaches; analyze and compare the different elements of the taxonomy; and illustrate and discuss the information that can be gained by using each approach. I view these different analytic methods as complementary rather than competing methods of providing information to decision makers, and argue that the complex nature of hospital objectives demands the use of more than one approach. Failure to do this may lead to biased evaluations and poor decision making. PMID:6768699

Application of a Consumer Health Information Needs Taxonomy to Questions in Maternal-Fetal Care

PubMed Central

Shenson, Jared A.; Ingram, Ebone; Colon, Nadja; Jackson, Gretchen Purcell

2015-01-01

Pregnancy is a time when expectant mothers may have numerous questions about their unborn children, especially when congenital anomalies are diagnosed prenatally. We sought to characterize information needs of pregnant women seen in the Vanderbilt Children’s Hospital Fetal Center. Participants recorded questions from diagnosis through delivery. Questions were categorized by two researchers using a hierarchical taxonomy describing consumer health information needs. Consensus category assignments were made, and inter-rater reliability was measured with Cohen’s Kappa. Sixteen participants reported 398 questions in 39 subcategories, of which the most common topics were prognosis (53 questions; 13.3%) and indications for intervention (31 questions; 7.8%). Inter-rater reliability of assignments showed moderate (κ=0.57) to substantial (κ=0.75) agreement for subcategories and primary categories, respectively. Pregnant women with prenatal diagnoses have diverse unmet information needs; a taxonomy of consumer health information needs may improve the ability to meet such needs through content and system design. PMID:26958254

Application of a Consumer Health Information Needs Taxonomy to Questions in Maternal-Fetal Care.

PubMed

Shenson, Jared A; Ingram, Ebone; Colon, Nadja; Jackson, Gretchen Purcell

2015-01-01

Pregnancy is a time when expectant mothers may have numerous questions about their unborn children, especially when congenital anomalies are diagnosed prenatally. We sought to characterize information needs of pregnant women seen in the Vanderbilt Children's Hospital Fetal Center. Participants recorded questions from diagnosis through delivery. Questions were categorized by two researchers using a hierarchical taxonomy describing consumer health information needs. Consensus category assignments were made, and inter-rater reliability was measured with Cohen's Kappa. Sixteen participants reported 398 questions in 39 subcategories, of which the most common topics were prognosis (53 questions; 13.3%) and indications for intervention (31 questions; 7.8%). Inter-rater reliability of assignments showed moderate (κ=0.57) to substantial (κ=0.75) agreement for subcategories and primary categories, respectively. Pregnant women with prenatal diagnoses have diverse unmet information needs; a taxonomy of consumer health information needs may improve the ability to meet such needs through content and system design.

Development of a taxonomy of interventions to organise the evidence on consumers' medicines use.

PubMed

Lowe, Dianne; Ryan, Rebecca; Santesso, Nancy; Hill, Sophie

2011-11-01

Safe, effective (quality) medicines use remains problematic worldwide, yet consumers' medicines use research is not well organised. This creates difficulties for decision makers in identifying evidence or research gaps and in understanding how or why interventions work. Developing a conceptual framework for this evidence helps to organise the evidence for application and raise awareness of the range of possible interventions. To scope the aims of interventions to improve consumers' medicines use we searched for and iteratively analysed policy documents, systematic reviews, and an existing consumer-oriented communication intervention taxonomy. We identified eight recurrent themes associated with the purpose of the interventions: to inform and educate; to support behaviour change; to teach skills; to facilitate communication and/or decision making; to support; to minimise risk and harms; to involve consumers at the system level; and to improve health care quality. The taxonomy accommodates the complexity and diversity of interventions in this field, by focussing on the purposes of interventions, rather than the intervention type. Currently used to organise the evidence on consumers' medicines use, the taxonomy provides a conceptual and practical map of the evidence which will aid decision making and future research investment in the area. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

A survey and taxonomy on energy efficient resource allocation techniques for cloud computing systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hameed, Abdul; Khoshkbarforoushha, Alireza; Ranjan, Rajiv

In a cloud computing paradigm, energy efficient allocation of different virtualized ICT resources (servers, storage disks, and networks, and the like) is a complex problem due to the presence of heterogeneous application (e.g., content delivery networks, MapReduce, web applications, and the like) workloads having contentious allocation requirements in terms of ICT resource capacities (e.g., network bandwidth, processing speed, response time, etc.). Several recent papers have tried to address the issue of improving energy efficiency in allocating cloud resources to applications with varying degree of success. However, to the best of our knowledge there is no published literature on this subjectmore » that clearly articulates the research problem and provides research taxonomy for succinct classification of existing techniques. Hence, the main aim of this paper is to identify open challenges associated with energy efficient resource allocation. In this regard, the study, first, outlines the problem and existing hardware and software-based techniques available for this purpose. Furthermore, available techniques already presented in the literature are summarized based on the energy-efficient research dimension taxonomy. The advantages and disadvantages of the existing techniques are comprehensively analyzed against the proposed research dimension taxonomy namely: resource adaption policy, objective function, allocation method, allocation operation, and interoperability.« less

Qualitative Data Analysis for Health Services Research: Developing Taxonomy, Themes, and Theory

PubMed Central

Bradley, Elizabeth H; Curry, Leslie A; Devers, Kelly J

2007-01-01

Objective To provide practical strategies for conducting and evaluating analyses of qualitative data applicable for health services researchers. Data Sources and Design We draw on extant qualitative methodological literature to describe practical approaches to qualitative data analysis. Approaches to data analysis vary by discipline and analytic tradition; however, we focus on qualitative data analysis that has as a goal the generation of taxonomy, themes, and theory germane to health services research. Principle Findings We describe an approach to qualitative data analysis that applies the principles of inductive reasoning while also employing predetermined code types to guide data analysis and interpretation. These code types (conceptual, relationship, perspective, participant characteristics, and setting codes) define a structure that is appropriate for generation of taxonomy, themes, and theory. Conceptual codes and subcodes facilitate the development of taxonomies. Relationship and perspective codes facilitate the development of themes and theory. Intersectional analyses with data coded for participant characteristics and setting codes can facilitate comparative analyses. Conclusions Qualitative inquiry can improve the description and explanation of complex, real-world phenomena pertinent to health services research. Greater understanding of the processes of qualitative data analysis can be helpful for health services researchers as they use these methods themselves or collaborate with qualitative researchers from a wide range of disciplines. PMID:17286625

Qualitative data analysis for health services research: developing taxonomy, themes, and theory.

PubMed

Bradley, Elizabeth H; Curry, Leslie A; Devers, Kelly J

2007-08-01

To provide practical strategies for conducting and evaluating analyses of qualitative data applicable for health services researchers. DATA SOURCES AND DESIGN: We draw on extant qualitative methodological literature to describe practical approaches to qualitative data analysis. Approaches to data analysis vary by discipline and analytic tradition; however, we focus on qualitative data analysis that has as a goal the generation of taxonomy, themes, and theory germane to health services research. We describe an approach to qualitative data analysis that applies the principles of inductive reasoning while also employing predetermined code types to guide data analysis and interpretation. These code types (conceptual, relationship, perspective, participant characteristics, and setting codes) define a structure that is appropriate for generation of taxonomy, themes, and theory. Conceptual codes and subcodes facilitate the development of taxonomies. Relationship and perspective codes facilitate the development of themes and theory. Intersectional analyses with data coded for participant characteristics and setting codes can facilitate comparative analyses. Qualitative inquiry can improve the description and explanation of complex, real-world phenomena pertinent to health services research. Greater understanding of the processes of qualitative data analysis can be helpful for health services researchers as they use these methods themselves or collaborate with qualitative researchers from a wide range of disciplines.

A taxonomy of dignity: a grounded theory study

PubMed Central

2009-01-01

Background This paper has its origins in Jonathan Mann's insight that the experience of dignity may explain the reciprocal relationships between health and human rights. It follows his call for a taxonomy of dignity: "a coherent vocabulary and framework to characterize dignity." Methods Grounded theory procedures were use to analyze literature pertaining to dignity and to conduct and analyze 64 semi-structured interviews with persons marginalized by their health or social status, individuals who provide health or social services to these populations, and people working in the field of health and human rights. Results The taxonomy presented identifies two main forms of dignity–human dignity and social dignity–and describes several elements of these forms, including the social processes that violate or promote them, the conditions under which such violations and promotions occur, the objects of violation and promotion, and the consequences of dignity violation. Together, these forms and elements point to a theory of dignity as a quality of individuals and collectives that is constituted through interaction and interpretation and structured by conditions pertaining to actors, relationships, settings, and the broader social order. Conclusion The taxonomy has several implications for work in health and human rights. It suggests a map to possible points of intervention and provides a language in which to talk about dignity. PMID:19239684

A taxonomy of dignity: a grounded theory study.

PubMed

Jacobson, Nora

2009-02-24

This paper has its origins in Jonathan Mann's insight that the experience of dignity may explain the reciprocal relationships between health and human rights. It follows his call for a taxonomy of dignity: "a coherent vocabulary and framework to characterize dignity." Grounded theory procedures were use to analyze literature pertaining to dignity and to conduct and analyze 64 semi-structured interviews with persons marginalized by their health or social status, individuals who provide health or social services to these populations, and people working in the field of health and human rights. The taxonomy presented identifies two main forms of dignity-human dignity and social dignity-and describes several elements of these forms, including the social processes that violate or promote them, the conditions under which such violations and promotions occur, the objects of violation and promotion, and the consequences of dignity violation. Together, these forms and elements point to a theory of dignity as a quality of individuals and collectives that is constituted through interaction and interpretation and structured by conditions pertaining to actors, relationships, settings, and the broader social order. The taxonomy has several implications for work in health and human rights. It suggests a map to possible points of intervention and provides a language in which to talk about dignity.

The ACTTION–APS–AAPM Pain Taxonomy (AAAPT) Multidimensional Approach to Classifying Acute Pain Conditions

PubMed Central

Kent, Michael L.; Tighe, Patrick J.; Belfer, Inna; Brennan, Timothy J.; Bruehl, Stephen; Brummett, Chad M.; Buckenmaier, Chester C.; Buvanendran, Asokumar; Cohen, Robert I.; Desjardins, Paul; Edwards, David; Fillingim, Roger; Gewandter, Jennifer; Gordon, Debra B.; Hurley, Robert W.; Kehlet, Henrik; Loeser, John D.; Mackey, Sean; McLean, Samuel A.; Polomano, Rosemary; Rahman, Siamak; Raja, Srinivasa; Rowbotham, Michael; Suresh, Santhanam; Schachtel, Bernard; Schreiber, Kristin; Schumacher, Mark; Stacey, Brett; Stanos, Steven; Todd, Knox; Turk, Dennis C.; Weisman, Steven J.; Wu, Christopher; Carr, Daniel B.; Dworkin, Robert H.; Terman, Gregory

2017-01-01

Objective. With the increasing societal awareness of the prevalence and impact of acute pain, there is a need to develop an acute pain classification system that both reflects contemporary mechanistic insights and helps guide future research and treatment. Existing classifications of acute pain conditions are limiting, with a predominant focus on the sensory experience (e.g., pain intensity) and pharmacologic consumption. Consequently, there is a need to more broadly characterize and classify the multidimensional experience of acute pain. Setting. Consensus report following expert panel involving the Analgesic, Anesthetic, and Addiction Clinical Trial Translations, Innovations, Opportunities, and Networks (ACTTION), American Pain Society (APS), and American Academy of Pain Medicine (AAPM). Methods. As a complement to a taxonomy recently developed for chronic pain, the ACTTION public-private partnership with the US Food and Drug Administration, the APS, and the AAPM convened a consensus meeting of experts to develop an acute pain taxonomy using prevailing evidence. Key issues pertaining to the distinct nature of acute pain are presented followed by the agreed-upon taxonomy. The ACTTION-APS-AAPM Acute Pain Taxonomy will include the following dimensions: 1) core criteria, 2) common features, 3) modulating factors, 4) impact/functional consequences, and 5) putative pathophysiologic pain mechanisms. Future efforts will consist of working groups utilizing this taxonomy to develop diagnostic criteria for a comprehensive set of acute pain conditions. Perspective. The ACTTION-APS-AAPM Acute Pain Taxonomy (AAAPT) is a multidimensional acute pain classification system designed to classify acute pain along the following dimensions: 1) core criteria, 2) common features, 3) modulating factors, 4) impact/functional consequences, and 5) putative pathophysiologic pain mechanisms. Conclusions. Significant numbers of patients still suffer from significant acute pain, despite the advent of modern multimodal analgesic strategies. Mismanaged acute pain has a broad societal impact as significant numbers of patients may progress to suffer from chronic pain. An acute pain taxonomy provides a much-needed standardization of clinical diagnostic criteria, which benefits clinical care, research, education, and public policy. For the purposes of the present taxonomy, acute pain is considered to last up to seven days, with prolongation to 30 days being common. The current understanding of acute pain mechanisms poorly differentiates between acute and chronic pain and is often insufficient to distinguish among many types of acute pain conditions. Given the usefulness of the AAPT multidimensional framework, the AAAPT undertook a similar approach to organizing various acute pain conditions. PMID:28482098

The ACTTION-APS-AAPM Pain Taxonomy (AAAPT) Multidimensional Approach to Classifying Acute Pain Conditions.

PubMed

Kent, Michael L; Tighe, Patrick J; Belfer, Inna; Brennan, Timothy J; Bruehl, Stephen; Brummett, Chad M; Buckenmaier, Chester C; Buvanendran, Asokumar; Cohen, Robert I; Desjardins, Paul; Edwards, David; Fillingim, Roger; Gewandter, Jennifer; Gordon, Debra B; Hurley, Robert W; Kehlet, Henrik; Loeser, John D; Mackey, Sean; McLean, Samuel A; Polomano, Rosemary; Rahman, Siamak; Raja, Srinivasa; Rowbotham, Michael; Suresh, Santhanam; Schachtel, Bernard; Schreiber, Kristin; Schumacher, Mark; Stacey, Brett; Stanos, Steven; Todd, Knox; Turk, Dennis C; Weisman, Steven J; Wu, Christopher; Carr, Daniel B; Dworkin, Robert H; Terman, Gregory

2017-05-01

With the increasing societal awareness of the prevalence and impact of acute pain, there is a need to develop an acute pain classification system that both reflects contemporary mechanistic insights and helps guide future research and treatment. Existing classifications of acute pain conditions are limiting, with a predominant focus on the sensory experience (eg, pain intensity) and pharmacologic consumption. Consequently, there is a need to more broadly characterize and classify the multidimensional experience of acute pain. Consensus report following expert panel involving the Analgesic, Anesthetic, and Addiction Clinical Trial Translations, Innovations, Opportunities, and Networks (ACTTION), American Pain Society (APS), and American Academy of Pain Medicine (AAPM). As a complement to a taxonomy recently developed for chronic pain, the ACTTION public-private partnership with the US Food and Drug Administration, the APS, and the AAPM convened a consensus meeting of experts to develop an acute pain taxonomy using prevailing evidence. Key issues pertaining to the distinct nature of acute pain are presented followed by the agreed-upon taxonomy. The ACTTION-APS-AAPM Acute Pain Taxonomy will include the following dimensions: 1) core criteria, 2) common features, 3) modulating factors, 4) impact/functional consequences, and 5) putative pathophysiologic pain mechanisms. Future efforts will consist of working groups utilizing this taxonomy to develop diagnostic criteria for a comprehensive set of acute pain conditions. The ACTTION-APS-AAPM Acute Pain Taxonomy (AAAPT) is a multidimensional acute pain classification system designed to classify acute pain along the following dimensions: 1) core criteria, 2) common features, 3) modulating factors, 4) impact/functional consequences, and 5) putative pathophysiologic pain mechanisms. Significant numbers of patients still suffer from significant acute pain, despite the advent of modern multimodal analgesic strategies. Mismanaged acute pain has a broad societal impact as significant numbers of patients may progress to suffer from chronic pain. An acute pain taxonomy provides a much-needed standardization of clinical diagnostic criteria, which benefits clinical care, research, education, and public policy. For the purposes of the present taxonomy, acute pain is considered to last up to seven days, with prolongation to 30 days being common. The current understanding of acute pain mechanisms poorly differentiates between acute and chronic pain and is often insufficient to distinguish among many types of acute pain conditions. Given the usefulness of the AAPT multidimensional framework, the AAAPT undertook a similar approach to organizing various acute pain conditions. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Identifying Complex Cultural Interactions in the Instructional Design Process: A Case Study of a Cross-Border, Cross-Sector Training for Innovation Program

ERIC Educational Resources Information Center

Russell, L. Roxanne; Kinuthia, Wanjira L.; Lokey-Vega, Anissa; Tsang-Kosma, Winnie; Madathany, Reeny

2013-01-01

The purpose of this research is to identify complex cultural dynamics in the instructional design process of a cross-sector, cross-border training environment by applying Young's (2009) Culture-Based Model (CBM) as a theoretical framework and taxonomy for description of the instructional design process under the conditions of one case. This…

Secondary science teachers' use of the affective domain in science education

NASA Astrophysics Data System (ADS)

Grauer, Bette L.

The purpose of this qualitative case study was to explore (a) the types of student affective responses that secondary science teachers reported emerged in science classes, (b) how those teachers worked with student affective responses, and (c) what interactions were present in the classroom when they worked with student affective responses. The study was motivated by research indicating that student interest and motivation for learning science is low. Eight secondary science teachers participated in the case study. The participants were selected from a pool of teachers who graduated from the same teacher education program at a large Midwest university. The primary sources of data were individual semi-structured interviews with the participants. Krathwohl's Taxonomy of the Affective Domain served as the research framework for the study. Student affective behavior reported by participants was classified within the five levels of Krathwohl's Affective Taxonomy: receiving, responding, valuing, organization, and characterization. Participants in the study reported student behavior representing all levels of the Affective Taxonomy. The types of behavior most frequently reported by participants were identified with the receiving and responding levels of the Affective Taxonomy. Organization behavior emerged during the study of perceived controversial science topics such as evolution. Participants in the study used student affective behavior to provide feedback on their lesson activities and instructional practices. Classroom interactions identified as collaboration and conversation contributed to the development of responding behavior. The researcher identified a process of affective progression in which teachers encouraged and developed student affective behavior changes from receiving to responding levels of the Affective Taxonomy.

Surveying hospital network structure in New York State: how are they structured?

PubMed

Nauenberg, E; Brewer, C S

2000-01-01

We determine the most common network structures in New York state. The taxonomy employed uses three structural dimensions: integration, complexity, and risk-sharing between organizations. Based on a survey conducted in 1996, the most common type of network (26.4 percent) had medium levels of integration, medium or high levels of complexity, and some risk-sharing. Also common were networks with low levels of integration, low levels of complexity, and no risk-sharing (22.1 percent).

Adult Mouse Cortical Cell Taxonomy by Single Cell Transcriptomics

PubMed Central

Tasic, Bosiljka; Menon, Vilas; Nguyen, Thuc Nghi; Kim, Tae Kyung; Jarsky, Tim; Yao, Zizhen; Levi, Boaz; Gray, Lucas T.; Sorensen, Staci A.; Dolbeare, Tim; Bertagnolli, Darren; Goldy, Jeff; Shapovalova, Nadiya; Parry, Sheana; Lee, Changkyu; Smith, Kimberly; Bernard, Amy; Madisen, Linda; Sunkin, Susan M.; Hawrylycz, Michael; Koch, Christof; Zeng, Hongkui

2016-01-01

Nervous systems are composed of various cell types, but the extent of cell type diversity is poorly understood. Here, we construct a cellular taxonomy of one cortical region, primary visual cortex, in adult mice based on single cell RNA-sequencing. We identify 49 transcriptomic cell types including 23 GABAergic, 19 glutamatergic and seven non-neuronal types. We also analyze cell-type specific mRNA processing and characterize genetic access to these transcriptomic types by many transgenic Cre lines. Finally, we show that some of our transcriptomic cell types display specific and differential electrophysiological and axon projection properties, thereby confirming that the single cell transcriptomic signatures can be associated with specific cellular properties. PMID:26727548

Personalized medicine in multiple sclerosis.

PubMed

Giovannoni, Gavin

2017-11-01

The therapeutic approach in multiple sclerosis (MS) requires a personalized medicine frame beyond the precision medicine concept, which is not currently implementable due to the lack of robust biomarkers and detailed understanding of MS pathogenesis. Personalized medicine demands a patient-focused approach, with disease taxonomy informed by characterization of pathophysiological processes. Important questions concerning MS taxonomy are: when does MS begin? When does the progressive phase begin? Is MS really two or three diseases? Does a therapeutic window truly exist? Newer evidence points to a disease spectrum and a therapeutic lag of several years for benefits to be observed from disease-modifying therapy. For personalized treatment, it is important to ascertain disease stage and any worsening of focal inflammatory lesions over time.

Hierarchical Ensemble Methods for Protein Function Prediction

PubMed Central

2014-01-01

Protein function prediction is a complex multiclass multilabel classification problem, characterized by multiple issues such as the incompleteness of the available annotations, the integration of multiple sources of high dimensional biomolecular data, the unbalance of several functional classes, and the difficulty of univocally determining negative examples. Moreover, the hierarchical relationships between functional classes that characterize both the Gene Ontology and FunCat taxonomies motivate the development of hierarchy-aware prediction methods that showed significantly better performances than hierarchical-unaware “flat” prediction methods. In this paper, we provide a comprehensive review of hierarchical methods for protein function prediction based on ensembles of learning machines. According to this general approach, a separate learning machine is trained to learn a specific functional term and then the resulting predictions are assembled in a “consensus” ensemble decision, taking into account the hierarchical relationships between classes. The main hierarchical ensemble methods proposed in the literature are discussed in the context of existing computational methods for protein function prediction, highlighting their characteristics, advantages, and limitations. Open problems of this exciting research area of computational biology are finally considered, outlining novel perspectives for future research. PMID:25937954

Collaborative Systems Testing

ERIC Educational Resources Information Center

Pocatilu, Paul; Ciurea, Cristian

2009-01-01

Collaborative systems are widely used today in various activity fields. Their complexity is high and the development involves numerous resources and costs. Testing collaborative systems has a very important role for the systems' success. In this paper we present taxonomy of collaborative systems. The collaborative systems are classified in many…

Taxonomic changes and description of two new species for the Phyllodactylus lanei complex (Gekkota: Phyllodactylidae) in Mexico.

PubMed

RamÍrez-Reyes, Tonatiuh; Flores-Villela, Oscar

2018-04-10

An integrative taxonomy approach was implemented based on analysis of genetic, phylogenetic, morphological and ecological data to identify the cryptic diversity within the Phyllodactylus lanei complex. At least six species can be identified, of which four are currently considered subspecies: Phyllodactylus lanei, Phyllodactylus rupinus, Phyllodactylus isabelae, Phyllodactylus lupitae and two corresponding to undescribed taxa, which are identified and described in this contribution. These differ from other Mexican geckos in several characters: genetic distance (DNAmt), position in molecular phylogeny (concatened data DNAmt+DNAnu), species tree, morphological characters such as snout-vent length, longitudinal scales, tubercles from head to tail, interorbital scales, scales across venter, third labial-snout scales and rows of tubercles across dorsum; there are also differences in their bioclimatic profiles (temperature and precipitation) and geographical distribution. The most recent studies on taxonomy and evolution of Mexican geckos (Phyllodactylus) show that the diversity of this group of reptiles is currently underestimated, suggesting that more research and conservation efforts are should be addressed at these lizards.

Screening and Characterization of RAPD Markers in Viscerotropic Leishmania Parasites

PubMed Central

Mkada–Driss, Imen; Talbi, Chiraz; Guerbouj, Souheila; Driss, Mehdi; Elamine, Elwaleed M.; Cupolillo, Elisa; Mukhtar, Moawia M.; Guizani, Ikram

2014-01-01

Visceral leishmaniasis (VL) is mainly due to the Leishmania donovani complex. VL is endemic in many countries worldwide including East Africa and the Mediterranean region where the epidemiology is complex. Taxonomy of these pathogens is under controversy but there is a correlation between their genetic diversity and geographical origin. With steady increase in genome knowledge, RAPD is still a useful approach to identify and characterize novel DNA markers. Our aim was to identify and characterize polymorphic DNA markers in VL Leishmania parasites in diverse geographic regions using RAPD in order to constitute a pool of PCR targets having the potential to differentiate among the VL parasites. 100 different oligonucleotide decamers having arbitrary DNA sequences were screened for reproducible amplification and a selection of 28 was used to amplify DNA from 12 L. donovani, L. archibaldi and L. infantum strains having diverse origins. A total of 155 bands were amplified of which 60.65% appeared polymorphic. 7 out of 28 primers provided monomorphic patterns. Phenetic analysis allowed clustering the parasites according to their geographical origin. Differentially amplified bands were selected, among them 22 RAPD products were successfully cloned and sequenced. Bioinformatic analysis allowed mapping of the markers and sequences and priming sites analysis. This study was complemented with Southern-blot to confirm assignment of markers to the kDNA. The bioinformatic analysis identified 16 nuclear and 3 minicircle markers. Analysis of these markers highlighted polymorphisms at RAPD priming sites with mainly 5′ end transversions, and presence of inter– and intra– taxonomic complex sequence and microsatellites variations; a bias in transitions over transversions and indels between the different sequences compared is observed, which is however less marked between L. infantum and L. donovani. The study delivers a pool of well-documented polymorphic DNA markers, to develop molecular diagnostics assays to characterize and differentiate VL causing agents. PMID:25313833

Characteristic variations in reflectance of surface soils

NASA Technical Reports Server (NTRS)

Stoner, E. R.; Baumgardner, M. F. (Principal Investigator)

1982-01-01

Surface soil samples from a wide range of naturally occurring soils were obtained for the purpose of studying the characteristic variations in soil reflectance as these variations relate to other soil properties and soil classification. A total 485 soil samples from the U.S. and Brazil representing 30 suborders of the 10 orders of 'Soil Taxonomy' was examined. The spectral bidirectional reflectance factor was measured on uniformly moist soils over the 0.52 to 2.32 micron wavelength range with a spectroradiometer adapted for indoor use. Five distinct soil spectral reflectance curve forms were identified according to curve shape, the presence or absence of absorption bands, and the predominance of soil organic matter and iron oxide composition. These curve forms were further characterized according to generically homogeneous soil properties in a manner similar to the subdivisions at the suborder level of 'Soil Taxonomy'. Results indicate that spectroradiometric measurements of soil spectral bidirectional reflectance factor can be used to characterize soil reflectance in terms that are meaningful to soil classification, genesis, and survey.

Structural Measures to Track the Evolution of SNOMED CT Hierarchies

PubMed Central

Wei, Duo; Gu, Huanying (Helen); Perl, Yehoshua; Halper, Michael; Ochs, Christopher; Elhanan, Gai; Chen, Yan

2015-01-01

The Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT) is an extensive reference terminology with an attendant amount of complexity. It has been updated continuously and revisions have been released semi-annually to meet users’ needs and to reflect the results of quality assurance (QA) activities. Two measures based on structural features are proposed to track the effects of both natural terminology growth and QA activities based on aspects of the complexity of SNOMED CT. These two measures, called the structural density measure and accumulated structural measure, are derived based on two abstraction networks, the area taxonomy and the partial-area taxonomy. The measures derive from attribute relationship distributions and various concept groupings that are associated with the abstraction networks. They are used to track the trends in the complexity of structures as SNOMED CT changes over time. The measures were calculated for consecutive releases of five SNOMED CT hierarchies, including the Specimen hierarchy. The structural density measure shows that natural growth tends to move a hierarchy’s structure toward a more complex state, whereas the accumulated structural measure shows that QA processes tend to move a hierarchy’s structure toward a less complex state. It is also observed that both the structural density and accumulated structural measures are useful tools to track the evolution of an entire SNOMED CT hierarchy and reveal internal concept migration within it. PMID:26260003

UniEuk: Time to Speak a Common Language in Protistology!

PubMed

Berney, Cédric; Ciuprina, Andreea; Bender, Sara; Brodie, Juliet; Edgcomb, Virginia; Kim, Eunsoo; Rajan, Jeena; Parfrey, Laura Wegener; Adl, Sina; Audic, Stéphane; Bass, David; Caron, David A; Cochrane, Guy; Czech, Lucas; Dunthorn, Micah; Geisen, Stefan; Glöckner, Frank Oliver; Mahé, Frédéric; Quast, Christian; Kaye, Jonathan Z; Simpson, Alastair G B; Stamatakis, Alexandros; Del Campo, Javier; Yilmaz, Pelin; de Vargas, Colomban

2017-05-01

Universal taxonomic frameworks have been critical tools to structure the fields of botany, zoology, mycology, and bacteriology as well as their large research communities. Animals, plants, and fungi have relatively solid, stable morpho-taxonomies built over the last three centuries, while bacteria have been classified for the last three decades under a coherent molecular taxonomic framework. By contrast, no such common language exists for microbial eukaryotes, even though environmental '-omics' surveys suggest that protists make up most of the organismal and genetic complexity of our planet's ecosystems! With the current deluge of eukaryotic meta-omics data, we urgently need to build up a universal eukaryotic taxonomy bridging the protist -omics age to the fragile, centuries-old body of classical knowledge that has effectively linked protist taxa to morphological, physiological, and ecological information. UniEuk is an open, inclusive, community-based and expert-driven international initiative to build a flexible, adaptive universal taxonomic framework for eukaryotes. It unites three complementary modules, EukRef, EukBank, and EukMap, which use phylogenetic markers, environmental metabarcoding surveys, and expert knowledge to inform the taxonomic framework. The UniEuk taxonomy is directly implemented in the European Nucleotide Archive at EMBL-EBI, ensuring its broad use and long-term preservation as a reference taxonomy for eukaryotes. © 2017 The Author(s) Journal of Eukaryotic Microbiology published by Wiley Periodicals, Inc. on behalf of International Society of Protistologists.

Skills for the 21st Century Supervisor: What Factory Personnel Think.

ERIC Educational Resources Information Center

Hotek, Douglas R.

2002-01-01

Discusses supervisory skills that factory personnel believe are important for leading and improving employee performance in complex manufacturing environments. Highlights include a historical perspective; manufacturing technologies; results of Pareto analysis, comparative analysis, and analysis of variance; and a Taxonomy of Supervisory Skills.…

Eight Ways to Do Inquiry

ERIC Educational Resources Information Center

Meyer, Daniel Z.; Kubarek-Sandor, Joy; Kedvesh, James; Heitzman, Cheryl; Pan, Yaozhen; Faik, Sima

2012-01-01

Creating inquiry activities is inherently difficult. Asking meaningful questions requires both background knowledge on the part of the students and complexity on the part of the phenomena. Yet numerous strategies can help teachers conduct inquiry activities. In this article, the authors share a taxonomy of teaching strategies used to create…

Generating a taxonomy of spatially cued attention for visual discrimination: Effects of judgment precision and set size on attention

PubMed Central

Hetley, Richard; Dosher, Barbara Anne; Lu, Zhong-Lin

2014-01-01

Attention precues improve the performance of perceptual tasks in many but not all circumstances. These spatial attention effects may depend upon display set size or workload, and have been variously attributed to external noise filtering, stimulus enhancement, contrast gain, or response gain, or to uncertainty or other decision effects. In this study, we document systematically different effects of spatial attention in low- and high-precision judgments, with and without external noise, and in different set sizes in order to contribute to the development of a taxonomy of spatial attention. An elaborated perceptual template model (ePTM) provides an integrated account of a complex set of effects of spatial attention with just two attention factors: a set-size dependent exclusion or filtering of external noise and a narrowing of the perceptual template to focus on the signal stimulus. These results are related to the previous literature by classifying the judgment precision and presence of external noise masks in those experiments, suggesting a taxonomy of spatially cued attention in discrimination accuracy. PMID:24939234

Generating a taxonomy of spatially cued attention for visual discrimination: effects of judgment precision and set size on attention.

PubMed

Hetley, Richard; Dosher, Barbara Anne; Lu, Zhong-Lin

2014-11-01

Attention precues improve the performance of perceptual tasks in many but not all circumstances. These spatial attention effects may depend upon display set size or workload, and have been variously attributed to external noise filtering, stimulus enhancement, contrast gain, or response gain, or to uncertainty or other decision effects. In this study, we document systematically different effects of spatial attention in low- and high-precision judgments, with and without external noise, and in different set sizes in order to contribute to the development of a taxonomy of spatial attention. An elaborated perceptual template model (ePTM) provides an integrated account of a complex set of effects of spatial attention with just two attention factors: a set-size dependent exclusion or filtering of external noise and a narrowing of the perceptual template to focus on the signal stimulus. These results are related to the previous literature by classifying the judgment precision and presence of external noise masks in those experiments, suggesting a taxonomy of spatially cued attention in discrimination accuracy.

Behaviour change techniques: the development and evaluation of a taxonomic method for reporting and describing behaviour change interventions (a suite of five studies involving consensus methods, randomised controlled trials and analysis of qualitative data).

PubMed

Michie, Susan; Wood, Caroline E; Johnston, Marie; Abraham, Charles; Francis, Jill J; Hardeman, Wendy

2015-11-01

Meeting global health challenges requires effective behaviour change interventions (BCIs). This depends on advancing the science of behaviour change which, in turn, depends on accurate intervention reporting. Current reporting often lacks detail, preventing accurate replication and implementation. Recent developments have specified intervention content into behaviour change techniques (BCTs) - the 'active ingredients', for example goal-setting, self-monitoring of behaviour. BCTs are 'the smallest components compatible with retaining the postulated active ingredients, i.e. the proposed mechanisms of change. They can be used alone or in combination with other BCTs' (Michie S, Johnston M. Theories and techniques of behaviour change: developing a cumulative science of behaviour change. Health Psychol Rev 2012;6:1-6). Domain-specific taxonomies of BCTs have been developed, for example healthy eating and physical activity, smoking cessation and alcohol consumption. We need to build on these to develop an internationally shared language for specifying and developing interventions. This technology can be used for synthesising evidence, implementing effective interventions and testing theory. It has enormous potential added value for science and global health. (1) To develop a method of specifying content of BCIs in terms of component BCTs; (2) to lay a foundation for a comprehensive methodology applicable to different types of complex interventions; (3) to develop resources to support application of the taxonomy; and (4) to achieve multidisciplinary and international acceptance for future development. Four hundred participants (systematic reviewers, researchers, practitioners, policy-makers) from 12 countries engaged in investigating, designing and/or delivering BCIs. Development of the taxonomy involved a Delphi procedure, an iterative process of revisions and consultation with 41 international experts; hierarchical structure of the list was developed using inductive 'bottom-up' and theory-driven 'top-down' open-sort procedures (n = 36); training in use of the taxonomy (1-day workshops and distance group tutorials) (n = 161) was evaluated by changes in intercoder reliability and validity (agreement with expert consensus); evaluating the taxonomy for coding interventions was assessed by reliability (intercoder; test-retest) and validity (n = 40 trained coders); and evaluating the taxonomy for writing descriptions was assessed by reliability (intercoder; test-retest) and by experimentally testing its value (n = 190). Ninety-three distinct, non-overlapping BCTs with clear labels and definitions formed Behaviour Change Technique Taxonomy version 1 (BCTTv1). BCTs clustered into 16 groupings using a 'bottom-up' open-sort procedure; there was overlap between these and groupings produced by a theory-driven, 'top-down' procedure. Both training methods improved validity (both p < 0.05), doubled the proportion of coders achieving competence and improved confidence in identifying BCTs in workshops (both p < 0.001) but did not improve intercoder reliability. Good intercoder reliability was observed for 80 of the 93 BCTs. Good within-coder agreement was observed after 1 month (p < 0.001). Validity was good for 14 of 15 BCTs in the descriptions. The usefulness of BCTTv1 to report descriptions of observed interventions had mixed results. The developed taxonomy (BCTTv1) provides a methodology for identifying content of complex BCIs and a foundation for international cross-disciplinary collaboration for developing more effective interventions to improve health. Further work is needed to examine its usefulness for reporting interventions. This project was funded by the Medical Research Council Ref: G0901474/1. Funding also came from the Peninsula Collaboration for Leadership in Applied Health Research and Care.

Transformation from manufacturing process taxonomy to repair process taxonomy: a phenetic approach

NASA Astrophysics Data System (ADS)

Raza, Umair; Ahmad, Wasim; Khan, Atif

2018-02-01

The need of taxonomy is vital for knowledge sharing. This need has been portrayed by through-life engineering services/systems. This paper addresses this issue by repair process taxonomy development. Framework for repair process taxonomy was developed followed by its implementation. The importance of repair process taxonomy has been highlighted.

Building Enterprise Transition Plans Through the Development of Collapsing Design Structure Matrices

DTIC Science & Technology

2015-09-17

processes from the earliest input to the final output to evaluate where change is needed to reduce costs, reduce waste, and improve the flow of information...from) integrating a large complex enterprise? • How should firms/enterprises evaluate systems prior to integration? What are some valid taxonomies

Linking Academic Emotions and Student Engagement: Mature-Aged Distance Students' Transition to University

ERIC Educational Resources Information Center

Kahu, Ella; Stephens, Christine; Leach, Linda; Zepke, Nick

2015-01-01

Research into both student engagement and student emotions is increasing, with widespread agreement that both are critical determinants of student success in higher education. Less researched are the complex, reciprocal relationships between these important influences. Two theoretical frameworks inform this paper: Pekrun's taxonomy of academic…

An integrative framework to reevaluate the Neotropical catfish genus Guyanancistrus (Siluriformes: Loricariidae) with particular emphasis on the Guyanancistrus brevispinis complex.

PubMed

Fisch-Muller, Sonia; Mol, Jan H A; Covain, Raphaël

2018-01-01

Characterizing and naming species becomes more and more challenging due to the increasing difficulty of accurately delineating specific bounderies. In this context, integrative taxonomy aims to delimit taxonomic units by leveraging the complementarity of multiple data sources (geography, morphology, genetics, etc.). However, while the theoretical framework of integrative taxonomy has been explicitly stated, methods for the simultaneous analysis of multiple data sets are poorly developed and in many cases different information sources are still explored successively. Multi-table methods developed in the field of community ecology provide such an intregrative framework. In particular, multiple co-inertia analysis is flexible enough to allow the integration of morphological, distributional, and genetic data in the same analysis. We have applied this powerfull approach to delimit species boundaries in a group of poorly differentiated catfishes belonging to the genus Guyanancistrus from the Guianas region of northeastern South America. Because the species G. brevispinis has been claimed to be a species complex consisting of five species, particular attention was paid to taxon. Separate analyses indicated the presence of eight distinct species of Guyanancistrus, including five new species and one new genus. However, none of the preliminary analyses revealed different lineages within G. brevispinis, and the multi-table analysis revealed three intraspecific lineages. After taxonomic clarifications and description of the new genus, species and subspecies, a reappraisal of the biogeography of Guyanancistrus members was performed. This analysis revealed three distinct dispersals from the Upper reaches of Amazonian tributaries toward coastal rivers of the Eastern Guianas Ecoregion. The central role played by the Maroni River, as gateway from the Amazon basin, was confirmed. The Maroni River was also found to be a center of speciation for Guyanancistrus (with three species and two subspecies), as well as a source of dispersal of G. brevispinis toward the other main basins of the Eastern Guianas.

An integrative framework to reevaluate the Neotropical catfish genus Guyanancistrus (Siluriformes: Loricariidae) with particular emphasis on the Guyanancistrus brevispinis complex

PubMed Central

Fisch-Muller, Sonia; Mol, Jan H. A.

2018-01-01

Characterizing and naming species becomes more and more challenging due to the increasing difficulty of accurately delineating specific bounderies. In this context, integrative taxonomy aims to delimit taxonomic units by leveraging the complementarity of multiple data sources (geography, morphology, genetics, etc.). However, while the theoretical framework of integrative taxonomy has been explicitly stated, methods for the simultaneous analysis of multiple data sets are poorly developed and in many cases different information sources are still explored successively. Multi-table methods developed in the field of community ecology provide such an intregrative framework. In particular, multiple co-inertia analysis is flexible enough to allow the integration of morphological, distributional, and genetic data in the same analysis. We have applied this powerfull approach to delimit species boundaries in a group of poorly differentiated catfishes belonging to the genus Guyanancistrus from the Guianas region of northeastern South America. Because the species G. brevispinis has been claimed to be a species complex consisting of five species, particular attention was paid to taxon. Separate analyses indicated the presence of eight distinct species of Guyanancistrus, including five new species and one new genus. However, none of the preliminary analyses revealed different lineages within G. brevispinis, and the multi-table analysis revealed three intraspecific lineages. After taxonomic clarifications and description of the new genus, species and subspecies, a reappraisal of the biogeography of Guyanancistrus members was performed. This analysis revealed three distinct dispersals from the Upper reaches of Amazonian tributaries toward coastal rivers of the Eastern Guianas Ecoregion. The central role played by the Maroni River, as gateway from the Amazon basin, was confirmed. The Maroni River was also found to be a center of speciation for Guyanancistrus (with three species and two subspecies), as well as a source of dispersal of G. brevispinis toward the other main basins of the Eastern Guianas. PMID:29298344

Quality assurance of the gene ontology using abstraction networks.

PubMed

Ochs, Christopher; Perl, Yehoshua; Halper, Michael; Geller, James; Lomax, Jane

2016-06-01

The gene ontology (GO) is used extensively in the field of genomics. Like other large and complex ontologies, quality assurance (QA) efforts for GO's content can be laborious and time consuming. Abstraction networks (AbNs) are summarization networks that reveal and highlight high-level structural and hierarchical aggregation patterns in an ontology. They have been shown to successfully support QA work in the context of various ontologies. Two kinds of AbNs, called the area taxonomy and the partial-area taxonomy, are developed for GO hierarchies and derived specifically for the biological process (BP) hierarchy. Within this framework, several QA heuristics, based on the identification of groups of anomalous terms which exhibit certain taxonomy-defined characteristics, are introduced. Such groups are expected to have higher error rates when compared to other terms. Thus, by focusing QA efforts on anomalous terms one would expect to find relatively more erroneous content. By automatically identifying these potential problem areas within an ontology, time and effort will be saved during manual reviews of GO's content. BP is used as a testbed, with samples of three kinds of anomalous BP terms chosen for a taxonomy-based QA review. Additional heuristics for QA are demonstrated. From the results of this QA effort, it is observed that different kinds of inconsistencies in the modeling of GO can be exposed with the use of the proposed heuristics. For comparison, the results of QA work on a sample of terms chosen from GO's general population are presented.

The ACTTION-APS-AAPM Pain Taxonomy (AAAPT) Multidimensional Approach to Classifying Acute Pain Conditions.

PubMed

Kent, Michael L; Tighe, Patrick J; Belfer, Inna; Brennan, Timothy J; Bruehl, Stephen; Brummett, Chad M; Buckenmaier, Chester C; Buvanendran, Asokumar; Cohen, Robert I; Desjardins, Paul; Edwards, David; Fillingim, Roger; Gewandter, Jennifer; Gordon, Debra B; Hurley, Robert W; Kehlet, Henrik; Loeser, John D; Mackey, Sean; McLean, Samuel A; Polomano, Rosemary; Rahman, Siamak; Raja, Srinivasa; Rowbotham, Michael; Suresh, Santhanam; Schachtel, Bernard; Schreiber, Kristin; Schumacher, Mark; Stacey, Brett; Stanos, Steven; Todd, Knox; Turk, Dennis C; Weisman, Steven J; Wu, Christopher; Carr, Daniel B; Dworkin, Robert H; Terman, Gregory

2017-05-01

With the increasing societal awareness of the prevalence and impact of acute pain, there is a need to develop an acute pain classification system that both reflects contemporary mechanistic insights and helps guide future research and treatment. Existing classifications of acute pain conditions are limiting, with a predominant focus on the sensory experience (e.g., pain intensity) and pharmacologic consumption. Consequently, there is a need to more broadly characterize and classify the multidimensional experience of acute pain. Consensus report following expert panel involving the Analgesic, Anesthetic, and Addiction Clinical Trial Translations, Innovations, Opportunities, and Networks (ACTTION), American Pain Society (APS), and American Academy of Pain Medicine (AAPM). As a complement to a taxonomy recently developed for chronic pain, the ACTTION public-private partnership with the US Food and Drug Administration, the APS, and the AAPM convened a consensus meeting of experts to develop an acute pain taxonomy using prevailing evidence. Key issues pertaining to the distinct nature of acute pain are presented followed by the agreed-upon taxonomy. The ACTTION-APS-AAPM Acute Pain Taxonomy will include the following dimensions: 1) core criteria, 2) common features, 3) modulating factors, 4) impact/functional consequences, and 5) putative pathophysiologic pain mechanisms. Future efforts will consist of working groups utilizing this taxonomy to develop diagnostic criteria for a comprehensive set of acute pain conditions. The ACTTION-APS-AAPM Acute Pain Taxonomy (AAAPT) is a multidimensional acute pain classification system designed to classify acute pain along the following dimensions: 1) core criteria, 2) common features, 3) modulating factors, 4) impact/functional consequences, and 5) putative pathophysiologic pain mechanisms. Significant numbers of patients still suffer from significant acute pain, despite the advent of modern multimodal analgesic strategies. Mismanaged acute pain has a broad societal impact as significant numbers of patients may progress to suffer from chronic pain. An acute pain taxonomy provides a much-needed standardization of clinical diagnostic criteria, which benefits clinical care, research, education, and public policy. For the purposes of the present taxonomy, acute pain is considered to last up to seven days, with prolongation to 30 days being common. The current understanding of acute pain mechanisms poorly differentiates between acute and chronic pain and is often insufficient to distinguish among many types of acute pain conditions. Given the usefulness of the AAPT multidimensional framework, the AAAPT undertook a similar approach to organizing various acute pain conditions. © 2017 American Academy of Pain Medicine. This article has been co-published in Pain Medicine and The Journal of Pain. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs licence (http://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial reproduction and distribution of the work, in any medium, provided the original work is not altered or transformed in any way, and that the work is properly cited. For commercial re-use, please contact journals.permissions@oup.com.

The Role of Integrative Taxonomy in the Conservation Management of Cryptic Species: The Taxonomic Status of Endangered Earless Dragons (Agamidae: Tympanocryptis) in the Grasslands of Queensland, Australia

PubMed Central

Melville, Jane; Smith, Katie; Hobson, Rod; Hunjan, Sumitha; Shoo, Luke

2014-01-01

Molecular phylogenetics is increasingly highlighting the prevalence of cryptic species, where morphologically similar organisms have long independent evolutionary histories. When such cryptic species are known to be declining in numbers and are at risk of extinction due to a range of threatening processes, the disjunction between molecular systematics research and conservation policy becomes a significant problem. We investigate the taxonomic status of Tympanocryptis populations in Queensland, which have previously been assigned to T. tetraporophora, using three species delimitation approaches. The taxonomic uncertainties in this species-group are of particular importance in the Darling Downs Earless Dragon (T. cf. tetraporophora), which is ranked as an endangered ‘species’ of high priority for conservation by the Queensland Department of Environment and Heritage Protection. We undertook a morphological study, integrated with a comprehensive genetic study and species delimitation analyses, to investigate the species status of populations in the region. Phylogenetic analyses of two gene regions (mtDNA: ND2; nuclear: RAG1) revealed high levels of genetic divergence between populations, indicating isolation over long evolutionary time frames, and strongly supporting two independent evolutionary lineages in southeastern Queensland, from the Darling Downs, and a third in the Gulf Region of northern Queensland. Of the three species delimitation protocols used, we found integrative taxonomy the most applicable to this cryptic species complex. Our study demonstrates the utility of integrative taxonomy as a species delimitation approach in cryptic complexes of species with conservation significance, where limited numbers of specimens are available. PMID:25076129

The role of integrative taxonomy in the conservation management of cryptic species: the taxonomic status of endangered earless dragons (Agamidae: Tympanocryptis) in the grasslands of Queensland, Australia.

PubMed

Melville, Jane; Smith, Katie; Hobson, Rod; Hunjan, Sumitha; Shoo, Luke

2014-01-01

Molecular phylogenetics is increasingly highlighting the prevalence of cryptic species, where morphologically similar organisms have long independent evolutionary histories. When such cryptic species are known to be declining in numbers and are at risk of extinction due to a range of threatening processes, the disjunction between molecular systematics research and conservation policy becomes a significant problem. We investigate the taxonomic status of Tympanocryptis populations in Queensland, which have previously been assigned to T. tetraporophora, using three species delimitation approaches. The taxonomic uncertainties in this species-group are of particular importance in the Darling Downs Earless Dragon (T. cf. tetraporophora), which is ranked as an endangered 'species' of high priority for conservation by the Queensland Department of Environment and Heritage Protection. We undertook a morphological study, integrated with a comprehensive genetic study and species delimitation analyses, to investigate the species status of populations in the region. Phylogenetic analyses of two gene regions (mtDNA: ND2; nuclear: RAG1) revealed high levels of genetic divergence between populations, indicating isolation over long evolutionary time frames, and strongly supporting two independent evolutionary lineages in southeastern Queensland, from the Darling Downs, and a third in the Gulf Region of northern Queensland. Of the three species delimitation protocols used, we found integrative taxonomy the most applicable to this cryptic species complex. Our study demonstrates the utility of integrative taxonomy as a species delimitation approach in cryptic complexes of species with conservation significance, where limited numbers of specimens are available.

Genetic structuring, dispersal and taxonomy of the high-alpine populations of the Geranium arabicum/kilimandscharicum complex in tropical eastern Africa

PubMed Central

Gizaw, Abel; Tusiime, Felly M.; Masao, Catherine A.; Abdi, Ahmed A.; Hou, Yan; Nemomissa, Sileshi; Brochmann, Christian

2017-01-01

The scattered eastern African high mountains harbor a renowned and highly endemic flora, but the taxonomy and phylogeographic history of many plant groups are still insufficiently known. The high-alpine populations of the Geranium arabicum/kilimandscharicum complex present intricate morphological variation and have recently been suggested to comprise two new endemic taxa. Here we aim to contribute to a clarification of the taxonomy of these populations by analyzing genetic (AFLP) variation in range-wide high-alpine samples, and we address whether hybridization has contributed to taxonomic problems. We identified only two genetic groups. One corresponded to G. kilimandscharicum, which has been reported as exclusively high-alpine and confined to the eastern Rift mountains in East Africa. The other corresponded to G. arabicum, reported from lower altitudes on the same mountains as well as from a wide altitudinal span in Ethiopia and on the western Rift mountains in East Africa. The four populations analyzed of a recently described species from the Bale Mts in Ethiopia were admixed, indicating that they result from recent long-distance dispersal of G. kilimandscharicum from East Africa followed by hybridization with local G. arabicum in naturally disturbed habitats. Some admixture between the two genetic groups was also inferred on other mountains, supporting earlier suggestions of introgression based on morphology. We did not find support for recognition of the recently suggested new subspecies of G. arabicum in Ethiopia. Interestingly, the high-alpine G. kilimandscharicum lacked clear geographic structuring, suggesting a recent history of colonization of the different mountains or extensive intermountain gene flow. PMID:28552970

"Assessment Drives Learning": Do Assessments Promote High-Level Cognitive Processing?

ERIC Educational Resources Information Center

Bezuidenhout, M. J.; Alt, H.

2011-01-01

Students tend to learn in the way they know, or think, they will be assessed. Therefore, to ensure deep, meaningful learning, assessments must be geared to promote cognitive processing that requires complex, contextualised thinking to construct meaning and create knowledge. Bloom's taxonomy of cognitive levels is used worldwide to assist in…

Elemental Learning as a Framework for E-Learning

ERIC Educational Resources Information Center

Dempsey, John V.; Litchfield, Brenda C.

2013-01-01

Analysis of learning outcomes can be a complex and esoteric instructional design process that is often ignored by educators and e-learning designers. This paper describes a model of analysis that fosters the real-life application of learning outcomes and explains why the model may be needed. The Elemental Learning taxonomy is a hierarchical model…

The Precalculus Concept Assessment: A Tool for Assessing Students' Reasoning Abilities and Understandings

ERIC Educational Resources Information Center

Carlson, Marilyn; Oehrtman, Michael; Engelke, Nicole

2010-01-01

This article describes the development of the Precalculus Concept Assessment (PCA) instrument, a 25-item multiple-choice exam. The reasoning abilities and understandings central to precalculus and foundational for beginning calculus were identified and characterized in a series of research studies and are articulated in the PCA Taxonomy. These…

History of east European chernozem soil degradation: Protection and restoration by tree windbreaks in the Russian steppe

USDA-ARS?s Scientific Manuscript database

The physiographic region of the Central Russian Upland, situated in the Central part of Eastern Europe, is characterized by the most fertile grassland soils – Chernozems (Mollisols in the USDA taxonomy). However, over the last several centuries this region has experienced intense land-use conversion...

Hard Incongruence Between ITS and Plastid Phylogenetic Trees in Amaryllidaceae Tribe Hippeastreae (Asparagales)

USDA-ARS?s Scientific Manuscript database

Amaryllidaceae tribe Hippeastreae constitutes a horticulturally valuable group of American endemics, characterized by disploidy and polyploidy (x = 5, 6, 8, 9, 10, 11, 12; 2n = 10-150). It is a clade putatively descended (in part) from an ancient hybridization event. Its taxonomy at the generic leve...

The Taxonomy of Intervention Intensity

ERIC Educational Resources Information Center

Fuchs, Lynn S.; Fuchs, Douglas; Malone, Amelia S.

2016-01-01

The purpose of this article is to describe the Taxonomy of Intervention Intensity, which articulates 7 dimensions for evaluating and building intervention intensity. We explain the Taxonomy's dimensions of intensity. In explaining the Taxonomy, we rely on a case study to illustrate how the Taxonomy can systematize the process by which special…

Integrative taxonomy of Anisakidae and Raphidascarididae (Nematoda) in Paralichthys patagonicus and Xystreurys rasile (Pisces: Teleostei) from Brazil.

PubMed

Fonseca, Michelle Cristie Gonçalves da; Knoff, Marcelo; Felizardo, Nilza Nunes; Di Azevedo, Maria Isabel N; Torres, Eduardo José Lopes; Gomes, Delir Corrêa; Iñiguez, Alena Mayo; São Clemente, Sérgio Carmona de

2016-10-17

Thirty-six Paralichthys patagonicus and 30 Xystreurys rasile were collected in the state of Rio de Janeiro, Brazil to investigate the presence of anisakid and raphidascaridid nematodes. Anisakis typica, Terranova sp., Contracaecum sp., Hysterothylacium deardorffoverstreetorum, and Raphidascaris sp. were identified using integrative taxonomy of morphological and genetic data. Morphological and morphometric analysis was conducted using bright field microscopy with scanning electron microscopy for topographic characterization of the cuticular surface. Phylogenetic analysis, using ITS and cox2 molecular targets, clearly demonstrated the species identification of A. typica and H. deardorffoverstreetorum and the high diversity of H. deardorffoverstreetorum. This is the first report of A. typica, H. deardorffoverstreetorum, and Raphidascaris sp. parasitizing P. patagonicus and X. rasile. Copyright © 2016 Elsevier B.V. All rights reserved.

New records of lampriform fishes (Teleostei: Lampriformes) from the Pacific coast of lower Central America, with comments on the diversity, taxonomy and distribution of the Lampriformes in the eastern Pacific Ocean.

PubMed

Angulo, Arturo; López-Sánchez, Myrna I

2017-02-23

New records of occurrence for four species of lampriform fishes (Teleostei: Lampriformes; Desmodema polystictum, Regalecus russelii, Trachipterus fukuzakii and Zu cristatus) poorly known or previously unknown for the Pacific coast of lower Central America (Costa Rica-Panama) are herein reported. Museum specimens supporting such records are characterized and described. Comparative morphometric and meristic data on other collections and species of lampriforms, as well as distributional information, are provided and discussed. Diversity, taxonomy and distribution of the eastern Pacific species of the order also are briefly discussed. Finally, a key to the eastern Pacific species of the Lampriformes, based on our research and data available in the literature, is presented.

Characterization of attacks on public telephone networks

NASA Astrophysics Data System (ADS)

Lorenz, Gary V.; Manes, Gavin W.; Hale, John C.; Marks, Donald; Davis, Kenneth; Shenoi, Sujeet

2001-02-01

The U.S. Public Telephone Network (PTN) is a massively connected distributed information systems, much like the Internet. PTN signaling, transmission and operations functions must be protected from physical and cyber attacks to ensure the reliable delivery of telecommunications services. The increasing convergence of PTNs with wireless communications systems, computer networks and the Internet itself poses serious threats to our nation's telecommunications infrastructure. Legacy technologies and advanced services encumber well-known and as of yet undiscovered vulnerabilities that render them susceptible to cyber attacks. This paper presents a taxonomy of cyber attacks on PTNs in converged environments that synthesizes exploits in computer and communications network domains. The taxonomy provides an opportunity for the systematic exploration of mitigative and preventive strategies, as well as for the identification and classification of emerging threats.

Lighten the Load: Scaffolding Visual Literacy in Biochemistry and Molecular Biology.

PubMed

Offerdahl, Erika G; Arneson, Jessie B; Byrne, Nicholas

2017-01-01

The development of scientific visual literacy has been identified as critical to the training of tomorrow's scientists and citizens alike. Within the context of the molecular life sciences in particular, visual representations frequently incorporate various components, such as discipline-specific graphical and diagrammatic features, varied levels of abstraction, and spatial arrangements of visual elements to convey information. Visual literacy is achieved when an individual understands the various ways in which a discipline uses these components to represent a particular way of knowing. Owing to the complex nature of visual representations, the activities through which visual literacy is developed have high cognitive load. Cognitive load can be reduced by first helping students to become fluent with the discrete components of visual representations before asking them to simultaneously integrate these components to extract the intended meaning of a representation. We present a taxonomy for characterizing one component of visual representations-the level of abstraction-as a first step in understanding the opportunities afforded students to develop fluency. Further, we demonstrate how our taxonomy can be used to analyze course assessments and spur discussions regarding the extent to which the development of visual literacy skills is supported by instruction within an undergraduate biochemistry curriculum. © 2017 E. G. Offerdahl et al. CBE—Life Sciences Education © 2017 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Integrative taxonomy reveals cryptic diversity in neotropical grasshoppers: taxonomy, phylogenetics, and evolution of the genus Sphenarium Charpentier, 1842 (Orthoptera: Pyrgomorphidae).

PubMed

Sanabria-Urbán, Salomón; Song, Hojun; Oyama, Ken; González-Rodríguez, Antonio; Castillo, Raúl Cueva Del

2017-06-08

The genus Sphenarium Charpentier, 1842 comprises the most diverse group of the New World Pyrgomorphidae. These grasshoppers show an extensive variation in external morphology, and are culturally and economically important for Mexican people since pre-Hispanic times. Nevertheless, the taxonomy of Sphenarium has been chaotic and remained incompletely resolved until now. Following an integrative taxonomic framework, we infer the number of species in this genus by species delimitation based on morphological, phylogenetic, and geographic information. Based on our results, we revise the genus and redefine 9 species and describe 8 new species (S. adelinae sp.n., S. crypticum sp.n., S. infernalis sp.n., S. miztecum sp.n., S. occidentalis sp.n., S. tarascum sp.n., S. totonacum sp.n. and S. zapotecum sp.n.). Moreover, we update the knowledge of the evolutionary relationships and biogeographic patterns of Sphenarium species. Our results also demonstrate the importance of historic geological and climatic events on the lineage diversification of this genus. Different levels of morphological and genetic differentiation among species suggest a complex interplay between evolutionary forces during the evolution of these neotropical grasshoppers.

Constructing Taxonomies to Identify Distinctive Forms of Primary Healthcare Organizations

PubMed Central

Borgès Da Silva, Roxane; Pineault, Raynald; Hamel, Marjolaine; Levesque, Jean-Frédéric; Roberge, Danièle; Lamarche, Paul

2013-01-01

Background. Primary healthcare (PHC) renewal gives rise to important challenges for policy makers, managers, and researchers in most countries. Evaluating new emerging forms of organizations is therefore of prime importance in assessing the impact of these policies. This paper presents a set of methods related to the configurational approach and an organizational taxonomy derived from our analysis. Methods. In 2005, we carried out a study on PHC in two health and social services regions of Quebec that included urban, suburban, and rural areas. An organizational survey was conducted in 473 PHC practices. We used multidimensional nonparametric statistical methods, namely, multiple correspondence and principal component analyses, and an ascending hierarchical classification method to construct a taxonomy of organizations. Results. PHC organizations were classified into five distinct models: four professional and one community. Study findings indicate that the professional integrated coordination and the community model have great potential for organizational development since they are closest to the ideal type promoted by current reforms. Conclusion. Results showed that the configurational approach is useful to assess complex phenomena such as the organization of PHC. The analysis highlights the most promising organizational models. Our study enhances our understanding of organizational change in health services organizations. PMID:24959575

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hameed, Abdul; Khoshkbarforoushha, Alireza; Ranjan, Rajiv

In a cloud computing paradigm, energy efficient allocation of different virtualized ICT resources (servers, storage disks, and networks, and the like) is a complex problem due to the presence of heterogeneous application (e.g., content delivery networks, MapReduce, web applications, and the like) workloads having contentious allocation requirements in terms of ICT resource capacities (e.g., network bandwidth, processing speed, response time, etc.). Several recent papers have tried to address the issue of improving energy efficiency in allocating cloud resources to applications with varying degree of success. However, to the best of our knowledge there is no published literature on this subjectmore » that clearly articulates the research problem and provides research taxonomy for succinct classification of existing techniques. Hence, the main aim of this paper is to identify open challenges associated with energy efficient resource allocation. In this regard, the study, first, outlines the problem and existing hardware and software-based techniques available for this purpose. Furthermore, available techniques already presented in the literature are summarized based on the energy-efficient research dimension taxonomy. The advantages and disadvantages of the existing techniques are comprehensively analyzed against the proposed research dimension taxonomy namely: resource adaption policy, objective function, allocation method, allocation operation, and interoperability.« less

Professional diversity and the productivity of cities.

PubMed

Bettencourt, Luís M A; Samaniego, Horacio; Youn, Hyejin

2014-06-23

Attempts to understand the relationship between diversity, productivity and scale have remained limited due to the scheme-dependent nature of the taxonomies describing complex systems. We analyze the diversity of US metropolitan areas in terms of profession diversity and employment to show how this frequency distribution takes a universal scale-invariant form, common to all cities, in the limit of infinite resolution of occupational taxonomies. We show that this limit is obtained under general conditions that follow from the analysis of the variation of the occupational frequency across taxonomies at different resolutions in a way analogous to finite-size scaling in statistical physical systems. We propose a theoretical framework that derives the form and parameters of the limiting distribution of professions based on the appearance, in urban social networks, of new occupations as the result of specialization and coordination of labor. By deriving classification scheme-independent measures of functional diversity and modeling cities as social networks embedded in infrastructural space, these results show how standard economic arguments of division and coordination of labor can be articulated in detail in cities and provide a microscopic basis for explaining increasing returns to population scale observed at the level of entire metropolitan areas.

Creating a Taxonomy of Local Boards of Health Based on Local Health Departments’ Perspectives

PubMed Central

Shah, Gulzar H.; Sotnikov, Sergey; Leep, Carolyn J.; Ye, Jiali; Van Wave, Timothy W.

2017-01-01

Objectives To develop a local board of health (LBoH) classification scheme and empirical definitions to provide a coherent framework for describing variation in the LBoHs. Methods This study is based on data from the 2015 Local Board of Health Survey, conducted among a nationally representative sample of local health department administrators, with 394 responses. The classification development consisted of the following steps: (1) theoretically guided initial domain development, (2) mapping of the survey variables to the proposed domains, (3) data reduction using principal component analysis and group consensus, and (4) scale development and testing for internal consistency. Results The final classification scheme included 60 items across 6 governance function domains and an additional domain—LBoH characteristics and strengths, such as meeting frequency, composition, and diversity of information sources. Application of this classification strongly supports the premise that LBoHs differ in their performance of governance functions and in other characteristics. Conclusions The LBoH taxonomy provides an empirically tested standardized tool for classifying LBoHs from the viewpoint of local health department administrators. Future studies can use this taxonomy to better characterize the impact of LBoHs. PMID:27854524

A taxonomy of accountable care organizations for policy and practice.

PubMed

Shortell, Stephen M; Wu, Frances M; Lewis, Valerie A; Colla, Carrie H; Fisher, Elliott S

2014-12-01

To develop an exploratory taxonomy of Accountable Care Organizations (ACOs) to describe and understand early ACO development and to provide a basis for technical assistance and future evaluation of performance. Data from the National Survey of Accountable Care Organizations, fielded between October 2012 and May 2013, of 173 Medicare, Medicaid, and commercial payer ACOs. Drawing on resource dependence and institutional theory, we develop measures of eight attributes of ACOs such as size, scope of services offered, and the use of performance accountability mechanisms. Data are analyzed using a two-step cluster analysis approach that accounts for both continuous and categorical data. We identified a reliable and internally valid three-cluster solution: larger, integrated systems that offer a broad scope of services and frequently include one or more postacute facilities; smaller, physician-led practices, centered in primary care, and that possess a relatively high degree of physician performance management; and moderately sized, joint hospital-physician and coalition-led groups that offer a moderately broad scope of services with some involvement of postacute facilities. ACOs can be characterized into three distinct clusters. The taxonomy provides a framework for assessing performance, for targeting technical assistance, and for diagnosing potential antitrust violations. © Health Research and Educational Trust.

Complete sequence and comparative analysis of the chloroplast genome of Plinia trunciflora

PubMed Central

Eguiluz, Maria; Yuyama, Priscila Mary; Guzman, Frank; Rodrigues, Nureyev Ferreira; Margis, Rogerio

2017-01-01

Abstract Plinia trunciflora is a Brazilian native fruit tree from the Myrtaceae family, also known as jaboticaba. This species has great potential by its fruit production. Due to the high content of essential oils in their leaves and of anthocyanins in the fruits, there is also an increasing interest by the pharmaceutical industry. Nevertheless, there are few studies focusing on its molecular biology and genetic characterization. We herein report the complete chloroplast (cp) genome of P. trunciflora using high-throughput sequencing and compare it to other previously sequenced Myrtaceae genomes. The cp genome of P. trunciflora is 159,512 bp in size, comprising inverted repeats of 26,414 bp and single-copy regions of 88,097 bp (LSC) and 18,587 bp (SSC). The genome contains 111 single-copy genes (77 protein-coding, 30 tRNA and four rRNA genes). Phylogenetic analysis using 57 cp protein-coding genes demonstrated that P. trunciflora, Eugenia uniflora and Acca sellowiana form a cluster with closer relationship to Syzygium cumini than with Eucalyptus. The complete cp sequence reported here can be used in evolutionary and population genetics studies, contributing to resolve the complex taxonomy of this species and fill the gap in genetic characterization. PMID:29111566

Phylogenetic species identification in Rattus highlights rapid radiation and morphological similarity of New Guinean species.

PubMed

Robins, Judith H; Tintinger, Vernon; Aplin, Ken P; Hingston, Melanie; Matisoo-Smith, Elizabeth; Penny, David; Lavery, Shane D

2014-01-01

The genus Rattus is highly speciose, the taxonomy is complex, and individuals are often difficult to identify to the species level. Previous studies have demonstrated the usefulness of phylogenetic approaches to identification in Rattus but some species, especially among the endemics of the New Guinean region, showed poor resolution. Possible reasons for this are simple misidentification, incomplete gene lineage sorting, hybridization, and phylogenetically distinct lineages that are unrecognised taxonomically. To assess these explanations we analysed 217 samples, representing nominally 25 Rattus species, collected in New Guinea, Asia, Australia and the Pacific. To reduce misidentification problems we sequenced museum specimens from earlier morphological studies and recently collected tissues from samples with associated voucher specimens. We also reassessed vouchers from previously sequenced specimens. We inferred combined and separate phylogenies from two mitochondrial DNA regions comprising 550 base pair D-loop sequences and both long (655 base pair) and short (150 base pair) cytochrome oxidase I sequences. Our phylogenetic species identification for 17 species was consistent with morphological designations and current taxonomy thus reinforcing the usefulness of this approach. We reduced misidentifications and consequently the number of polyphyletic species in our phylogenies but the New Guinean Rattus clades still exhibited considerable complexity. Only three of our eight New Guinean species were monophyletic. We found good evidence for either incomplete mitochondrial lineage sorting or hybridization between species within two pairs, R. leucopus/R. cf. verecundus and R. steini/R. praetor. Additionally, our results showed that R. praetor, R. niobe and R. verecundus each likely encompass more than one species. Our study clearly points to the need for a revised taxonomy of the rats of New Guinea, based on broader sampling and informed by both morphology and phylogenetics. The remaining taxonomic complexity highlights the recent and rapid radiation of Rattus in the Australo-Papuan region.

Phylogenetic Species Identification in Rattus Highlights Rapid Radiation and Morphological Similarity of New Guinean Species

PubMed Central

Robins, Judith H.; Tintinger, Vernon; Aplin, Ken P.; Hingston, Melanie; Matisoo-Smith, Elizabeth; Penny, David; Lavery, Shane D.

2014-01-01

The genus Rattus is highly speciose, the taxonomy is complex, and individuals are often difficult to identify to the species level. Previous studies have demonstrated the usefulness of phylogenetic approaches to identification in Rattus but some species, especially among the endemics of the New Guinean region, showed poor resolution. Possible reasons for this are simple misidentification, incomplete gene lineage sorting, hybridization, and phylogenetically distinct lineages that are unrecognised taxonomically. To assess these explanations we analysed 217 samples, representing nominally 25 Rattus species, collected in New Guinea, Asia, Australia and the Pacific. To reduce misidentification problems we sequenced museum specimens from earlier morphological studies and recently collected tissues from samples with associated voucher specimens. We also reassessed vouchers from previously sequenced specimens. We inferred combined and separate phylogenies from two mitochondrial DNA regions comprising 550 base pair D-loop sequences and both long (655 base pair) and short (150 base pair) cytochrome oxidase I sequences. Our phylogenetic species identification for 17 species was consistent with morphological designations and current taxonomy thus reinforcing the usefulness of this approach. We reduced misidentifications and consequently the number of polyphyletic species in our phylogenies but the New Guinean Rattus clades still exhibited considerable complexity. Only three of our eight New Guinean species were monophyletic. We found good evidence for either incomplete mitochondrial lineage sorting or hybridization between species within two pairs, R. leucopus/R. cf. verecundus and R. steini/R. praetor. Additionally, our results showed that R. praetor, R. niobe and R. verecundus each likely encompass more than one species. Our study clearly points to the need for a revised taxonomy of the rats of New Guinea, based on broader sampling and informed by both morphology and phylogenetics. The remaining taxonomic complexity highlights the recent and rapid radiation of Rattus in the Australo-Papuan region. PMID:24865350

Janthinocins A, B and C, novel peptide lactone antibiotics produced by Janthinobacterium lividum. I. Taxonomy, fermentation, isolation, physico-chemical and biological characterization.

PubMed

O'Sullivan, J; McCullough, J; Johnson, J H; Bonner, D P; Clark, J C; Dean, L; Trejo, W H

1990-08-01

Janthinocins A, B and C are novel antibacterial agents produced by Janthinobacterium lividum. They were isolated from fermentation broths and characterized by UV, IR, NMR and mass spectroscopy. They are cyclic decapeptide lactones with marked activity against aerobic and anaerobic Gram-positive bacteria and are 2 to 4 times more potent in vitro than vancomycin. Janthinocins A and B were also found to be effective in a Staphylococcus aureus systemic infection in mice.

Designing a New Taxonomy of Educational Objectives. Experts in Assessment.

ERIC Educational Resources Information Center

Marzano, Robert J.

This volume is an attempt to articulate a taxonomy of educational objectives that uses the best available research and theory accumulated since the publication of the taxonomy of educational objectives of B. Bloom and others in 1956. Like Bloom's taxonomy, this taxonomy defines six levels of mental processing: self-system thinking (Level 6);…

Does the name really matter? The importance of botanical nomenclature and plant taxonomy in biomedical research.

PubMed

Bennett, Bradley C; Balick, Michael J

2014-03-28

Medical research on plant-derived compounds requires a breadth of expertise from field to laboratory and clinical skills. Too often basic botanical skills are evidently lacking, especially with respect to plant taxonomy and botanical nomenclature. Binomial and familial names, synonyms and author citations are often misconstrued. The correct botanical name, linked to a vouchered specimen, is the sine qua non of phytomedical research. Without the unique identifier of a proper binomial, research cannot accurately be linked to the existing literature. Perhaps more significant, is the ambiguity of species determinations that ensues of from poor taxonomic practices. This uncertainty, not surprisingly, obstructs reproducibility of results-the cornerstone of science. Based on our combined six decades of experience with medicinal plants, we discuss the problems of inaccurate taxonomy and botanical nomenclature in biomedical research. This problems appear all too frequently in manuscripts and grant applications that we review and they extend to the published literature. We also review the literature on the importance of taxonomy in other disciplines that relate to medicinal plant research. In most cases, questions regarding orthography, synonymy, author citations, and current family designations of most plant binomials can be resolved using widely-available online databases and other electronic resources. Some complex problems require consultation with a professional plant taxonomist, which also is important for accurate identification of voucher specimens. Researchers should provide the currently accepted binomial and complete author citation, provide relevant synonyms, and employ the Angiosperm Phylogeny Group III family name. Taxonomy is a vital adjunct not only to plant-medicine research but to virtually every field of science. Medicinal plant researchers can increase the precision and utility of their investigations by following sound practices with respect to botanical nomenclature. Correct spellings, accepted binomials, author citations, synonyms, and current family designations can readily be found on reliable online databases. When questions arise, researcher should consult plant taxonomists. © 2013 Published by Elsevier Ireland Ltd.

Taxonomy for Common-Cause Failure Vulnerability and Mitigation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wood, Richard Thomas; Korsah, Kofi; Mullens, James Allen

2015-09-01

Applying current guidance and practices for common-cause failure (CCF) mitigation to digital instrumentation and control (I&C) systems has proven problematic, and the regulatory environment has been unpredictable. The potential for CCF vulnerability inhibits I&C modernization, thereby challenging the long-term sustainability of existing plants. For new plants and advanced reactor concepts, concern about CCF vulnerability in highly integrated digital I&C systems imposes a design burden that results in higher costs and increased complexity. The regulatory uncertainty in determining which mitigation strategies will be acceptable (e.g., what diversity is needed and how much is sufficient) drives designers to adopt complicated, costly solutionsmore » devised for existing plants. To address the conditions that constrain the transition to digital I&C technology by the US nuclear industry, crosscutting research is needed to resolve uncertainty, demonstrate necessary characteristics, and establish an objective basis for qualification of digital technology for nuclear power plant (NPP) I&C applications. To fulfill this research need, Oak Ridge National Laboratory is investigating mitigation of CCF vulnerability for nuclear-qualified applications. The outcome of this research is expected to contribute to a fundamentally sound, comprehensive basis to qualify digital technology for nuclear power applications. This report documents the development of a CCF taxonomy. The basis for the CCF taxonomy was generated by determining consistent terminology and establishing a classification approach. The terminology is based on definitions from standards, guides, and relevant nuclear power industry technical reports. The classification approach is derived from identified classification schemes focused on I&C systems and key characteristics, including failure modes. The CCF taxonomy provides the basis for a systematic organization of key systems aspects relevant to analyzing the potential for CCF vulnerability and the suitability of mitigation techniques. Development of an effective CCF taxonomy will help to provide a framework for establishing the objective analysis and assessment capabilities desired to facilitate rigorous identification of fault types and triggers that are the fundamental elements of CCF.« less

Development and Validation of a Taxonomy for Characterizing Measurements in Health Self-Quantification.

PubMed

Almalki, Manal; Gray, Kathleen; Martin-Sanchez, Fernando

2017-11-03

The use of wearable tools for health self-quantification (SQ) introduces new ways of thinking about one's body and about how to achieve desired health outcomes. Measurements from individuals, such as heart rate, respiratory volume, skin temperature, sleep, mood, blood pressure, food consumed, and quality of surrounding air can be acquired, quantified, and aggregated in a holistic way that has never been possible before. However, health SQ still lacks a formal common language or taxonomy for describing these kinds of measurements. Establishing such taxonomy is important because it would enable systematic investigations that are needed to advance in the use of wearable tools in health self-care. For a start, a taxonomy would help to improve the accuracy of database searching when doing systematic reviews and meta-analyses in this field. Overall, more systematic research would contribute to build evidence of sufficient quality to determine whether and how health SQ is a worthwhile health care paradigm. The aim of this study was to investigate a sample of SQ tools and services to build and test a taxonomy of measurements in health SQ, titled: the classification of data and activity in self-quantification systems (CDA-SQS). Eight health SQ tools and services were selected to be examined: Zeo Sleep Manager, Fitbit Ultra, Fitlinxx Actipressure, MoodPanda, iBGStar, Sensaris Senspod, 23andMe, and uBiome. An open coding analytical approach was used to find all the themes related to the research aim. This study distinguished three types of measurements in health SQ: body structures and functions, body actions and activities, and around the body. The CDA-SQS classification should be applicable to align health SQ measurement data from people with many different health objectives, health states, and health conditions. CDA-SQS is a critical contribution to a much more consistent way of studying health SQ. ©Manal Almalki, Kathleen Gray, Fernando Martin-Sanchez. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 03.11.2017.

Development and Validation of a Taxonomy for Characterizing Measurements in Health Self-Quantification

PubMed Central

2017-01-01

Background The use of wearable tools for health self-quantification (SQ) introduces new ways of thinking about one’s body and about how to achieve desired health outcomes. Measurements from individuals, such as heart rate, respiratory volume, skin temperature, sleep, mood, blood pressure, food consumed, and quality of surrounding air can be acquired, quantified, and aggregated in a holistic way that has never been possible before. However, health SQ still lacks a formal common language or taxonomy for describing these kinds of measurements. Establishing such taxonomy is important because it would enable systematic investigations that are needed to advance in the use of wearable tools in health self-care. For a start, a taxonomy would help to improve the accuracy of database searching when doing systematic reviews and meta-analyses in this field. Overall, more systematic research would contribute to build evidence of sufficient quality to determine whether and how health SQ is a worthwhile health care paradigm. Objective The aim of this study was to investigate a sample of SQ tools and services to build and test a taxonomy of measurements in health SQ, titled: the classification of data and activity in self-quantification systems (CDA-SQS). Methods Eight health SQ tools and services were selected to be examined: Zeo Sleep Manager, Fitbit Ultra, Fitlinxx Actipressure, MoodPanda, iBGStar, Sensaris Senspod, 23andMe, and uBiome. An open coding analytical approach was used to find all the themes related to the research aim. Results This study distinguished three types of measurements in health SQ: body structures and functions, body actions and activities, and around the body. Conclusions The CDA-SQS classification should be applicable to align health SQ measurement data from people with many different health objectives, health states, and health conditions. CDA-SQS is a critical contribution to a much more consistent way of studying health SQ. PMID:29101092

ClassyFire: automated chemical classification with a comprehensive, computable taxonomy.

PubMed

Djoumbou Feunang, Yannick; Eisner, Roman; Knox, Craig; Chepelev, Leonid; Hastings, Janna; Owen, Gareth; Fahy, Eoin; Steinbeck, Christoph; Subramanian, Shankar; Bolton, Evan; Greiner, Russell; Wishart, David S

2016-01-01

Scientists have long been driven by the desire to describe, organize, classify, and compare objects using taxonomies and/or ontologies. In contrast to biology, geology, and many other scientific disciplines, the world of chemistry still lacks a standardized chemical ontology or taxonomy. Several attempts at chemical classification have been made; but they have mostly been limited to either manual, or semi-automated proof-of-principle applications. This is regrettable as comprehensive chemical classification and description tools could not only improve our understanding of chemistry but also improve the linkage between chemistry and many other fields. For instance, the chemical classification of a compound could help predict its metabolic fate in humans, its druggability or potential hazards associated with it, among others. However, the sheer number (tens of millions of compounds) and complexity of chemical structures is such that any manual classification effort would prove to be near impossible. We have developed a comprehensive, flexible, and computable, purely structure-based chemical taxonomy (ChemOnt), along with a computer program (ClassyFire) that uses only chemical structures and structural features to automatically assign all known chemical compounds to a taxonomy consisting of >4800 different categories. This new chemical taxonomy consists of up to 11 different levels (Kingdom, SuperClass, Class, SubClass, etc.) with each of the categories defined by unambiguous, computable structural rules. Furthermore each category is named using a consensus-based nomenclature and described (in English) based on the characteristic common structural properties of the compounds it contains. The ClassyFire webserver is freely accessible at http://classyfire.wishartlab.com/. Moreover, a Ruby API version is available at https://bitbucket.org/wishartlab/classyfire_api, which provides programmatic access to the ClassyFire server and database. ClassyFire has been used to annotate over 77 million compounds and has already been integrated into other software packages to automatically generate textual descriptions for, and/or infer biological properties of over 100,000 compounds. Additional examples and applications are provided in this paper. ClassyFire, in combination with ChemOnt (ClassyFire's comprehensive chemical taxonomy), now allows chemists and cheminformaticians to perform large-scale, rapid and automated chemical classification. Moreover, a freely accessible API allows easy access to more than 77 million "ClassyFire" classified compounds. The results can be used to help annotate well studied, as well as lesser-known compounds. In addition, these chemical classifications can be used as input for data integration, and many other cheminformatics-related tasks.

Development of tools to study personal weight control strategies: OxFAB taxonomy

PubMed Central

Aveyard, Paul; Koshiaris, Constantinos; Jebb, Susan A.

2016-01-01

Objective To describe the development of the Oxford Food and Activity Behaviors (OxFAB) taxonomy and questionnaire to explore the cognitive and behavioral strategies used by individuals during weight management attempts. Methods The taxonomy was constructed through a qualitative analysis of existing resources and a review of existing behavior change taxonomies and theories. The taxonomy was translated into a questionnaire to identify strategies used by individuals. Think‐aloud interviews were conducted to test the face/concept validity of the questionnaire, and test–retest reliability was assessed in a sample of 138 participants. Results The OxFAB taxonomy consists of 117 strategies grouped into 23 domains. Compared to taxonomies used to describe interventions, around half of the domains and strategies identified are unique to the OxFAB taxonomy. The OxFAB questionnaire consists of 117 questions, one for each strategy from the taxonomy. Test–retest resulted in a mean PABAK score of 0.61 (SD 0.15). Questions were revised where appropriate. Conclusions The OxFAB taxonomy and questionnaire provide a conceptual framework to identify the cognitive and behavioral strategies used by individuals during attempts at weight control. PMID:26748902

Development of tools to study personal weight control strategies: OxFAB taxonomy.

PubMed

Hartmann-Boyce, Jamie; Aveyard, Paul; Koshiaris, Constantinos; Jebb, Susan A

2016-02-01

To describe the development of the Oxford Food and Activity Behaviors (OxFAB) taxonomy and questionnaire to explore the cognitive and behavioral strategies used by individuals during weight management attempts. The taxonomy was constructed through a qualitative analysis of existing resources and a review of existing behavior change taxonomies and theories. The taxonomy was translated into a questionnaire to identify strategies used by individuals. Think-aloud interviews were conducted to test the face/concept validity of the questionnaire, and test-retest reliability was assessed in a sample of 138 participants. The OxFAB taxonomy consists of 117 strategies grouped into 23 domains. Compared to taxonomies used to describe interventions, around half of the domains and strategies identified are unique to the OxFAB taxonomy. The OxFAB questionnaire consists of 117 questions, one for each strategy from the taxonomy. Test-retest resulted in a mean PABAK score of 0.61 (SD 0.15). Questions were revised where appropriate. The OxFAB taxonomy and questionnaire provide a conceptual framework to identify the cognitive and behavioral strategies used by individuals during attempts at weight control. © 2016 The Authors. Obesity published by Wiley Periodicals, Inc. on behalf of The Obesity Society (TOS).

Development and evaluation of a new taxonomy of mobility-related assistive technology devices.

PubMed

Shoemaker, Laura L; Lenker, James A; Fuhrer, Marcus J; Jutai, Jeffrey W; Demers, Louise; DeRuyter, Frank

2010-10-01

This article reports on the development of a new taxonomy for mobility-related assistive technology devices. A prototype taxonomy was created based on the extant literature. Five mobility device experts were engaged in a modified Delphi process to evaluate and refine the taxonomy. Multiple iterations of expert feedback and revision yielded consensual agreement on the structure and terminology of a new mobility device taxonomy. The taxonomy uses a hierarchical framework to classify ambulation aids and wheeled mobility devices, including their key features that impact mobility. Five attributes of the new taxonomy differentiate it from previous mobility-related device classifications: (1) hierarchical structure, (2) primary device categories are grouped based on their intended mobility impact, (3) comprehensive inclusion of technical features, (4) a capacity to assimilate reimbursement codes, and (5) availability of a detailed glossary. The taxonomy is intended to support assistive technology outcomes research. The taxonomy will enable researchers to capture mobility-related assistive technology device interventions with precision and provide a common terminology that will allow comparisons among studies. The prominence of technical features within the new taxonomy will hopefully promote research that helps clinicians predict how devices will perform, thus aiding clinical decision making and supporting funding recommendations.

DNA barcodes to identify species and explore diversity in the Adelgidae (Insecta: Hemiptera: Aphidoidea)

Treesearch

R.G. Foottit; H.E.L. Maw; N.P. Havill; R.G. Ahern; M.E. Montgomery

2009-01-01

The Adelgidae are relatively small, cryptic insects, exhibiting complex life cycles with parthenogenetic reproduction. Due to these characteristics, the taxonomy of the group is problematic. Here, we test the effectiveness of the standard 658-bp barcode fragment from the 5'-end of the mitochondrial cytochrome c oxidase 1 gene (COI) in...

Individual Differences in Study Processes and the Quality of Learning Outcomes.

ERIC Educational Resources Information Center

Biggs, John

1979-01-01

The relationship between students' study processes and the structural complexity of their learning is examined. Study processes are viewed in terms of three dimensions and are assessed by a questionnaire. Learning quality is expressed in levels of a taxonomy. A study that relates taxonomic levels and retention to study processes is reported.…

A Web-Based Adaptive Tutor to Teach PCR Primer Design

ERIC Educational Resources Information Center

van Seters, Janneke R.; Wellink, Joan; Tramper, Johannes; Goedhart, Martin J.; Ossevoort, Miriam A.

2012-01-01

When students have varying prior knowledge, personalized instruction is desirable. One way to personalize instruction is by using adaptive e-learning to offer training of varying complexity. In this study, we developed a web-based adaptive tutor to teach PCR primer design: the PCR Tutor. We used part of the Taxonomy of Educational Objectives (the…

Draft Genome Sequence of Fish Pathogen Aeromonas bestiarum GA97-22.

PubMed

Kumru, Salih; Tekedar, Hasan C; Griffin, Matt J; Waldbieser, Geoffrey C; Liles, Mark R; Sonstegard, Tad; Schroeder, Steven G; Lawrence, Mark L; Karsi, Attila

2018-06-14

Aeromonas bestiarum is a Gram-negative mesophilic motile bacterium causing acute hemorrhagic septicemia or chronic skin ulcers in fish. Here, we report the draft genome sequence of A. bestiarum strain GA97-22, which was isolated from rainbow trout in 1997. This genome sequence will improve our understanding of the complex taxonomy of motile aeromonads.

Breast cancer pathology: the impact of molecular taxonomy on morphological taxonomy.

PubMed

Masuda, Shinobu

2012-05-01

The concept of having an 'intrinsic subtype,' or a molecular taxonomy, lets us clearly recognize that breast cancers have characteristically different patterns of gene expression, thus giving newfound significance to morphological taxonomy. In this review, the concept of the 'intrinsic subtype' is discussed, research questions are introduced to refine the significance of morphological taxonomy, and a corresponding example is presented between microarray analysis and 'immunohistochemical subtype,' or histological taxonomy. © 2012 The Author. Pathology International © 2012 Japanese Society of Pathology and Blackwell Publishing Asia Pty Ltd.

A taxonomy of multinational ethical and methodological standards for clinical trials of therapeutic interventions

PubMed Central

Ashton, Carol M; Wray, Nelda P; Jarman, Anna F; Kolman, Jacob M; Wenner, Danielle M; Brody, Baruch A

2013-01-01

Background If trials of therapeutic interventions are to serve society’s interests, they must be of high methodological quality and must satisfy moral commitments to human subjects. The authors set out to develop a clinical-trials compendium in which standards for the ethical treatment of human subjects are integrated with standards for research methods. Methods The authors rank-ordered the world’s nations and chose the 31 with >700 active trials as of 24 July 2008. Governmental and other authoritative entities of the 31 countries were searched, and 1004 English-language documents containing ethical and/or methodological standards for clinical trials were identified. The authors extracted standards from 144 of those: 50 designated as ‘core’, 39 addressing trials of invasive procedures and a 5% sample (N=55) of the remainder. As the integrating framework for the standards we developed a coherent taxonomy encompassing all elements of a trial’s stages. Findings Review of the 144 documents yielded nearly 15 000 discrete standards. After duplicates were removed, 5903 substantive standards remained, distributed in the taxonomy as follows: initiation, 1401 standards, 8 divisions; design, 1869 standards, 16 divisions; conduct, 1473 standards, 8 divisions; analysing and reporting results, 997 standards, four divisions; and post-trial standards, 168 standards, 5 divisions. Conclusions The overwhelming number of source documents and standards uncovered in this study was not anticipated beforehand and confirms the extraordinary complexity of the clinical trials enterprise. This taxonomy of multinational ethical and methodological standards may help trialists and overseers improve the quality of clinical trials, particularly given the globalisation of clinical research. PMID:21429960

A taxonomy of multinational ethical and methodological standards for clinical trials of therapeutic interventions.

PubMed

Ashton, Carol M; Wray, Nelda P; Jarman, Anna F; Kolman, Jacob M; Wenner, Danielle M; Brody, Baruch A

2011-06-01

If trials of therapeutic interventions are to serve society's interests, they must be of high methodological quality and must satisfy moral commitments to human subjects. The authors set out to develop a clinical-trials compendium in which standards for the ethical treatment of human subjects are integrated with standards for research methods. The authors rank-ordered the world's nations and chose the 31 with >700 active trials as of 24 July 2008. Governmental and other authoritative entities of the 31 countries were searched, and 1004 English-language documents containing ethical and/or methodological standards for clinical trials were identified. The authors extracted standards from 144 of those: 50 designated as 'core', 39 addressing trials of invasive procedures and a 5% sample (N=55) of the remainder. As the integrating framework for the standards we developed a coherent taxonomy encompassing all elements of a trial's stages. Review of the 144 documents yielded nearly 15 000 discrete standards. After duplicates were removed, 5903 substantive standards remained, distributed in the taxonomy as follows: initiation, 1401 standards, 8 divisions; design, 1869 standards, 16 divisions; conduct, 1473 standards, 8 divisions; analysing and reporting results, 997 standards, four divisions; and post-trial standards, 168 standards, 5 divisions. The overwhelming number of source documents and standards uncovered in this study was not anticipated beforehand and confirms the extraordinary complexity of the clinical trials enterprise. This taxonomy of multinational ethical and methodological standards may help trialists and overseers improve the quality of clinical trials, particularly given the globalisation of clinical research.

External details revisited - A new taxonomy for coding 'non-episodic' content during autobiographical memory retrieval.

PubMed

Strikwerda-Brown, Cherie; Mothakunnel, Annu; Hodges, John R; Piguet, Olivier; Irish, Muireann

2018-04-24

Autobiographical memory (ABM) is typically held to comprise episodic and semantic elements, with the vast majority of studies to date focusing on profiles of episodic details in health and disease. In this context, 'non-episodic' elements are often considered to reflect semantic processing or are discounted from analyses entirely. Mounting evidence suggests that rather than reflecting one unitary entity, semantic autobiographical information may contain discrete subcomponents, which vary in their relative degree of semantic or episodic content. This study aimed to (1) review the existing literature to formally characterize the variability in analysis of 'non-episodic' content (i.e., external details) on the Autobiographical Interview and (2) use these findings to create a theoretically grounded framework for coding external details. Our review exposed discrepancies in the reporting and interpretation of external details across studies, reinforcing the need for a new, consistent approach. We validated our new external details scoring protocol (the 'NExt' taxonomy) in patients with Alzheimer's disease (n = 18) and semantic dementia (n = 13), and 20 healthy older Control participants and compared profiles of the NExt subcategories across groups and time periods. Our results revealed increased sensitivity of the NExt taxonomy in discriminating between ABM profiles of patient groups, when compared to traditionally used internal and external detail metrics. Further, remote and recent autobiographical memories displayed distinct compositions of the NExt detail types. This study is the first to provide a fine-grained and comprehensive taxonomy to parse external details into intuitive subcategories and to validate this protocol in neurodegenerative disorders. © 2018 The British Psychological Society.

The Hierarchical Taxonomy of Psychopathology (HiTOP): A dimensional alternative to traditional nosologies.

PubMed

Kotov, Roman; Krueger, Robert F; Watson, David; Achenbach, Thomas M; Althoff, Robert R; Bagby, R Michael; Brown, Timothy A; Carpenter, William T; Caspi, Avshalom; Clark, Lee Anna; Eaton, Nicholas R; Forbes, Miriam K; Forbush, Kelsie T; Goldberg, David; Hasin, Deborah; Hyman, Steven E; Ivanova, Masha Y; Lynam, Donald R; Markon, Kristian; Miller, Joshua D; Moffitt, Terrie E; Morey, Leslie C; Mullins-Sweatt, Stephanie N; Ormel, Johan; Patrick, Christopher J; Regier, Darrel A; Rescorla, Leslie; Ruggero, Camilo J; Samuel, Douglas B; Sellbom, Martin; Simms, Leonard J; Skodol, Andrew E; Slade, Tim; South, Susan C; Tackett, Jennifer L; Waldman, Irwin D; Waszczuk, Monika A; Widiger, Thomas A; Wright, Aidan G C; Zimmerman, Mark

2017-05-01

The reliability and validity of traditional taxonomies are limited by arbitrary boundaries between psychopathology and normality, often unclear boundaries between disorders, frequent disorder co-occurrence, heterogeneity within disorders, and diagnostic instability. These taxonomies went beyond evidence available on the structure of psychopathology and were shaped by a variety of other considerations, which may explain the aforementioned shortcomings. The Hierarchical Taxonomy Of Psychopathology (HiTOP) model has emerged as a research effort to address these problems. It constructs psychopathological syndromes and their components/subtypes based on the observed covariation of symptoms, grouping related symptoms together and thus reducing heterogeneity. It also combines co-occurring syndromes into spectra, thereby mapping out comorbidity. Moreover, it characterizes these phenomena dimensionally, which addresses boundary problems and diagnostic instability. Here, we review the development of the HiTOP and the relevant evidence. The new classification already covers most forms of psychopathology. Dimensional measures have been developed to assess many of the identified components, syndromes, and spectra. Several domains of this model are ready for clinical and research applications. The HiTOP promises to improve research and clinical practice by addressing the aforementioned shortcomings of traditional nosologies. It also provides an effective way to summarize and convey information on risk factors, etiology, pathophysiology, phenomenology, illness course, and treatment response. This can greatly improve the utility of the diagnosis of mental disorders. The new classification remains a work in progress. However, it is developing rapidly and is poised to advance mental health research and care significantly as the relevant science matures. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

A test of color-based taxonomy in nudibranchs: Molecular phylogeny and species delimitation of the Felimida clenchi (Mollusca: Chromodorididae) species complex.

PubMed

Padula, Vinicius; Bahia, Juliana; Stöger, Isabella; Camacho-García, Yolanda; Malaquias, Manuel António E; Cervera, Juan Lucas; Schrödl, Michael

2016-10-01

Traditionally, species identification in nudibranch gastropods relies heavily on body color pattern. The Felimida clenchi species complex, a group of brightly colored Atlantic and Mediterranean species in the family Chromodorididae, has a history of exceptional controversy and discussion among taxonomists. The most widely accepted hypothesis is that the complex includes four species (Felimida clenchi, F. neona, F. binza and F. britoi), each with a characteristic body color pattern. In this study, we investigated the taxonomic value of coloration in the Felimida clenchi complex, using molecular phylogenetics, species-delimitation analyses (ABGD, GMYC, PTP), haplotype-network methods, and the anatomy of the reproductive system. None of our analyses recovered the traditional separation into four species. Our results indicated the existence of three species, a result inconsistent with previous taxonomic hypotheses. We distinguished an undescribed species of Felimida and redefined the concepts of F. clenchi and F. binza, both highly polychromatic species. For the first time, molecular data support the existence of extreme color polymorphism in chromatic nudibranch species, with direct implications for the taxonomy of the group and its diversity. The polychromatism observed in the F. clenchi complex apparently correlates with the regional occurrence of similar color patterns in congeneric species, suggesting different mimicry circles. This may represent a parallel in the marine environment to the mechanisms that play a major role in the diversification of color in terrestrial and fresh-water chromatic groups, such as heliconian butterflies. Copyright © 2016 Elsevier Inc. All rights reserved.

Summarizing an Ontology: A "Big Knowledge" Coverage Approach.

PubMed

Zheng, Ling; Perl, Yehoshua; Elhanan, Gai; Ochs, Christopher; Geller, James; Halper, Michael

2017-01-01

Maintenance and use of a large ontology, consisting of thousands of knowledge assertions, are hampered by its scope and complexity. It is important to provide tools for summarization of ontology content in order to facilitate user "big picture" comprehension. We present a parameterized methodology for the semi-automatic summarization of major topics in an ontology, based on a compact summary of the ontology, called an "aggregate partial-area taxonomy", followed by manual enhancement. An experiment is presented to test the effectiveness of such summarization measured by coverage of a given list of major topics of the corresponding application domain. SNOMED CT's Specimen hierarchy is the test-bed. A domain-expert provided a list of topics that serves as a gold standard. The enhanced results show that the aggregate taxonomy covers most of the domain's main topics.

Auditing Complex Concepts in Overlapping Subsets of SNOMED

PubMed Central

Wang, Yue; Wei, Duo; Xu, Junchuan; Elhanan, Gai; Perl, Yehoshua; Halper, Michael; Chen, Yan; Spackman, Kent A.; Hripcsak, George

2008-01-01

Limited resources and the sheer volume of concepts make auditing a large terminology, such as SNOMED CT, a daunting task. It is essential to devise techniques that can aid an auditor by automatically identifying concepts that deserve attention. A methodology for this purpose based on a previously introduced abstraction network (called the p-area taxonomy) for a SNOMED CT hierarchy is presented. The methodology algorithmically gathers concepts appearing in certain overlapping subsets, defined exclusively with respect to the p-area taxonomy, for review. The results of applying the methodology to SNOMED’s Specimen hierarchy are presented. These results are compared against a control sample composed of concepts residing in subsets without the overlaps. With the use of the double bootstrap, the concept group produced by our methodology is shown to yield a statistically significant higher proportion of error discoveries. PMID:18998838

Auditing complex concepts in overlapping subsets of SNOMED.

PubMed

Wang, Yue; Wei, Duo; Xu, Junchuan; Elhanan, Gai; Perl, Yehoshua; Halper, Michael; Chen, Yan; Spackman, Kent A; Hripcsak, George

2008-11-06

Limited resources and the sheer volume of concepts make auditing a large terminology, such as SNOMED CT, a daunting task. It is essential to devise techniques that can aid an auditor by automatically identifying concepts that deserve attention. A methodology for this purpose based on a previously introduced abstraction network (called the p-area taxonomy) for a SNOMED CT hierarchy is presented. The methodology algorithmically gathers concepts appearing in certain overlapping subsets, defined exclusively with respect to the p-area taxonomy, for review. The results of applying the methodology to SNOMED's Specimen hierarchy are presented. These results are compared against a control sample composed of concepts residing in subsets without the overlaps. With the use of the double bootstrap, the concept group produced by our methodology is shown to yield a statistically significant higher proportion of error discoveries.

Transporter taxonomy - a comparison of different transport protein classification schemes.

PubMed

Viereck, Michael; Gaulton, Anna; Digles, Daniela; Ecker, Gerhard F

2014-06-01

Currently, there are more than 800 well characterized human membrane transport proteins (including channels and transporters) and there are estimates that about 10% (approx. 2000) of all human genes are related to transport. Membrane transport proteins are of interest as potential drug targets, for drug delivery, and as a cause of side effects and drug–drug interactions. In light of the development of Open PHACTS, which provides an open pharmacological space, we analyzed selected membrane transport protein classification schemes (Transporter Classification Database, ChEMBL, IUPHAR/BPS Guide to Pharmacology, and Gene Ontology) for their ability to serve as a basis for pharmacology driven protein classification. A comparison of these membrane transport protein classification schemes by using a set of clinically relevant transporters as use-case reveals the strengths and weaknesses of the different taxonomy approaches.

Taxonomy, phylogeny and molecular epidemiology of Echinococcus multilocularis: From fundamental knowledge to health ecology.

PubMed

Knapp, Jenny; Gottstein, Bruno; Saarma, Urmas; Millon, Laurence

2015-10-30

Alveolar echinococcosis, caused by the tapeworm Echinococcus multilocularis, is one of the most severe parasitic diseases in humans and represents one of the 17 neglected diseases prioritised by the World Health Organisation (WHO) in 2012. Considering the major medical and veterinary importance of this parasite, the phylogeny of the genus Echinococcus is of considerable importance; yet, despite numerous efforts with both mitochondrial and nuclear data, it has remained unresolved. The genus is clearly complex, and this is one of the reasons for the incomplete understanding of its taxonomy. Although taxonomic studies have recognised E. multilocularis as a separate entity from the Echinococcus granulosus complex and other members of the genus, it would be premature to draw firm conclusions about the taxonomy of the genus before the phylogeny of the whole genus is fully resolved. The recent sequencing of E. multilocularis and E. granulosus genomes opens new possibilities for performing in-depth phylogenetic analyses. In addition, whole genome data provide the possibility of inferring phylogenies based on a large number of functional genes, i.e. genes that trace the evolutionary history of adaptation in E. multilocularis and other members of the genus. Moreover, genomic data open new avenues for studying the molecular epidemiology of E. multilocularis: genotyping studies with larger panels of genetic markers allow the genetic diversity and spatial dynamics of parasites to be evaluated with greater precision. There is an urgent need for international coordination of genotyping of E. multilocularis isolates from animals and human patients. This could be fundamental for a better understanding of the transmission of alveolar echinococcosis and for designing efficient healthcare strategies. Copyright © 2015 Elsevier B.V. All rights reserved.

Living Behaviors and Molecular Characterization of Benthic Foraminifera in the Arabian Gulf

NASA Astrophysics Data System (ADS)

Arslan, Muhammad; Kaminski, Michael; Khalil, Amjad; Holzmann, Maria

2016-04-01

The benthic foraminifera are among the major carbonate producers in modern Arabian Gulf waters and are found living in all marine habitats. They have been recognized as proxies to assess paleoenvironmental changes, however, their biological behaviors in modern environments needs to be further studied. The current study attempts to explain the biology of benthic foraminifera in terms of their living behaviors and molecular characterization, from different regions of the western side of the Arabian Gulf. Accordingly, two major groups of benthic foraminifera, namely rotaliids and miliolids, are examined under laboratory conditions. Results illustrate that the rotaliids are more resistant to environmental changes than miliolids, as their granular reticulopodial network is stronger than among the miliolids, with high cytoplasmic streaming. The pseudopodia extend out from both primary and secondary apertures, and aid the organism in locomotion by attaching to the wall of hard substrate. As a result they drag their whole bodies toward the direction of motion. In rotaliids, the movement rate is high and is attributed to the extension of pseudopodia through all apertures, compared with miliolids in which pseudopodia extend out from the primary aperture only. The innate behavior of both groups was observed as a function of external stimulus, i.e., light, nutrients, and availability of substrate. The observation on average life span reflected that the rotaliids was able to survive longer than miliolids. Molecular analysis reveals the presence of four groups, i.e., Ammonia, Murrayinella, Glabratellina, and Elphidium which support the morphological taxonomy at the genus level. However, BLAST analysis contradicts the species level taxonomy, which challenges the classification based upon hard-shell morphology. Nevertheless, monophyletic clustering is observed among all major groups. The study concludes that the morphological taxonomy needs to be augmented by molecular analysis, in order to develop a new inventory of species.

Molecular characterization of the species Salvinia (Salviniaceae) from the upper Paraná River floodplain.

PubMed

Machado, S A; Oliveira, A V; Fabrin, T M C; Prioli, S M A P; Prioli, A J

2016-08-12

The pteridophytes Salvinia minima, S. herzogii, and S. auriculata are among the most abundant aquatic macrophytes in the upper Paraná River floodplain. Since some species have highly similar morphological features, it is very difficult to identify members of this genus to the species level. An indication of this difficulty is a set of poorly differentiated taxa comprising S. auriculata and S. herzogii known as the 'S. auriculata complex', which is found in the Paraná River together with other Salvinia species such as S. biloba and S. molesta. Some authors have reported the existence of inter-species hybrids. Despite the complex Salvinia taxonomy, few genetic studies have been performed on purported species within the genus to resolve this complexity. The present study was conducted to determine useful molecular sequences for the discrimination of Salvinia species of the upper Paraná River floodplain. Molecular data were compared with data of other species of the genus to clarify phylogenetic relationships, employing the nucleotide sequence trnL-trnF from the chloroplast DNA. The results revealed that Salvinia populations in the upper Paraná River floodplain belong to different species and indicated that species of the S. auriculata complex may be distinguished from one another after the division of the S. minima group, corroborating results by other researchers. Although the taxonomic position of S. oblongifolia was clarified, as high closeness between S. oblongifolia and the S. auriculata complex was reported, Salvinia kinship is still not thoroughly established and further investigations in morphology and molecular diversity are required.

Structural and functional MRI- findings in children and adolescents with antisocial behavior.

PubMed

Vloet, Timo D; Konrad, Kerstin; Huebner, Thomas; Herpertz, Sabine; Herpertz-Dahlmann, Beate

2008-01-01

The developmental course of children with conduct disorder (CD) is heterogeneous. Especially children who exhibit symptoms early in their lifetimes are characterized by a negative outcome. Neurobiological aspects of CD have been investigated in these children but little is known about structural and functional brain aberrations. We describe the developmental taxonomy of children with CD and focus on those with the early onset subtype. Structural MRI data of these children and antisocial adults are recapitulated. The impact of investigating neurobiological underpinnings of antisocial behavior and how this might contribute to future forensic and psychiatric assessments is discussed. RESULTS/ CONCLUSION: Children display similar structural aberrations of fronto-limbic structures to adults with antisocial behavior, and amygdala dysfunction might be closely related to dysregulated emotions. Though the investigation of biological factors in antisocial subjects has made great progress in recent years, today MRI is still a rather complex, expensive and indistinct method for forensic assessment. (c) 2008 John Wiley & Sons, Ltd.

A cognitive taxonomy of medical errors.

PubMed

Zhang, Jiajie; Patel, Vimla L; Johnson, Todd R; Shortliffe, Edward H

2004-06-01

Propose a cognitive taxonomy of medical errors at the level of individuals and their interactions with technology. Use cognitive theories of human error and human action to develop the theoretical foundations of the taxonomy, develop the structure of the taxonomy, populate the taxonomy with examples of medical error cases, identify cognitive mechanisms for each category of medical error under the taxonomy, and apply the taxonomy to practical problems. Four criteria were used to evaluate the cognitive taxonomy. The taxonomy should be able (1) to categorize major types of errors at the individual level along cognitive dimensions, (2) to associate each type of error with a specific underlying cognitive mechanism, (3) to describe how and explain why a specific error occurs, and (4) to generate intervention strategies for each type of error. The proposed cognitive taxonomy largely satisfies the four criteria at a theoretical and conceptual level. Theoretically, the proposed cognitive taxonomy provides a method to systematically categorize medical errors at the individual level along cognitive dimensions, leads to a better understanding of the underlying cognitive mechanisms of medical errors, and provides a framework that can guide future studies on medical errors. Practically, it provides guidelines for the development of cognitive interventions to decrease medical errors and foundation for the development of medical error reporting system that not only categorizes errors but also identifies problems and helps to generate solutions. To validate this model empirically, we will next be performing systematic experimental studies.

Of Moving Targets and Chameleons: Why the Concept of Difficulty Is So Hard to Pin Down

ERIC Educational Resources Information Center

DeKeyser, Robert

2016-01-01

In this short article I try to present a taxonomy of sources of difficulty, in particular complexity. I emphasize how these factors interact with each other and with individual differences and treatments, before illustrating some of these interactions and the methodological issues involved in studying them with examples from the empirical studies…

On Developing a Taxonomy for Multidisciplinary Design Optimization: A Decision-Based Perspective

NASA Technical Reports Server (NTRS)

Lewis, Kemper; Mistree, Farrokh

1995-01-01

In this paper, we approach MDO from a Decision-Based Design (DBD) perspective and explore classification schemes for designing complex systems and processes. Specifically, we focus on decisions, which are only a small portion of the Decision Support Problem (DSP) Technique, our implementation of DBD. We map coupled nonhierarchical and hierarchical representations from the DSP Technique into the Balling-Sobieski (B-S) framework (Balling and Sobieszczanski-Sobieski, 1994), and integrate domain-independent linguistic terms to complete our taxonomy. Application of DSPs to the design of complex, multidisciplinary systems include passenger aircraft, ships, damage tolerant structural and mechanical systems, and thermal energy systems. In this paper we show that Balling-Sobieski framework is consistent with that of the Decision Support Problem Technique through the use of linguistic entities to describe the same type of formulations. We show that the underlying linguistics of the solution approaches are the same and can be coalesced into a homogeneous framework with which to base the research, application, and technology MDO upon. We introduce, in the Balling-Sobieski framework, examples of multidisciplinary design, namely, aircraft, damage tolerant structural and mechanical systems, and thermal energy systems.

A Taxonomy of Learning through Asynchronous Discussion

ERIC Educational Resources Information Center

Knowlton, Dave S.

2005-01-01

This article presents a five-tiered taxonomy that describes the nature of participation in, and learning through, asynchronous discussion. The taxonomy is framed by a constructivist view of asynchronous discussion. The five tiers of the taxonomy include the following: (a) passive participation, (b) developmental participation, (c) generative…

Teaching Taxonomy: How Many Kingdoms?

ERIC Educational Resources Information Center

Case, Emily

2008-01-01

Taxonomy, the identification, naming, and classification of living things, is an indispensable unit in any biology curriculum and indeed, an integral part of biological science. Taxonomy catalogues life's diversity and is an essential tool for communication. Textbook discussions of taxonomy range anywhere from three to eight domains of kingdoms.…

Information needs of case managers caring for persons living with HIV.

PubMed

Schnall, Rebecca; Cimino, James J; Currie, Leanne M; Bakken, Suzanne

2011-05-01

The goals of this study were to explore the information needs of case managers who provide services to persons living with HIV (PLWH) and to assess the applicability of the Information Needs Event Taxonomy in a new population. The study design was observational with data collection via an online survey. Responses to open-ended survey questions about the information needs of case managers (n=94) related to PLWH of three levels of care complexity were categorized using the Information Needs Event Taxonomy. The most frequently identified needs were related to patient education resources (33%), patient data (23%), and referral resources (22%) accounting for 79% of all (N=282) information needs. Study limitations include selection bias, recall bias, and a relatively narrow focus of the study on case-manager information needs in the context of caring for PLWH. The study findings contribute to the evidence base regarding information needs in the context of patient interactions by: (1) supporting the applicability of the Information Needs Event Taxonomy and extending it through addition of a new generic question; (2) providing a foundation for the addition of context-specific links to external information resources within information systems; (3) applying a new approach for elicitation of information needs; and (4) expanding the literature regarding addressing information needs in community-based settings for HIV services.

Building a Framework for a Dual Task Taxonomy

PubMed Central

McIsaac, Tara L.; Lamberg, Eric M.; Muratori, Lisa M.

2015-01-01

The study of dual task interference has gained increasing attention in the literature for the past 35 years, with six MEDLINE citations in 1979 growing to 351 citations indexed in 2014 and a peak of 454 cited papers in 2013. Increasingly, researchers are examining dual task cost in individuals with pathology, including those with neurodegenerative diseases. While the influence of these papers has extended from the laboratory to the clinic, the field has evolved without clear definitions of commonly used terms and with extreme variations in experimental procedures. As a result, it is difficult to examine the interference literature as a single body of work. In this paper we present a new taxonomy for classifying cognitive-motor and motor-motor interference within the study of dual task behaviors that connects traditional concepts of learning and principles of motor control with current issues of multitasking analysis. As a first step in the process we provide an operational definition of dual task, distinguishing it from a complex single task. We present this new taxonomy, inclusive of both cognitive and motor modalities, as a working model; one that we hope will generate discussion and create a framework from which one can view previous studies and develop questions of interest. PMID:25961027

The harms of screening: a proposed taxonomy and application to lung cancer screening.

PubMed

Harris, Russell P; Sheridan, Stacey L; Lewis, Carmen L; Barclay, Colleen; Vu, Maihan B; Kistler, Christine E; Golin, Carol E; DeFrank, Jessica T; Brewer, Noel T

2014-02-01

Making rational decisions about screening requires information about its harms, but high-quality evidence is often either not available or not used. One reason may be that we lack a coherent framework, a taxonomy, for conceptualizing and studying these harms. To create a taxonomy, we categorized harms from several sources: systematic reviews of screening, other published literature, and informal discussions with clinicians and patients. We used this information to develop an initial taxonomy and vetted it with local and national experts, making revisions as needed. We propose a taxonomy with 4 domains of harm from screening: physical effects, psychological effects, financial strain, and opportunity costs. Harms can occur at any step of the screening cascade. We provide definitions for each harm domain and illustrate the taxonomy using the example of screening for lung cancer. The taxonomy provides a systematic way to conceptualize harms as experienced by patients. As shown in the lung cancer screening example, the taxonomy also makes clear where (which domains of harms and which parts of the screening cascade) we have useful information and where there are gaps in our knowledge. The taxonomy needs further testing and validation across a broad range of screening programs. We hope that further development of this taxonomy can improve our thinking about the harms of screening, thus informing our research, policy making, and decision making with patients about the wisdom of screening.

A Taxonomy of Accountable Care Organizations for Policy and Practice

PubMed Central

Shortell, Stephen M; Wu, Frances M; Lewis, Valerie A; Colla, Carrie H; Fisher, Elliott S

2014-01-01

Objective To develop an exploratory taxonomy of Accountable Care Organizations (ACOs) to describe and understand early ACO development and to provide a basis for technical assistance and future evaluation of performance. Data Sources/Study Setting Data from the National Survey of Accountable Care Organizations, fielded between October 2012 and May 2013, of 173 Medicare, Medicaid, and commercial payer ACOs. Study Design Drawing on resource dependence and institutional theory, we develop measures of eight attributes of ACOs such as size, scope of services offered, and the use of performance accountability mechanisms. Data are analyzed using a two-step cluster analysis approach that accounts for both continuous and categorical data. Principal Findings We identified a reliable and internally valid three-cluster solution: larger, integrated systems that offer a broad scope of services and frequently include one or more postacute facilities; smaller, physician-led practices, centered in primary care, and that possess a relatively high degree of physician performance management; and moderately sized, joint hospital–physician and coalition-led groups that offer a moderately broad scope of services with some involvement of postacute facilities. Conclusions ACOs can be characterized into three distinct clusters. The taxonomy provides a framework for assessing performance, for targeting technical assistance, and for diagnosing potential antitrust violations. PMID:25251146

Bloom's Taxonomy: Improving Assessment and Teaching-Learning Process

ERIC Educational Resources Information Center

Chandio, Muhammad Tufail; Pandhiani, Saima Murtaza; Iqbal, Rabia

2016-01-01

This research study critically analyzes the scope and contribution of Bloom's Taxonomy in both assessment and teaching-learning process. Bloom's Taxonomy consists of six stages, namely; remembering, understanding, applying, analyzing, evaluating and creating and moves from lower degree to the higher degree. The study applies Bloom's Taxonomy to…

BioWarehouse: a bioinformatics database warehouse toolkit

PubMed Central

Lee, Thomas J; Pouliot, Yannick; Wagner, Valerie; Gupta, Priyanka; Stringer-Calvert, David WJ; Tenenbaum, Jessica D; Karp, Peter D

2006-01-01

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. PMID:16556315

BioWarehouse: a bioinformatics database warehouse toolkit.

PubMed

Lee, Thomas J; Pouliot, Yannick; Wagner, Valerie; Gupta, Priyanka; Stringer-Calvert, David W J; Tenenbaum, Jessica D; Karp, Peter D

2006-03-23

This article addresses the problem of interoperation of heterogeneous bioinformatics databases. 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. BioWarehouse embodies significant progress on the database integration problem for bioinformatics.

SSU rDNA divergence in planktonic foraminifera: molecular taxonomy and biogeographic implications.

PubMed

André, Aurore; Quillévéré, Frédéric; Morard, Raphaël; Ujiié, Yurika; Escarguel, Gilles; de Vargas, Colomban; de Garidel-Thoron, Thibault; Douady, Christophe J

2014-01-01

The use of planktonic foraminifera in paleoceanography requires taxonomic consistency and precise assessment of the species biogeography. Yet, ribosomal small subunit (SSUr) DNA analyses have revealed that most of the modern morpho-species of planktonic foraminifera are composed of a complex of several distinct genetic types that may correspond to cryptic or pseudo-cryptic species. These genetic types are usually delimitated using partial sequences located at the 3'end of the SSUrDNA, but typically based on empirical delimitation. Here, we first use patristic genetic distances calculated within and among genetic types of the most common morpho-species to show that intra-type and inter-type genetic distances within morpho-species may significantly overlap, suggesting that genetic types have been sometimes inconsistently defined. We further apply two quantitative and independent methods, ABGD (Automatic Barcode Gap Detection) and GMYC (General Mixed Yule Coalescent) to a dataset of published and newly obtained partial SSU rDNA for a more objective assessment of the species status of these genetic types. Results of these complementary approaches are highly congruent and lead to a molecular taxonomy that ranks 49 genetic types of planktonic foraminifera as genuine (pseudo)cryptic species. Our results advocate for a standardized sequencing procedure allowing homogenous delimitations of (pseudo)cryptic species. On the ground of this revised taxonomic framework, we finally provide an integrative taxonomy synthesizing geographic, ecological and morphological differentiations that can occur among the genuine (pseudo)cryptic species. Due to molecular, environmental or morphological data scarcities, many aspects of our proposed integrative taxonomy are not yet fully resolved. On the other hand, our study opens up the potential for a correct interpretation of environmental sequence datasets.

SSU rDNA Divergence in Planktonic Foraminifera: Molecular Taxonomy and Biogeographic Implications

PubMed Central

André, Aurore; Quillévéré, Frédéric; Morard, Raphaël; Ujiié, Yurika; Escarguel, Gilles; de Vargas, Colomban; de Garidel-Thoron, Thibault; Douady, Christophe J.

2014-01-01

The use of planktonic foraminifera in paleoceanography requires taxonomic consistency and precise assessment of the species biogeography. Yet, ribosomal small subunit (SSUr) DNA analyses have revealed that most of the modern morpho-species of planktonic foraminifera are composed of a complex of several distinct genetic types that may correspond to cryptic or pseudo-cryptic species. These genetic types are usually delimitated using partial sequences located at the 3′end of the SSUrDNA, but typically based on empirical delimitation. Here, we first use patristic genetic distances calculated within and among genetic types of the most common morpho-species to show that intra-type and inter-type genetic distances within morpho-species may significantly overlap, suggesting that genetic types have been sometimes inconsistently defined. We further apply two quantitative and independent methods, ABGD (Automatic Barcode Gap Detection) and GMYC (General Mixed Yule Coalescent) to a dataset of published and newly obtained partial SSU rDNA for a more objective assessment of the species status of these genetic types. Results of these complementary approaches are highly congruent and lead to a molecular taxonomy that ranks 49 genetic types of planktonic foraminifera as genuine (pseudo)cryptic species. Our results advocate for a standardized sequencing procedure allowing homogenous delimitations of (pseudo)cryptic species. On the ground of this revised taxonomic framework, we finally provide an integrative taxonomy synthesizing geographic, ecological and morphological differentiations that can occur among the genuine (pseudo)cryptic species. Due to molecular, environmental or morphological data scarcities, many aspects of our proposed integrative taxonomy are not yet fully resolved. On the other hand, our study opens up the potential for a correct interpretation of environmental sequence datasets. PMID:25119900

Social Media Use in Chronic Disease: A Systematic Review and Novel Taxonomy.

PubMed

Patel, Rajesh; Chang, Tammy; Greysen, S Ryan; Chopra, Vineet

2015-12-01

The purpose of this study is to evaluate clinical outcomes from applications of contemporary social media in chronic disease; to develop a conceptual taxonomy to categorize, summarize, and then analyze the current evidence base; and to suggest a framework for future studies on this topic. We performed a systematic review of MEDLINE via PubMed (January 2000 to January 2015) of studies reporting clinical outcomes on leading contemporary social media (ie, Facebook, Twitter, Wikipedia, YouTube) use in 10 chronic diseases. Two reviewers independently performed data extraction and quality assessment; characterization of study outcomes as positive, negative, neutral, or undefined impact; and inductive, thematic analysis to develop our taxonomy. Of 378 citations identified, 42 studies examining the use of Facebook (n = 16), blogs (n = 13), Twitter (n = 8), wikis (n = 5), and YouTube (n = 4) on outcomes in cancer (n = 14), depression (n = 13), obesity (n = 9), diabetes (n = 4), heart disease (n = 3), stroke (n = 2), and chronic lower respiratory tract infection (n = 1) were included. Studies were classified as support (n = 16), patient education (n = 10), disease modification (n = 6), disease management (n = 5), and diagnosis (n = 5) within our taxonomy. The overall impact of social media on chronic disease was variable, with 48% of studies indicating benefit, 45% neutral or undefined, and 7% suggesting harm. Among studies that showed benefit, 85% used either Facebook or blogs, and 40% were based within the domain of support. Using social media to provide social, emotional, or experiential support in chronic disease, especially with Facebook and blogs, appears most likely to improve patient care. Copyright © 2015 Elsevier Inc. All rights reserved.

Flexible taxonomic assignment of ambiguous sequencing reads

PubMed Central

2011-01-01

Background To characterize the diversity of bacterial populations in metagenomic studies, sequencing reads need to be accurately assigned to taxonomic units in a given reference taxonomy. Reads that cannot be reliably assigned to a unique leaf in the taxonomy (ambiguous reads) are typically assigned to the lowest common ancestor of the set of species that match it. This introduces a potentially severe error in the estimation of bacteria present in the sample due to false positives, since all species in the subtree rooted at the ancestor are implicitly assigned to the read even though many of them may not match it. Results We present a method that maps each read to a node in the taxonomy that minimizes a penalty score while balancing the relevance of precision and recall in the assignment through a parameter q. This mapping can be obtained in time linear in the number of matching sequences, because LCA queries to the reference taxonomy take constant time. When applied to six different metagenomic datasets, our algorithm produces different taxonomic distributions depending on whether coverage or precision is maximized. Including information on the quality of the reads reduces the number of unassigned reads but increases the number of ambiguous reads, stressing the relevance of our method. Finally, two measures of performance are described and results with a set of artificially generated datasets are discussed. Conclusions The assignment strategy of sequencing reads introduced in this paper is a versatile and a quick method to study bacterial communities. The bacterial composition of the analyzed samples can vary significantly depending on how ambiguous reads are assigned depending on the value of the q parameter. Validation of our results in an artificial dataset confirm that a combination of values of q produces the most accurate results. PMID:21211059

Heuristic for learning common emitter amplification with bipolar transistors

NASA Astrophysics Data System (ADS)

Staffas, Kjell

2017-11-01

Mathematics in engineering education causes many thresholds in the courses because of the demand of abstract conceptualisation. Electronics depend heavily on more or less complex mathematics. Therefore the concepts of analogue electronics are hard to learn since a great deal of students struggle with the calculations and procedures needed. A survey was done focusing on students' struggle to pass a course in analogue electronics by introducing a top-down perspective and the revised taxonomy of Bloom. From a top-down perspective you can create learning environments from any spot in the taxonomy using a step-by-step approach of the verbs understand and apply. Three textbooks with a top-down perspective on analogue electronics are analysed on the concept of amplifying with a transistor circuit. The study claims issues when losing the top-down perspective to present concepts and procedures of the content to be learned.

A Molecular Phylogeny of Living Primates

PubMed Central

Perelman, Polina; Johnson, Warren E.; Roos, Christian; Seuánez, Hector N.; Horvath, Julie E.; Moreira, Miguel A. M.; Kessing, Bailey; Pontius, Joan; Roelke, Melody; Rumpler, Yves; Schneider, Maria Paula C.; Silva, Artur; O'Brien, Stephen J.; Pecon-Slattery, Jill

2011-01-01

Comparative genomic analyses of primates offer considerable potential to define and understand the processes that mold, shape, and transform the human genome. However, primate taxonomy is both complex and controversial, with marginal unifying consensus of the evolutionary hierarchy of extant primate species. Here we provide new genomic sequence (∼8 Mb) from 186 primates representing 61 (∼90%) of the described genera, and we include outgroup species from Dermoptera, Scandentia, and Lagomorpha. The resultant phylogeny is exceptionally robust and illuminates events in primate evolution from ancient to recent, clarifying numerous taxonomic controversies and providing new data on human evolution. Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered. Our resolution of the primate phylogeny provides an essential evolutionary framework with far-reaching applications including: human selection and adaptation, global emergence of zoonotic diseases, mammalian comparative genomics, primate taxonomy, and conservation of endangered species. PMID:21436896

A Taxonomy of Object-Oriented Measures Modeling the Object-Oriented Space

NASA Technical Reports Server (NTRS)

Neal, Ralph D.; Weistroffer, H. Roland; Coppins, Richard J.

1997-01-01

In order to control the quality of software and the software development process, it is important to understand the measurement of software. A first step toward a better comprehension of software measurement is the categorization of software measures by some meaningful taxonomy. The most worthwhile taxonomy would capture the fundamental nature of the object-oriented (O-O) space. The principal characteristics of object-oriented software offer a starting point for such a categorization of measures. This paper introduces a taxonomy of measures based upon fourteen characteristics of object-oriented software gathered from the literature. This taxonomy allows us to easily see gaps or redundancies in the existing O-O measures. The taxonomy also clearly differentiates among taxa so that there is no ambiguity as to the taxon to which a measure belongs. The taxonomy has been populated with measures taken from the literature.

A Taxonomy of Object-Oriented Measures Modeling the Object Oriented Space

NASA Technical Reports Server (NTRS)

Neal, Ralph D.; Weistroffer, H. Roland; Coppins, Richard J.

1997-01-01

In order to control the quality of software and the software development process, it is important to understand the measurement of software. A first step toward a better comprehension of software measurement is the categorization of software measures by some meaningful taxonomy. The most worthwhile taxonomy would capture the fundamental nature of the object-oriented (O-O) space. The principal characteristics of object-oriented software offer a starting point for such a categorization of measures. This paper introduces a taxonomy of measures based upon fourteen characteristics of object-oriented software gathered from the literature. This taxonomy allows us to easily see gaps or redundancies in the existing O-O measures. The taxonomy also clearly differentiates among taxa so that there is no ambiguity as to the taxon to which a measure belongs. The taxonomy has been populated with measures taken from the literature.

Parent Training in Autism Spectrum Disorder: What’s in a Name?

PubMed Central

Bearss, Karen; Burrell, T. Lindsey; Stewart, Lindsay M.; Scahill, Lawrence

2015-01-01

Parent training (PT) is well understood as an evidence-based treatment for typically developing children with disruptive behavior. Within the field of autism spectrum disorder (ASD), the term parent training has been used to describe a wide range of interventions including care coordination, psychoeducation, treatments for language or social development, as well as programs designed to address maladaptive behaviors. As a result, the meaning of “parent training” in ASD is profoundly uncertain. This paper describes the need to delineate the variants of PT in ASD and offers a coherent taxonomy. Uniform characterization of PT programs can facilitate communication with families, professionals, administrators and third-party payers. Moreover, it may also serve as a framework for comparing and contrasting PT programs. In support of the taxonomy, a purposive sampling of the literature is presented to illustrate the range of parent training interventions in ASD. PMID:25722072

Taxonomy and Systematics of the Genus Makatinus Heyns, 1965 (Nematoda: Dorylaimida: Aporcelaimidae)

PubMed Central

Varela, Ingrid

2017-01-01

The taxonomy and the systematics of the genus Makatinus are discussed by means of the characterization of its morphological pattern and the first molecular (D2–D3 expansion segments of 28S rDNA) analysis of a representative of this taxon, Makatinus crassiformis from Costa Rica. The presence of two or more pairs of male ad-cloacal genital papillae is the most characteristic autapomorphy of the genus, but the status of its species on this concern differ among them. Both morphological and molecular data support a relationship with Aporcelaimellus, which, however, might not be as close as usually assumed. An emended diagnosis of the genus, a key to species identification, and a compendium of their morphometrics are provided. Makatinus siddiqii is regarded as species inquirenda, Makatinus simus is retained under Eudorylaimus, and Makatinus tritici becomes a junior synonym of Aporcelaimellus tritici. PMID:29062147

Learning Collaboratives: Insights And A New Taxonomy From AHRQ's Two Decades Of Experience.

PubMed

Nix, Mary; McNamara, Peggy; Genevro, Janice; Vargas, Natalia; Mistry, Kamila; Fournier, Alaina; Shofer, Margie; Lomotan, Edwin; Miller, Therese; Ricciardi, Richard; Bierman, Arlene S

2018-02-01

Learning collaboratives are increasingly used as mechanisms to support and hasten the diffusion and implementation of innovation, clinical evidence, and effective models of care. Factors contributing to the collaboratives' success or failure are poorly understood. The Agency for Healthcare Research and Quality (AHRQ) has sponsored collaboratives for nearly two decades to support improvements in health care quality and value by accelerating the diffusion and implementation of innovation. We examined AHRQ's experience with these collaboratives to characterize their attributes, identify factors that might contribute to their success or failure, and assess the challenges they encountered. Building on the literature and insights from AHRQ's experience, we propose a taxonomy that can offer guidance to decision makers and funders about the factors they should consider in developing collaboratives and planning their evaluation, as well as to researchers who seek to conduct research that will ultimately help decision makers make better investments in diffusing innovation and evidence.

Advances in Dendrobium molecular research: Applications in genetic variation, identification and breeding.

PubMed

Teixeira da Silva, Jaime A; Jin, Xiaohua; Dobránszki, Judit; Lu, Jiangjie; Wang, Huizhong; Zotz, Gerhard; Cardoso, Jean Carlos; Zeng, Songjun

2016-02-01

Orchids of the genus Dendrobium are of great economic importance in global horticultural trade and in Asian traditional medicine. For both areas, research yielding solid information on taxonomy, phylogeny, and breeding of this genus are essential. Traditional morphological and cytological characterization are used in combination with molecular results in classification and identification. Markers may be useful when used alone but are not always reliable in identification. The number of species studied and identified by molecular markers is small at present. Conventional breeding methods are time-consuming and laborious. In the past two decades, promising advances have been made in taxonomy, phylogeny and breeding of Dendrobium species due to the intensive use of molecular markers. In this review, we focus on the main molecular techniques used in 121 published studies and discuss their importance and possibilities in speeding up the breeding of new cultivars and hybrids. Copyright © 2015 Elsevier Inc. All rights reserved.

Taxonomies of Educational Technology Uses: Dewey, Chip and Me

ERIC Educational Resources Information Center

Levin, James A.

2014-01-01

In the early 1990s, Chip Bruce created a taxonomy of education technology uses, which the author of the article helped to expand and evaluate. This taxonomy is based on John Dewey's "four impulses of the child": inquiry, construction, communication, and expression. This taxonomy has helped people interested in the uses of…

48 CFR 237.102-74 - Taxonomy for the acquisition of services, and supplies and equipment.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 48 Federal Acquisition Regulations System 3 2014-10-01 2014-10-01 false Taxonomy for the... CONTRACTING SERVICE CONTRACTING Service Contracts-General 237.102-74 Taxonomy for the acquisition of services, and supplies and equipment. See PGI 237.102-74 for further guidance on the taxonomy for the...

Cryptic or pseudocryptic: can morphological methods inform copepod taxonomy? An analysis of publications and a case study of the Eurytemora affinis species complex

PubMed Central

Lajus, Dmitry; Sukhikh, Natalia; Alekseev, Victor

2015-01-01

Interest in cryptic species has increased significantly with current progress in genetic methods. The large number of cryptic species suggests that the resolution of traditional morphological techniques may be insufficient for taxonomical research. However, some species now considered to be cryptic may, in fact, be designated pseudocryptic after close morphological examination. Thus the “cryptic or pseudocryptic” dilemma speaks to the resolution of morphological analysis and its utility for identifying species. We address this dilemma first by systematically reviewing data published from 1980 to 2013 on cryptic species of Copepoda and then by performing an in-depth morphological study of the former Eurytemora affinis complex of cryptic species. Analyzing the published data showed that, in 5 of 24 revisions eligible for systematic review, cryptic species assignment was based solely on the genetic variation of forms without detailed morphological analysis to confirm the assignment. Therefore, some newly described cryptic species might be designated pseudocryptic under more detailed morphological analysis as happened with Eurytemora affinis complex. Recent genetic analyses of the complex found high levels of heterogeneity without morphological differences; it is argued to be cryptic. However, next detailed morphological analyses allowed to describe a number of valid species. Our study, using deep statistical analyses usually not applied for new species describing, of this species complex confirmed considerable differences between former cryptic species. In particular, fluctuating asymmetry (FA), the random variation of left and right structures, was significantly different between forms and provided independent information about their status. Our work showed that multivariate statistical approaches, such as principal component analysis, can be powerful techniques for the morphological discrimination of cryptic taxons. Despite increasing cryptic species designations, morphological techniques have great potential in determining copepod taxonomy. PMID:26120427

Developing a taxonomy of coordination behaviours in nuclear power plant control rooms during emergencies.

PubMed

Wang, Dunxing; Gao, Qin; Li, Zhizhong; Song, Fei; Ma, Liang

2017-12-01

This study aims to develop a taxonomy of coordination behaviours during emergencies in nuclear power plants (NPPs). We summarised basic coordination behaviours from literature in aviation, health care and nuclear field and identified coordination behaviours specific to the nuclear domain by interviewing and surveying control crew operators. The established taxonomy includes 7 workflow stages and 24 basic coordination behaviours. To evaluate the reliability and feasibility of the taxonomy, we analysed 12 videos of operators' training sessions by coding coordination behaviours with the taxonomy and the inter-rater reliability was acceptable. Further analysis of the frequency, the duration and the direction of the coordination behaviours revealed four coordination problems. This taxonomy provides a foundation of systematic observation of coordination behaviours among NPP crews, advances researchers' understanding of the coordination mechanism during emergencies in NPPs and facilitate the possibility to deepen the understanding of the relationships between coordination behaviours and team performance. Practitioner Summary: A taxonomy of coordination behaviours during emergencies in nuclear power plants was developed. Reliability and feasibility of the taxonomy was verified through the analysis of 12 training sessions. The taxonomy can serve as an observation system for analysis of coordination behaviours and help to identify coordination problems of control crews.

NASA Taxonomies for Searching Problem Reports and FMEAs

NASA Technical Reports Server (NTRS)

Malin, Jane T.; Throop, David R.

2006-01-01

Many types of hazard and risk analyses are used during the life cycle of complex systems, including Failure Modes and Effects Analysis (FMEA), Hazard Analysis, Fault Tree and Event Tree Analysis, Probabilistic Risk Assessment, Reliability Analysis and analysis of Problem Reporting and Corrective Action (PRACA) databases. The success of these methods depends on the availability of input data and the analysts knowledge. Standard nomenclature can increase the reusability of hazard, risk and problem data. When nomenclature in the source texts is not standard, taxonomies with mapping words (sets of rough synonyms) can be combined with semantic search to identify items and tag them with metadata based on a rich standard nomenclature. Semantic search uses word meanings in the context of parsed phrases to find matches. The NASA taxonomies provide the word meanings. Spacecraft taxonomies and ontologies (generalization hierarchies with attributes and relationships, based on terms meanings) are being developed for types of subsystems, functions, entities, hazards and failures. The ontologies are broad and general, covering hardware, software and human systems. Semantic search of Space Station texts was used to validate and extend the taxonomies. The taxonomies have also been used to extract system connectivity (interaction) models and functions from requirements text. Now the Reconciler semantic search tool and the taxonomies are being applied to improve search in the Space Shuttle PRACA database, to discover recurring patterns of failure. Usual methods of string search and keyword search fall short because the entries are terse and have numerous shortcuts (irregular abbreviations, nonstandard acronyms, cryptic codes) and modifier words cannot be used in sentence context to refine the search. The limited and fixed FMEA categories associated with the entries do not make the fine distinctions needed in the search. The approach assigns PRACA report titles to problem classes in the taxonomy. Each ontology class includes mapping words - near-synonyms naming different manifestations of that problem class. The mapping words for Problems, Entities and Functions are converted to a canonical form plus any of a small set of modifier words (e.g. non-uniformity NOT + UNIFORM.) The report titles are parsed as sentences if possible, or treated as a flat sequence of word tokens if parsing fails. When canonical forms in the title match mapping words, the PRACA entry is associated with the corresponding Problem, Entity or Function in the ontology. The user can search for types of failures associated with types of equipment, clustering by type of problem (e.g., all bearings found with problems of being uneven: rough, irregular, gritty ). The results could also be used for tagging PRACA report entries with rich metadata. This approach could also be applied to searching and tagging failure modes, failure effects and mitigations in FMEAs. In the pilot work, parsing 52K+ truncated titles (the test cases that were available), has resulted in identification of both a type of equipment and type of problem in about 75% of the cases. The results are displayed in a manner analogous to Google search results. The effort has also led to the enrichment of the taxonomy, adding some new categories and many new mapping words. Further work would make enhancements that have been identified for improving the clustering and further reducing the false alarm rate. (In searching for recurring problems, good clustering is more important than reducing false alarms). Searching complete PRACA reports should lead to immediate improvement.

A taxonomy of behaviour change methods: an Intervention Mapping approach.

PubMed

Kok, Gerjo; Gottlieb, Nell H; Peters, Gjalt-Jorn Y; Mullen, Patricia Dolan; Parcel, Guy S; Ruiter, Robert A C; Fernández, María E; Markham, Christine; Bartholomew, L Kay

2016-09-01

In this paper, we introduce the Intervention Mapping (IM) taxonomy of behaviour change methods and its potential to be developed into a coding taxonomy. That is, although IM and its taxonomy of behaviour change methods are not in fact new, because IM was originally developed as a tool for intervention development, this potential was not immediately apparent. Second, in explaining the IM taxonomy and defining the relevant constructs, we call attention to the existence of parameters for effectiveness of methods, and explicate the related distinction between theory-based methods and practical applications and the probability that poor translation of methods may lead to erroneous conclusions as to method-effectiveness. Third, we recommend a minimal set of intervention characteristics that may be reported when intervention descriptions and evaluations are published. Specifying these characteristics can greatly enhance the quality of our meta-analyses and other literature syntheses. In conclusion, the dynamics of behaviour change are such that any taxonomy of methods of behaviour change needs to acknowledge the importance of, and provide instruments for dealing with, three conditions for effectiveness for behaviour change methods. For a behaviour change method to be effective: (1) it must target a determinant that predicts behaviour; (2) it must be able to change that determinant; (3) it must be translated into a practical application in a way that preserves the parameters for effectiveness and fits with the target population, culture, and context. Thus, taxonomies of methods of behaviour change must distinguish the specific determinants that are targeted, practical, specific applications, and the theory-based methods they embody. In addition, taxonomies should acknowledge that the lists of behaviour change methods will be used by, and should be used by, intervention developers. Ideally, the taxonomy should be readily usable for this goal; but alternatively, it should be clear how the information in the taxonomy can be used in practice. The IM taxonomy satisfies these requirements, and it would be beneficial if other taxonomies would be extended to also meet these needs.

Speciation in Indo-Pacific swiftlets (Aves: Apodidae): integrating molecular and phenotypic data for a new provisional taxonomy of the Collocalia esculenta complex.

PubMed

Rheindt, Frank E; Christidis, Les; Norman, Janette A; Eaton, James A; Sadanandan, Keren R; Schodde, Richard

2017-04-07

White-bellied swiftlets of the Collocalia esculenta complex constitute a radiation of colony-breeding swifts distributed throughout the tropical Indo-Pacific region. Resolution of their taxonomy is challenging due to their morphological uniformity. To analyze the evolutionary history of this complex, we combine new biometric measurements and results from plumage assessment of museum specimens with novel as well as previously published molecular data. Together, this body of information constitutes the largest systematic dataset for white-bellied swiftlets yet compiled, drawn from 809 individuals belonging to 32 taxa for which new molecular, biometric, and/or plumage data are presented. We propose changing the classification of white-bellied swiftlets, for which two species are currently recognized, to elevate eight regional forms to species level, and we also describe two new subspecies. The ten taxa we recommend recognizing at the species level are: Collocalia linchi (Java to Lombok, Sumatran hills), C. dodgei (montane Borneo), C. natalis (Christmas Island), C. affinis (Greater Sundas, including the Thai-Malay Peninsula and Andaman-Nicobar Islands), C. marginata (Philippines), C. isonota (Philippines), C. sumbawae (west Lesser Sundas), C. neglecta (east Lesser Sundas), C. esculenta (Sulawesi, Moluccas, New Guinea, Bismarck Archipelago, Solomon Islands), and C. uropygialis (Vanuatu, New Caledonia). Future molecular and morphological work is needed to resolve questions of speciation and population affinities in the Philippines, Christmas Island, Wallacea and central Melanesia, and to shed light on historic diversification and patterns of gene flow in the complex.

HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts

PubMed Central

Laffy, Patrick W.; Wood-Charlson, Elisha M.; Turaev, Dmitrij; Weynberg, Karen D.; Botté, Emmanuelle S.; van Oppen, Madeleine J. H.; Webster, Nicole S.; Rattei, Thomas

2016-01-01

Abundant bioinformatics resources are available for the study of complex microbial metagenomes, however their utility in viral metagenomics is limited. HoloVir is a robust and flexible data analysis pipeline that provides an optimized and validated workflow for taxonomic and functional characterization of viral metagenomes derived from invertebrate holobionts. Simulated viral metagenomes comprising varying levels of viral diversity and abundance were used to determine the optimal assembly and gene prediction strategy, and multiple sequence assembly methods and gene prediction tools were tested in order to optimize our analysis workflow. HoloVir performs pairwise comparisons of single read and predicted gene datasets against the viral RefSeq database to assign taxonomy and additional comparison to phage-specific and cellular markers is undertaken to support the taxonomic assignments and identify potential cellular contamination. Broad functional classification of the predicted genes is provided by assignment of COG microbial functional category classifications using EggNOG and higher resolution functional analysis is achieved by searching for enrichment of specific Swiss-Prot keywords within the viral metagenome. Application of HoloVir to viral metagenomes from the coral Pocillopora damicornis and the sponge Rhopaloeides odorabile demonstrated that HoloVir provides a valuable tool to characterize holobiont viral communities across species, environments, or experiments. PMID:27375564

Construction of Military Intelligence Military Occupational Specialty Taxonomy

DTIC Science & Technology

1990-11-01

Ji ARI Research Note 91-10 Construction of Military Intelligence Military Occupational Specialty N Taxonomy IFrederick A. Muckler, Sally Seven, and...11. TITLE (Include Security Classification) Construction of Military Intelligence Military Occupational Specialty Taxonomy 12. PERSONAL AUTHOR(S...Continue on reverse if necessary and identify by block number) FIELD GROUP SUB-GROUP Military intelligence Evaluation taxonomy MOS restructuring

48 CFR 237.102-74 - Taxonomy for the acquisition of services.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 48 Federal Acquisition Regulations System 3 2012-10-01 2012-10-01 false Taxonomy for the... Service Contracts-General 237.102-74 Taxonomy for the acquisition of services. See PGI 237.102-74 for OUSD(AT&L) DPAP memorandum, “Taxonomy for the Acquisition of Services,” dated November 23, 2010. [75 FR...

48 CFR 237.102-74 - Taxonomy for the acquisition of services.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 48 Federal Acquisition Regulations System 3 2011-10-01 2011-10-01 false Taxonomy for the... Service Contracts-General 237.102-74 Taxonomy for the acquisition of services. See PGI 237.102-74 for OUSD(AT&L) DPAP memorandum, “Taxonomy for the Acquisition of Services,” dated November 23, 2010. [75 FR...

48 CFR 237.102-74 - Taxonomy for the acquisition of services.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 48 Federal Acquisition Regulations System 3 2013-10-01 2013-10-01 false Taxonomy for the... Service Contracts-General 237.102-74 Taxonomy for the acquisition of services. See PGI 237.102-74 for OUSD(AT&L) DPAP memorandum, “Taxonomy for the Acquisition of Services,” dated November 23, 2010. [75 FR...

Taxonomy of Learning Skills. Interim Technical Report for the Period February 1986-1987.

ERIC Educational Resources Information Center

Kyllonen, Patrick C.; Shute, Valerie J.

Questions concerning individual differences in learning ability may be more precisely addressed in light of an agreed-upon taxonomy of learning skills. Existing taxonomies are reviewed, and their shortcomings are described. A taxonomy is then proposed based on a synthesis of current thought consisting of four dimensions: the forms of knowledge;…

Distributed computer taxonomy based on O/S structure

NASA Technical Reports Server (NTRS)

Foudriat, Edwin C.

1985-01-01

The taxonomy considers the resource structure at the operating system level. It compares a communication based taxonomy with the new taxonomy to illustrate how the latter does a better job when related to the client's view of the distributed computer. The results illustrate the fundamental features and what is required to construct fully distributed processing systems. The problem of using network computers on the space station is addressed. A detailed discussion of the taxonomy is not given here. Information is given in the form of charts and diagrams that were used to illustrate a talk.

Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2018).

PubMed

King, Andrew M Q; Lefkowitz, Elliot J; Mushegian, Arcady R; Adams, Michael J; Dutilh, Bas E; Gorbalenya, Alexander E; Harrach, Balázs; Harrison, Robert L; Junglen, Sandra; Knowles, Nick J; Kropinski, Andrew M; Krupovic, Mart; Kuhn, Jens H; Nibert, Max L; Rubino, Luisa; Sabanadzovic, Sead; Sanfaçon, Hélène; Siddell, Stuart G; Simmonds, Peter; Varsani, Arvind; Zerbini, Francisco Murilo; Davison, Andrew J

2018-05-12

This article lists the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses in February 2018. A total of 451 species, 69 genera, 11 subfamilies, 9 families and one new order were added to the taxonomy. The current totals at each taxonomic level now stand at 9 orders, 131 families, 46 subfamilies, 803 genera and 4853 species. A change was made to the International Code of Virus Classification and Nomenclature to allow the use of the names of people in taxon names under appropriate circumstances. An updated Master Species List incorporating the approved changes was released in March 2018 ( https://talk.ictvonline.org/taxonomy/ ).

Keys to soil taxonomy by soil survey staff (sixth edition)

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1994-12-31

This publication, Keys to Soil Taxonomy, serves two purposes. It provides the taxonomic keys necessary for the classification of soils according to Soil Taxonomy in a form that can be used easily in the field, and it also acquaints users of Soil Taxonomy with recent changes in the classification system. This volume includes all revisions of the keys that have so far been approved, replacing the original keys in Soil Taxonomy: A Basic System of Soil Classification for Making and Interpreting Soil Surveys (1975), the work on which this abridged version, first published in 1983, is based. This publication incorporatesmore » all amendments approved to date and published in National Soil Taxonomy Handbook (NSTH) Issues 1-17.« less

Methods of Conceptual Clustering and their Relation to Numerical Taxonomy.

DTIC Science & Technology

1985-07-22

the conceptual clustering problem is to first solve theaggregation problem, and then the characterization problem. In machine learning, the...cluster- ings by first generating some number of possible clusterings. For each clustering generated, one calls a learning from examples subroutine, which...class 1 from class 2, and vice versa, only the first combination implies a partition over the set of theoretically possible objects. The first

Cuticular hydrocarbons and soldier defense secretions of Reticulitermes in southern California: a critical analysis of the taxonomy of the genus in North America

Treesearch

Lori J. Nelson; Laurence G. Cool; Christopher W. Solek; Michael I. Haverty

2008-01-01

Cuticular hydrocarbons (CHC) and soldier defense secretions (SDS) were characterized for collections of Reticulitermes from six counties (Los Angeles, Orange, Riverside, San Bernardino, San Diego, and Santa Barbara) in southern California. Collection sites included the type locality for R. hesperus, Lake Arrowhead (formerly known as Little Bear Lake) in the San...

Training and Personnel Systems Technology R and D Program Description FY 93

DTIC Science & Technology

1992-07-24

instructional strategies provide the best training in ICAT applications, and (c) demonstration of microcomputer authoring techniques for rapid development...learning strategies for language training, (b) develop a behavioral taxonomy to evaluate Military Intelligence (MI) performance and to characterize the...training requirements for collective tasks. In FY93, plans are to: (a) develop training strategies for sustaining command and control skills, and (b

Physical studies of small asteroids. I - Lightcurves and taxonomy of 10 asteroids

NASA Technical Reports Server (NTRS)

Wisniewski, W. Z.

1991-01-01

Photometric observations of 10 small asteroids (10 km or less in diameter), obtained using the 1.5-m Mt. Lemmon and 2.3-m Kitt Peak telescopes of the University of Arizona during 1986-1987, are reported. The instrumentation and data-reduction techniques employed are described, and the results are presented in tables and light-curve plots and briefly characterized.

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.

PubMed

McDonald, Daniel; Price, Morgan N; Goodrich, Julia; Nawrocki, Eric P; DeSantis, Todd Z; Probst, Alexander; Andersen, Gary L; Knight, Rob; Hugenholtz, Philip

2012-03-01

Reference phylogenies are crucial for providing a taxonomic framework for interpretation of marker gene and metagenomic surveys, which continue to reveal novel species at a remarkable rate. Greengenes is a dedicated full-length 16S rRNA gene database that provides users with a curated taxonomy based on de novo tree inference. We developed a 'taxonomy to tree' approach for transferring group names from an existing taxonomy to a tree topology, and used it to apply the Greengenes, National Center for Biotechnology Information (NCBI) and cyanoDB (Cyanobacteria only) taxonomies to a de novo tree comprising 408,315 sequences. We also incorporated explicit rank information provided by the NCBI taxonomy to group names (by prefixing rank designations) for better user orientation and classification consistency. The resulting merged taxonomy improved the classification of 75% of the sequences by one or more ranks relative to the original NCBI taxonomy with the most pronounced improvements occurring in under-classified environmental sequences. We also assessed candidate phyla (divisions) currently defined by NCBI and present recommendations for consolidation of 34 redundantly named groups. All intermediate results from the pipeline, which includes tree inference, jackknifing and transfer of a donor taxonomy to a recipient tree (tax2tree) are available for download. The improved Greengenes taxonomy should provide important infrastructure for a wide range of megasequencing projects studying ecosystems on scales ranging from our own bodies (the Human Microbiome Project) to the entire planet (the Earth Microbiome Project). The implementation of the software can be obtained from http://sourceforge.net/projects/tax2tree/.

Student perceptions regarding the usefulness of explicit discussion of "Structure of the Observed Learning Outcome" taxonomy.

PubMed

Prakash, E S; Narayan, K A; Sethuraman, K R

2010-09-01

One method of grading responses of the descriptive type is by using Structure of Observed Learning Outcomes (SOLO) taxonomy. The basis of this study was the expectation that if students were oriented to SOLO taxonomy, it would provide them an opportunity to understand some of the factors that teachers consider while grading descriptive responses and possibly develop strategies to improve scores. We first sampled the perceptions of 68 second-year undergraduate medical students doing the Respiratory System course regarding the usefulness of explicit discussion of SOLO taxonomy. Subsequently, in a distinct cohort of 20 second-year medical students doing the Central Nervous System course, we sought to determine whether explicit illustration of SOLO taxonomy combined with some advice on better answering descriptive test questions (to an experimental group) resulted in better student scores in a continuous assessment test compared with providing advice for better answering test questions but without any reference to SOLO taxonomy (the control group). Student ratings of the clarity of the presentation on SOLO taxonomy appeared satisfactory to the authors, as was student understanding of our presentation. The majority of participants indicated that knowledge of SOLO taxonomy would help them study and prepare better answers for questions of the descriptive type. Although scores in the experimental and control group were comparable, this experience nonetheless provided us with the motivation to orient students to SOLO taxonomy early on in the medical program and further research factors that affect students' development of strategies based on knowledge of SOLO taxonomy.

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

PubMed Central

McDonald, Daniel; Price, Morgan N; Goodrich, Julia; Nawrocki, Eric P; DeSantis, Todd Z; Probst, Alexander; Andersen, Gary L; Knight, Rob; Hugenholtz, Philip

2012-01-01

Reference phylogenies are crucial for providing a taxonomic framework for interpretation of marker gene and metagenomic surveys, which continue to reveal novel species at a remarkable rate. Greengenes is a dedicated full-length 16S rRNA gene database that provides users with a curated taxonomy based on de novo tree inference. We developed a ‘taxonomy to tree' approach for transferring group names from an existing taxonomy to a tree topology, and used it to apply the Greengenes, National Center for Biotechnology Information (NCBI) and cyanoDB (Cyanobacteria only) taxonomies to a de novo tree comprising 408 315 sequences. We also incorporated explicit rank information provided by the NCBI taxonomy to group names (by prefixing rank designations) for better user orientation and classification consistency. The resulting merged taxonomy improved the classification of 75% of the sequences by one or more ranks relative to the original NCBI taxonomy with the most pronounced improvements occurring in under-classified environmental sequences. We also assessed candidate phyla (divisions) currently defined by NCBI and present recommendations for consolidation of 34 redundantly named groups. All intermediate results from the pipeline, which includes tree inference, jackknifing and transfer of a donor taxonomy to a recipient tree (tax2tree) are available for download. The improved Greengenes taxonomy should provide important infrastructure for a wide range of megasequencing projects studying ecosystems on scales ranging from our own bodies (the Human Microbiome Project) to the entire planet (the Earth Microbiome Project). The implementation of the software can be obtained from http://sourceforge.net/projects/tax2tree/. PMID:22134646

DNA barcoding and traditional taxonomy: an integrated approach for biodiversity conservation.

PubMed

Sheth, Bhavisha P; Thaker, Vrinda S

2017-07-01

Biological diversity is depleting at an alarming rate. Additionally, a vast amount of biodiversity still remains undiscovered. Taxonomy has been serving the purpose of describing, naming, and classifying species for more than 250 years. DNA taxonomy and barcoding have accelerated the rate of this process, thereby providing a tool for conservation practice. DNA barcoding and traditional taxonomy have their own inherent merits and demerits. The synergistic use of both methods, in the form of integrative taxonomy, has the potential to contribute to biodiversity conservation in a pragmatic timeframe and overcome their individual drawbacks. In this review, we discuss the basics of both these methods of biological identification (traditional taxonomy and DNA barcoding), the technical advances in integrative taxonomy, and future trends. We also present a comprehensive compilation of published examples of integrative taxonomy that refer to nine topics within biodiversity conservation. Morphological and molecular species limits were observed to be congruent in ∼41% of the 58 source studies. The majority of the studies highlighted the description of cryptic diversity through the use of molecular data, whereas research areas like endemism, biological invasion, and threatened species were less discussed in the literature.

Developing an integrative level-dimensional taxonomy model for rehabilitation psychology research and practice.

PubMed

Mermis, Bernie J

2018-02-01

The present article concerns the development of a taxonomy model for organizing and classifying all aspects of rehabilitation psychology from an integrative level-dimensional conceptualization. This conceptualization is presented as an alternative to a primarily categorical approach to classification. It also assumes a continuity perspective for all aspects of behavior and experience. Development of this taxonomy model involves organizing information relevant to levels/domains of all aspects of behavior and experience, and to constructs describing their underlying components conceptually as well as dimensions which constitute the measurable basis of constructs. A taxonomy model with levels/domains, representative examples of constructs and dimensions is presented as a foundation for development of the present taxonomy model, with specific relevance to rehabilitation psychology. This integrative level-dimensional taxonomy model provides a structure for organizing all aspects of rehabilitation psychology relevant to understanding, assessing, and influencing the rehabilitation process. Suggestions for development and research are provided for the taxonomy model. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

GEM Building Taxonomy (Version 2.0)

USGS Publications Warehouse

Brzev, S.; Scawthorn, C.; Charleson, A.W.; Allen, L.; Greene, M.; Jaiswal, Kishor; Silva, V.

2013-01-01

/7/8/IRRE9/10/RSH3+RWO211/FW12/13/ which can be read as (1) Direction = [DX or DY] (the building has the same lateral load-resisting system in both directions); (2) Material = [Unreinforced Masonry + solid fired clay bricks + cement: lime mortar]; (3) Lateral Load-Resisting System = [Wall]; (4) Date of construction = [pre-1939]; (5) Heaight = [exactly 2 storeys]; (6) Occupancy = [residential, unknown type]; (7) Building Position = [unknown = no entry]; (8) Shape of building plan = [unknown = no entry]; (9) Structural irregularity = [regular]; (10) Exterior walls = [unknown = no entry]; (11) Roof = [Shape: pitched and hipped, Roof covering: clay tiles, Roof system material: wood, Roof system type: wood trusses]; (12) Floor = [Floor system: Wood, unknown]; (13) Foundation = [unknown = no entry]. Mapping of GEM Building Taxonomy to selected taxonomies is included in the report -- for example, the above building would be referenced by previous structural taxonomies as: PAGER-STR as UFB or UFB4, by the World Housing Encyclopedia as 7 or 8 and by the European Macroseismic Scale (98) as M5. The Building Taxonomy data model is highly flexible and has been incorporated within a relational database architecture. Due to its ability to represent building typologies using a shorthand form, it is also possible to use the taxonomy for non-database applications, and we discuss possible application of adaptation for Building Information Modelling (BIM) systems, and for the insurance industry. The GEM Building Taxonomy was independently evaluated and tested by the Earthquake Engineering Research Institute (EERI), which received 217 TaxT reports from 49 countries, representing a wide range of building typologies, including single and multi-storey buildings, reinforced and unreinforced masonry, confined masonry, concrete, steel, wood, and earthern buildings used for residential, commercial, industrial, and educational occupancy. Based on these submissions and other feedback, the EERI team validated that the GEM Building Taxonomy is highly functional, robust and able to describe different buildings around the world. The GEM Building Taxonomy is accompanied by supplementary resources. All terms have been explained in a companion online Glossary, which provides both text and graphic descriptions. The Taxonomy is accompanied by TaxT, a computer application that enables a user record information about a building or a building typology using the attributes of the GEM Building Taxonomy v2.0. TaxT can generate a taxonomy string and enable a user to generate a report in PDF format which summarizes the attribute values (s)he has chosen as representative of the building typology under consideration. The report concludes with recommendations for future development of the GEM Building Taxonomy. Appendices provide the detailed GEM Building Taxonomy tables and additional resource, as well as mappings to other taxonomies.

Teaching the New Taxonomy.

ERIC Educational Resources Information Center

Texley, Juliana

2002-01-01

Points out that today's taxonomy is very different than what many biology teachers learned when they were in school. Traces the history of some of the changes and describes the current taxonomy. (DDR)

Corpus-based Customization for an Ontology

DOE Office of Scientific and Technical Information (OSTI.GOV)

2010-09-14

CCAT scans a corpus of text for terms, and computes lexical similarity between corpus terms and taxonomy terms. Based on a set of metrics and a learning algorithm, the system inserts corpus terms into the taxonomy. Conversely, terms from the taxonomy are disambiguated based on the text in the corpus. Unused terms are discarded, and infrequently used senses of terms are collapsed to make the taxonomy more manageable.

Virtual Workshop Environment (VWE): A Taxonomy and Service Oriented Architecture (SOA) Framework for Modularized Virtual Learning Environments (VLE)--Applying the Learning Object Concept to the VLE

ERIC Educational Resources Information Center

Paulsson, Fredrik; Naeve, Ambjorn

2006-01-01

Based on existing Learning Object taxonomies, this article suggests an alternative Learning Object taxonomy, combined with a general Service Oriented Architecture (SOA) framework, aiming to transfer the modularized concept of Learning Objects to modularized Virtual Learning Environments. The taxonomy and SOA-framework exposes a need for a clearer…

A taxonomy of behaviour change methods: an Intervention Mapping approach

PubMed Central

Kok, Gerjo; Gottlieb, Nell H.; Peters, Gjalt-Jorn Y.; Mullen, Patricia Dolan; Parcel, Guy S.; Ruiter, Robert A.C.; Fernández, María E.; Markham, Christine; Bartholomew, L. Kay

2016-01-01

ABSTRACT In this paper, we introduce the Intervention Mapping (IM) taxonomy of behaviour change methods and its potential to be developed into a coding taxonomy. That is, although IM and its taxonomy of behaviour change methods are not in fact new, because IM was originally developed as a tool for intervention development, this potential was not immediately apparent. Second, in explaining the IM taxonomy and defining the relevant constructs, we call attention to the existence of parameters for effectiveness of methods, and explicate the related distinction between theory-based methods and practical applications and the probability that poor translation of methods may lead to erroneous conclusions as to method-effectiveness. Third, we recommend a minimal set of intervention characteristics that may be reported when intervention descriptions and evaluations are published. Specifying these characteristics can greatly enhance the quality of our meta-analyses and other literature syntheses. In conclusion, the dynamics of behaviour change are such that any taxonomy of methods of behaviour change needs to acknowledge the importance of, and provide instruments for dealing with, three conditions for effectiveness for behaviour change methods. For a behaviour change method to be effective: (1) it must target a determinant that predicts behaviour; (2) it must be able to change that determinant; (3) it must be translated into a practical application in a way that preserves the parameters for effectiveness and fits with the target population, culture, and context. Thus, taxonomies of methods of behaviour change must distinguish the specific determinants that are targeted, practical, specific applications, and the theory-based methods they embody. In addition, taxonomies should acknowledge that the lists of behaviour change methods will be used by, and should be used by, intervention developers. Ideally, the taxonomy should be readily usable for this goal; but alternatively, it should be clear how the information in the taxonomy can be used in practice. The IM taxonomy satisfies these requirements, and it would be beneficial if other taxonomies would be extended to also meet these needs. PMID:26262912

Morphometric and molecular characterization of fungus Pestalotiopsis using nuclear ribosomal DNA analysis.

PubMed

Gehlot, Praveen; Singh, S K; Pathak, Rakesh

2012-09-01

Taxonomy of the fungus Pestalotiopsis based on morphological characters has been equivocal. Molecular characterization often Pestalotiopsis species was done based on nuclear ribosomal DNA internal transcribed spacer (ITS) amplifications. Results of the analyses showed that species of genus Pestalotiopsis are monophyletic. We report ITS length variations, single nucleotide polymorphisms (SNPs) and insertions/ deletions (INDELS) among ten species of Pestalotiopsis that did not cause any phylogenetic error at either genus or species designation levels. New gene sequences have been assigned (Gen Accession numbers from HM 190146 to HM 190155) by the National Centre for Biotechnology Information, USA.

Infra-specific folk taxonomy in sorghum (Sorghum bicolor (L.) Moench) in Ethiopia: folk nomenclature, classification, and criteria

PubMed Central

Mekbib, Firew

2007-01-01

Background Sorghum is one of the main staple food crops for the poorest and most food insecure people of the world. As Ethiopia is the centre of origin and diversity for sorghum, the crop has been cultivated for many thousands of years. Hence, indigenous knowledge based sorghum classification and naming has a long tradition. Methods In order to assess folk taxonomy, various research methods were employed, including, focus group interviews with 360 farmers, direct on-farm participatory monitoring with 120 farmers, key informant interviews with 60 farmers and development agents and semi-structured interviews with 250 farmers. In addition, diversity fairs were conducted with over 1200 farmers. Assessment of folk taxonomy consistency was assessed by 30 farmers' evaluation of 44 folk species. Results Farmers have been growing sorghum for at least 500 years (20 generations). Sorghum is named as Mishinga in the region. Farmers used twenty five morphological, sixty biotic and abiotic and twelve use-related traits in folk taxonomy of sorghum. Farmers classified their gene-pool by hierarchical classifications into parts that represented distinguishable groups of accessions. Folk taxonomy trees were generated in the highland, intermediate and lowland sorghum ecologies. Over 78 folk species have been identified. The folk species were named after morphological, use-related and breeding methodology used. Relative distribution of folk species over the region, folk taxonomy consistency, and comparison of folk and formal taxonomy are described. Conclusion New folk taxonomy descriptors have been identified and suggested to be used as formal taxonomy descriptors. It is concluded that integrated folk-formal taxonomy has to be used for enhanced collection, characterisation and utilization of on farm genetic resources. PMID:18162135

Infra-specific folk taxonomy in sorghum (Sorghum bicolor (L.) Moench) in Ethiopia: folk nomenclature, classification, and criteria.

PubMed

Mekbib, Firew

2007-12-27

Sorghum is one of the main staple food crops for the poorest and most food insecure people of the world. As Ethiopia is the centre of origin and diversity for sorghum, the crop has been cultivated for many thousands of years. Hence, indigenous knowledge based sorghum classification and naming has a long tradition. In order to assess folk taxonomy, various research methods were employed, including, focus group interviews with 360 farmers, direct on-farm participatory monitoring with 120 farmers, key informant interviews with 60 farmers and development agents and semi-structured interviews with 250 farmers. In addition, diversity fairs were conducted with over 1200 farmers. Assessment of folk taxonomy consistency was assessed by 30 farmers' evaluation of 44 folk species. Farmers have been growing sorghum for at least 500 years (20 generations). Sorghum is named as Mishinga in the region. Farmers used twenty five morphological, sixty biotic and abiotic and twelve use-related traits in folk taxonomy of sorghum. Farmers classified their gene-pool by hierarchical classifications into parts that represented distinguishable groups of accessions. Folk taxonomy trees were generated in the highland, intermediate and lowland sorghum ecologies. Over 78 folk species have been identified. The folk species were named after morphological, use-related and breeding methodology used. Relative distribution of folk species over the region, folk taxonomy consistency, and comparison of folk and formal taxonomy are described. New folk taxonomy descriptors have been identified and suggested to be used as formal taxonomy descriptors. It is concluded that integrated folk-formal taxonomy has to be used for enhanced collection, characterisation and utilization of on farm genetic resources.

What influences the impact of pressure ulcers on health-related quality of life? A qualitative patient-focused exploration of contributory factors.

PubMed

Gorecki, C; Nixon, J; Madill, A; Firth, J; Brown, J M

2012-02-01

With the recognition of health-related quality of life (HRQL) as an important and relevant outcome in pressure ulceration, it is important to gain better understanding of the complex relationship among the various factors that affect it. A problem with existing literature in this area is that the impact of having a pressure ulcer on HRQL is combined conceptually with contributory factors which may influence outcome. This study identified contributory factors affecting pressure ulcer-related HRQL and explored interrelationships between factors based on views of adults with pressure ulcers. We obtained patient-reported qualitative data through semi-structured interviews with 30 patients with pressure ulcers recruited from hospital and community settings around England and Northern Ireland. Patients described how pressure ulcers affected their lives by recounting specific relevant events. Events (patient-reported issues) were sorted into categories and data framework analysed to produce a taxonomy of contributory factors. Inter-rater reliability established the extent of agreement between two independent raters. We identified 16 contributory factors, into two theme taxonomy: experience-of-care and individual-patient factors, defined by descriptive components. Our taxonomy is a comprehensive theoretical model of factors that contribute to pressure ulcer-related HRQL. We have also identified further research priorities to inform clinical practice. Copyright © 2011 Tissue Viability Society. Published by Elsevier Ltd. All rights reserved.

An Updated Taxonomy and a Graphical Summary Tool for Optimal Classification and Comprehension of Omics Research.

PubMed

Pirih, Nina; Kunej, Tanja

2018-05-01

The volume of publications and the type of research approaches used in omics system sciences are vast and continue to expand rapidly. This increased complexity and heterogeneity of omics data are challenging data extraction, sensemaking, analyses, knowledge translation, and interpretation. An extended and dynamic taxonomy for the classification and summary of omics studies are essential. We present an updated taxonomy for classification of omics research studies based on four criteria: (1) type and number of genomic loci in a research study, (2) number of species and biological samples, (3) the type of omics technology (e.g., genomics, transcriptomics, and proteomics) and omics technology application type (e.g., pharmacogenomics and nutrigenomics), and (4) phenotypes. In addition, we present a graphical summary approach that enables the researchers to define the main characteristics of their study in a single figure, and offers the readers to rapidly grasp the published study and omics data. We searched the PubMed and the Web of Science from 09/2002 to 02/2018, including research and review articles, and identified 90 scientific publications. We propose a call toward omics studies' standardization for reporting in scientific literature. We anticipate the proposed classification scheme will usefully contribute to improved classification of published reports in genomics and other omics fields, and help data extraction from publications for future multiomics data integration.

Pedoinformatics Approach to Soil Text Analytics

NASA Astrophysics Data System (ADS)

Furey, J.; Seiter, J.; Davis, A.

2017-12-01

The several extant schema for the classification of soils rely on differing criteria, but the major soil science taxonomies, including the United States Department of Agriculture (USDA) and the international harmonized World Reference Base for Soil Resources systems, are based principally on inferred pedogenic properties. These taxonomies largely result from compiled individual observations of soil morphologies within soil profiles, and the vast majority of this pedologic information is contained in qualitative text descriptions. We present text mining analyses of hundreds of gigabytes of parsed text and other data in the digitally available USDA soil taxonomy documentation, the Soil Survey Geographic (SSURGO) database, and the National Cooperative Soil Survey (NCSS) soil characterization database. These analyses implemented iPython calls to Gensim modules for topic modelling, with latent semantic indexing completed down to the lowest taxon level (soil series) paragraphs. Via a custom extension of the Natural Language Toolkit (NLTK), approximately one percent of the USDA soil series descriptions were used to train a classifier for the remainder of the documents, essentially by treating soil science words as comprising a novel language. While location-specific descriptors at the soil series level are amenable to geomatics methods, unsupervised clustering of the occurrence of other soil science words did not closely follow the usual hierarchy of soil taxa. We present preliminary phrasal analyses that may account for some of these effects.

A Taxonomy of Delivery and Documentation Deviations During Delivery of High-Fidelity Simulations.

PubMed

McIvor, William R; Banerjee, Arna; Boulet, John R; Bekhuis, Tanja; Tseytlin, Eugene; Torsher, Laurence; DeMaria, Samuel; Rask, John P; Shotwell, Matthew S; Burden, Amanda; Cooper, Jeffrey B; Gaba, David M; Levine, Adam; Park, Christine; Sinz, Elizabeth; Steadman, Randolph H; Weinger, Matthew B

2017-02-01

We developed a taxonomy of simulation delivery and documentation deviations noted during a multicenter, high-fidelity simulation trial that was conducted to assess practicing physicians' performance. Eight simulation centers sought to implement standardized scenarios over 2 years. Rules, guidelines, and detailed scenario scripts were established to facilitate reproducible scenario delivery; however, pilot trials revealed deviations from those rubrics. A taxonomy with hierarchically arranged terms that define a lack of standardization of simulation scenario delivery was then created to aid educators and researchers in assessing and describing their ability to reproducibly conduct simulations. Thirty-six types of delivery or documentation deviations were identified from the scenario scripts and study rules. Using a Delphi technique and open card sorting, simulation experts formulated a taxonomy of high-fidelity simulation execution and documentation deviations. The taxonomy was iteratively refined and then tested by 2 investigators not involved with its development. The taxonomy has 2 main classes, simulation center deviation and participant deviation, which are further subdivided into as many as 6 subclasses. Inter-rater classification agreement using the taxonomy was 74% or greater for each of the 7 levels of its hierarchy. Cohen kappa calculations confirmed substantial agreement beyond that expected by chance. All deviations were classified within the taxonomy. This is a useful taxonomy that standardizes terms for simulation delivery and documentation deviations, facilitates quality assurance in scenario delivery, and enables quantification of the impact of deviations upon simulation-based performance assessment.

Learning to change taxonomies

NASA Astrophysics Data System (ADS)

Eneva, Elena; Petrushin, Valery A.

2002-03-01

Taxonomies are valuable tools for structuring and representing our knowledge about the world. They are widely used in many domains, where information about species, products, customers, publications, etc. needs to be organized. In the absence of standards, many taxonomies of the same entities can co-exist. A problem arises when data categorized in a particular taxonomy needs to be used by a procedure (methodology or algorithm) that uses a different taxonomy. Usually, a labor-intensive manual approach is used to solve this problem. This paper describes a machine learning approach which aids domain experts in changing taxonomies. It allows learning relationships between two taxonomies and mapping the data from one taxonomy into another. The proposed approach uses decision trees and bootstrapping for learning mappings of instances from the source to the target taxonomies. A C4.5 decision tree classifier is trained on a small manually labeled training set and applied to a randomly selected sample from the unlabeled data. The classification results are analyzed and the misclassified items are corrected and all items are added to the training set. This procedure is iterated until unlabeled data is available or an acceptable error rate is reached. In the latter case the last classifier is used to label all the remaining data. We test our approach on a database of products obtained from as grocery store chain and find that it performs well, reaching 92.6% accuracy while requiring the human expert to explicitly label only 18% of the entire data.

Taxonomy for Education and Training in Clinical Neuropsychology: past, present, and future.

PubMed

Sperling, Scott A; Cimino, Cynthia R; Stricker, Nikki H; Heffelfinger, Amy K; Gess, Jennifer L; Osborn, Katie E; Roper, Brad L

2017-07-01

Historically, the clinical neuropsychology training community has not clearly or consistently defined education or training opportunities. The lack of consistency has limited students' and trainees' ability to accurately assess and compare the intensity of neuropsychology-specific training provided by programs. To address these issues and produce greater 'truth in advertising' across programs, CNS, with SCN's Education Advisory Committee (EAC), ADECN, AITCN, and APPCN constructed a specialty-specific taxonomy, namely, the Taxonomy for Education and Training in Clinical Neuropsychology. The taxonomy provides consensus in the description of training offered by doctoral, internship, and postdoctoral programs, as well as at the post-licensure stage. Although the CNS approved the taxonomy in February 2015, many programs have not adopted its language. Increased awareness of the taxonomy and the reasons behind its development and structure, as well as its potential benefits, are warranted. In 2016, a working group of clinical neuropsychologists from the EAC and APPCN, all authors of this manuscript, was created and tasked with disseminating information about the taxonomy. Group members held regular conference calls, leading to the generation of this manuscript. This manuscript is the primary byproduct of the working group. Its purpose is to (1) outline the history behind the development of the taxonomy, (2) detail its structure and utility, (3) address the expected impact of its adoption, and (4) call for its adoption across training programs. This manuscript outlines the development and structure of the clinical neuropsychology taxonomy and addresses the need for its adoption across training programs.

Towards an Artificial Space Object Taxonomy

DTIC Science & Technology

2013-09-01

demonstrate how to implement this taxonomy in Figaro, an open source probabilistic programming language. 2. INTRODUCTION Currently, US Space Command...Taxonomy 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7...demonstrate how to implement this taxonomy in Figaro, an open source probabilistic programming language. 15. SUBJECT TERMS 16. SECURITY CLASSIFICATION OF

Commercial Mobile Alert Service (CMAS) Alerting Pipeline Taxonomy

DTIC Science & Technology

2012-03-01

for the consumer at the mo- ment but will soon become a commoditized, basic requirement. For example, as the baby boomers grow older, mobile services...Commercial Mobile Alert Service (CMAS) Alerting Pipeline Taxonomy The WEA Project Team March 2012 SPECIAL REPORT CMU/SEI-2012-TR-019 CERT...report presents a taxonomy developed for the Commercial Mobile Alert Service (CMAS). The CMAS Alerting Pipeline Taxonomy is a hierarchical classification

Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV)

PubMed Central

Dempsey, Donald M; Hendrickson, Robert Curtis; Orton, Richard J; Siddell, Stuart G; Smith, Donald B

2018-01-01

Abstract The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa; maintaining a database detailing the currently approved taxonomy; and providing the database, supporting proposals, and other virus-related information from an open-access, public web site. The ICTV web site (http://ictv.global) provides access to the current taxonomy database in online and downloadable formats, and maintains a complete history of virus taxa back to the first release in 1971. The ICTV has also published the ICTV Report on Virus Taxonomy starting in 1971. This Report provides a comprehensive description of all virus taxa covering virus structure, genome structure, biology and phylogenetics. The ninth ICTV report, published in 2012, is available as an open-access online publication from the ICTV web site. The current, 10th report (http://ictv.global/report/), is being published online, and is replacing the previous hard-copy edition with a completely open access, continuously updated publication. No other database or resource exists that provides such a comprehensive, fully annotated compendium of information on virus taxa and taxonomy. PMID:29040670

A Taxonomy of Network Centric Warfare Architectures

DTIC Science & Technology

2008-01-01

mound structure emerges as a result of the termites following very simple rules, and exchanging very simple pheromone signals (Solé & Goodwin 2000...only fairly simple decisions.” For example, in far northern Australia, “magnetic termites ” build large termite mounds which are oriented north-south...and contain a complex ventilation system which controls temperature, humidity, and oxygen levels. But termite brains are too small to store a plan

Ongoing Speciation and Gene Flow between Taxonomically Challenging Trochulus Species Complex (Gastropoda: Hygromiidae).

PubMed

Proćków, Małgorzata; Strzała, Tomasz; Kuźnik-Kowalska, Elżbieta; Proćków, Jarosław; Mackiewicz, Paweł

2017-01-01

Geographical isolation, selection and genetic drift can cause the geographical diversification of populations and lead to speciation. Land snail species in the genus Trochulus show overlaps in geographical ranges as well as in morphology, but genetic data do not always support the species-level taxonomy based on morphological characters. Such a group offers an excellent opportunity to explore the processes involved. We have addressed the problem by determining the status of the restricted endemic T. graminicola within the larger context of Trochulus taxonomy. We used an integrated approach based on morphological features, ecological preferences and two molecular markers: mitochondrial COI sequences and microsatellites. Comparison of these results demonstrated: (i) conchological distinction of T. striolatus and T. sericeus; (ii) anatomical, ecological and genetic differentiation of T. graminicola and (iii) concordance between morphological characters and mtDNA markers in T. striolatus. Moreover, our data showed an intricate evolutionary history within the genus Trochulus, which can be best explained by: (i) recent or ongoing gene flow between taxa or (ii) their large ancestral polymorphism. Both of these hypotheses suggest that diversification within this group of snails has occurred relatively recently. The mismatches between species defined on morphology and on molecular genetics indicate the complexity of the processes involved in the diversification of this genus.

Ongoing Speciation and Gene Flow between Taxonomically Challenging Trochulus Species Complex (Gastropoda: Hygromiidae)

PubMed Central

Proćków, Małgorzata; Strzała, Tomasz; Kuźnik-Kowalska, Elżbieta; Proćków, Jarosław; Mackiewicz, Paweł

2017-01-01

Geographical isolation, selection and genetic drift can cause the geographical diversification of populations and lead to speciation. Land snail species in the genus Trochulus show overlaps in geographical ranges as well as in morphology, but genetic data do not always support the species-level taxonomy based on morphological characters. Such a group offers an excellent opportunity to explore the processes involved. We have addressed the problem by determining the status of the restricted endemic T. graminicola within the larger context of Trochulus taxonomy. We used an integrated approach based on morphological features, ecological preferences and two molecular markers: mitochondrial COI sequences and microsatellites. Comparison of these results demonstrated: (i) conchological distinction of T. striolatus and T. sericeus; (ii) anatomical, ecological and genetic differentiation of T. graminicola and (iii) concordance between morphological characters and mtDNA markers in T. striolatus. Moreover, our data showed an intricate evolutionary history within the genus Trochulus, which can be best explained by: (i) recent or ongoing gene flow between taxa or (ii) their large ancestral polymorphism. Both of these hypotheses suggest that diversification within this group of snails has occurred relatively recently. The mismatches between species defined on morphology and on molecular genetics indicate the complexity of the processes involved in the diversification of this genus. PMID:28107432

A singular value decomposition approach for improved taxonomic classification of biological sequences

PubMed Central

2011-01-01

Background Singular value decomposition (SVD) is a powerful technique for information retrieval; it helps uncover relationships between elements that are not prima facie related. SVD was initially developed to reduce the time needed for information retrieval and analysis of very large data sets in the complex internet environment. Since information retrieval from large-scale genome and proteome data sets has a similar level of complexity, SVD-based methods could also facilitate data analysis in this research area. Results We found that SVD applied to amino acid sequences demonstrates relationships and provides a basis for producing clusters and cladograms, demonstrating evolutionary relatedness of species that correlates well with Linnaean taxonomy. The choice of a reasonable number of singular values is crucial for SVD-based studies. We found that fewer singular values are needed to produce biologically significant clusters when SVD is employed. Subsequently, we developed a method to determine the lowest number of singular values and fewest clusters needed to guarantee biological significance; this system was developed and validated by comparison with Linnaean taxonomic classification. Conclusions By using SVD, we can reduce uncertainty concerning the appropriate rank value necessary to perform accurate information retrieval analyses. In tests, clusters that we developed with SVD perfectly matched what was expected based on Linnaean taxonomy. PMID:22369633

Taxonaut: an application software for comparative display of multiple taxonomies with a use case of GBIF Species API.

PubMed

Ytow, Nozomi

2016-01-01

The Species API of the Global Biodiversity Information Facility (GBIF) provides public access to taxonomic data aggregated from multiple data sources. Each data source follows its own classification which can be inconsistent with classifications from other sources. Even with a reference classification e.g. the GBIF Backbone taxonomy, a comprehensive method to compare classifications in the data aggregation is essential, especially for non-expert users. A Java application was developed to compare multiple taxonomies graphically using classification data acquired from GBIF's ChecklistBank via the GBIF Species API. It uses a table to display taxonomies where each column represents a taxonomy under comparison, with an aligner column to organise taxa by name. Each cell contains the name of a taxon if the classification in that column contains the name. Each column also has a cell showing the hierarchy of the taxonomy by a folder metaphor where taxa are aligned and synchronised in the aligner column. A set of those comparative tables shows taxa categorised by relationship between taxonomies. The result set is also available as tables in an Excel format file.

The Development of a Taxonomy of Wrongdoing in Medical Practice and Research

PubMed Central

DuBois, James M.; Yates, Elena; Vasher, Meghan

2011-01-01

“Ethical disasters” or egregious violations of professional ethics in medicine often receive substantial amounts of publicity, leading to mistrust of the medical system. Efforts to understand wrongdoing in medical practice and research are hampered by the absence of a clear taxonomy. This article describes the authors’ process of developing a taxonomy based on: (1) reviews of academic literature, ethics codes, government regulations, and cases of wrongdoing; (2) consultation with experts in health law and healthcare ethics; and (3) application of the taxonomy to published cases of wrongdoing in medical research and practice. The resulting taxonomy includes 14 categories of wrongdoing in medical practice, and 15 categories of wrongdoing in medical research. This taxonomy may be useful to oversight bodies, researchers who seek to understand and reduce the prevalence of wrongdoing in medicine, and librarians who index literature on wrongdoing. PMID:22176853

Modeling the Object-Oriented Space Through Validated Measures

NASA Technical Reports Server (NTRS)

Neal, Ralph D.

1996-01-01

In order to truly understand software and the software development process, software measurement must be better understood. A beginning step toward a better understanding of software measurement is the categorization of the measurements by some meaningful taxonomy. The most meaningful taxonomy would capture the basic nature of the subject oriented (O-O) space. The interesting characteristics of object oriented software offer a starting point for such a categorization of measures. A taxonomy has been developed based on fourteen characteristics of object-oriented software gathered from the literature This taxonomy allows us to easily see gaps and redundancies in the O-O measures. The taxonomy also clearly differentiates among taxa so that there is no ambiguity as to the taxon to which a measure belongs. The taxonomy has been populated with thirty-two measures that have been validated in the narrow sense of Fenton, using measurement theory with Zuse's augmentation.

Comprehensive Social Skills Taxonomy: Development and Application.

PubMed

Kauffman, Nancy A; Kinnealey, Moya

2015-01-01

We developed a comprehensive social skills taxonomy based on archived children's social skill goal sheets, and we applied the taxonomy to 6,897 goals of children in 6 diagnostic categories to explore patterns related to diagnosis. We used a grounded theory approach to code and analyze social skill goals and develop the taxonomy. Multivariate analysis of variance and Tukey post hoc honestly significant difference test were used to analyze differences in social skill needs among diagnostic groups. We developed a taxonomy of 7 social skill constructs or categories, descriptions, and behavioral indicators. The 7 social skill categories were reflected across 6 diagnostic groups, and differences in social skill needs among groups were identified. This comprehensive taxonomy of social skills can be useful in developing research-based individual, group, or institutional programming to improve social skills. Copyright © 2015 by the American Occupational Therapy Association, Inc.

Taxonomy for Modeling Demand Response Resources

DOE Office of Scientific and Technical Information (OSTI.GOV)

Olsen, Daniel; Kiliccote, Sila; Sohn, Michael

2014-08-01

Demand response resources are an important component of modern grid management strategies. Accurate characterizations of DR resources are needed to develop systems of optimally managed grid operations and to plan future investments in generation, transmission, and distribution. The DOE Demand Response and Energy Storage Integration Study (DRESIS) project researched the degree to which demand response (DR) and energy storage can provide grid flexibility and stability in the Western Interconnection. In this work, DR resources were integrated with traditional generators in grid forecasting tools, specifically a production cost model of the Western Interconnection. As part of this study, LBNL developed amore » modeling framework for characterizing resource availability and response attributes of DR resources consistent with the governing architecture of the simulation modeling platform. In this report, we identify and describe the following response attributes required to accurately characterize DR resources: allowable response frequency, maximum response duration, minimum time needed to achieve load changes, necessary pre- or re-charging of integrated energy storage, costs of enablement, magnitude of controlled resources, and alignment of availability. We describe a framework for modeling these response attributes, and apply this framework to characterize 13 DR resources including residential, commercial, and industrial end-uses. We group these end-uses into three broad categories based on their response capabilities, and define a taxonomy for classifying DR resources within these categories. The three categories of resources exhibit different capabilities and differ in value to the grid. Results from the production cost model of the Western Interconnection illustrate that minor differences in resource attributes can have significant impact on grid utilization of DR resources. The implications of these findings will be explored in future DR valuation studies.« less

Family Baculoviridae

USDA-ARS?s Scientific Manuscript database

The International Committee on Taxonomy of Viruses (ICTV) has been charged with the task of developing, refining, and maintaining a universal virus taxonomy. The Online (10th) ICTV Report depicts the current status of virus taxonomy. This chapter of the Report details the classification, nomenclat...

[Concepts of rational taxonomy].

PubMed

Pavlinov, I Ia

2011-01-01

The problems are discussed related to development of concepts of rational taxonomy and rational classifications (taxonomic systems) in biology. Rational taxonomy is based on the assumption that the key characteristic of rationality is deductive inference of certain partial judgments about reality under study from other judgments taken as more general and a priory true. Respectively, two forms of rationality are discriminated--ontological and epistemological ones. The former implies inference of classifications properties from general (essential) properties of the reality being investigated. The latter implies inference of the partial rules of judgments about classifications from more general (formal) rules. The following principal concepts of ontologically rational biological taxonomy are considered: "crystallographic" approach, inference of the orderliness of organismal diversity from general laws of Nature, inference of the above orderliness from the orderliness of ontogenetic development programs, based on the concept of natural kind and Cassirer's series theory, based on the systemic concept, based on the idea of periodic systems. Various concepts of ontologically rational taxonomy can be generalized by an idea of the causal taxonomy, according to which any biologically sound classification is founded on a contentwise model of biological diversity that includes explicit indication of general causes responsible for that diversity. It is asserted that each category of general causation and respective background model may serve as a basis for a particular ontologically rational taxonomy as a distinctive research program. Concepts of epistemologically rational taxonomy and classifications (taxonomic systems) can be interpreted in terms of application of certain epistemological criteria of substantiation of scientific status of taxonomy in general and of taxonomic systems in particular. These concepts include: consideration of taxonomy consistency from the standpoint of inductive and hypothetico-deductive argumentation schemes and such fundamental criteria of classifications naturalness as their prognostic capabilities; foundation of a theory of "general taxonomy" as a "general logic", including elements of the axiomatic method. The latter concept constitutes a core of the program of general classiology; it is inconsistent due to absence of anything like "general logic". It is asserted that elaboration of a theory of taxonomy as a biological discipline based on the formal principles of epistemological rationality is not feasible. Instead, it is to be elaborated as ontologically rational one based on biologically sound metatheories about biological diversity causes.

Bayesian approach to transforming public gene expression repositories into disease diagnosis databases.

PubMed

Huang, Haiyan; Liu, Chun-Chi; Zhou, Xianghong Jasmine

2010-04-13

The rapid accumulation of gene expression data has offered unprecedented opportunities to study human diseases. The National Center for Biotechnology Information Gene Expression Omnibus is currently the largest database that systematically documents the genome-wide molecular basis of diseases. However, thus far, this resource has been far from fully utilized. This paper describes the first study to transform public gene expression repositories into an automated disease diagnosis database. Particularly, we have developed a systematic framework, including a two-stage Bayesian learning approach, to achieve the diagnosis of one or multiple diseases for a query expression profile along a hierarchical disease taxonomy. Our approach, including standardizing cross-platform gene expression data and heterogeneous disease annotations, allows analyzing both sources of information in a unified probabilistic system. A high level of overall diagnostic accuracy was shown by cross validation. It was also demonstrated that the power of our method can increase significantly with the continued growth of public gene expression repositories. Finally, we showed how our disease diagnosis system can be used to characterize complex phenotypes and to construct a disease-drug connectivity map.

Why bottom-up taxonomies are unlikely to satisfy the quest for a definitive taxonomy of situations.

PubMed

Reis, Harry T

2018-03-01

The recent advent of methods for large-scale data collection has provided an unprecedented opportunity for researchers who seek to develop a taxonomy of situations. Parrigon, Woo, Tay, and Wang's (2017) CAPTIONs model is the latest such effort. In this comment, I argue that although bottom-up approaches of this sort have clear value, they are unlikely to provide the sort of definitive, comprehensive, and theoretically integrative taxonomy that the field wants and needs. In large part, this is because bottom-up taxonomies represent what is common about situations and not what is theoretically important and influential about them. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Molecular Evidences of a Hidden Complex Scenario in Leporinus cf. friderici

PubMed Central

Silva-Santos, Rosane; Ramirez, Jorge L.; Galetti, Pedro M.; Freitas, Patrícia D.

2018-01-01

The megadiversity of the neotropical ichthyofauna has been associated to recent diversification processes, reflecting in subtle or lacking morphological differentiation between species, challenging the classical taxonomic identification. Leporinus friderici occurs in several river basins of South America, and its nominal taxonomic validity has been questioned. Its wide distribution within the Brazilian Shield suggests that this species could be genetically structured among the hydrographic basins, despite a sharp morphological similarity. In this study, we performed phylogenetic analyses, based on three nuclear (recombination activating gene 1, RAG1, recombination activating gene 2, RAG2, and myosin heavy chain 6 cardiac muscle alpha gene, Myh6) and two mitochondrial (COI and Cytochrome b, Cytb) markers, in specimens morphologically similar to L. friderici and related species from different hydrographic basins in South America. Our phylogenetic tree identified four well-supported clades, which point out to the existence of taxonomic inconsistencies within this fish group. A clade named L. cf. friderici sensu stricto included eight Molecular Operational Taxonomic Units recently diversified in the Brazilian Shield basins. These results were also confirmed by a single-gene species delimitation analysis. It is suggested that this clade includes a species complex, characterizing taxonomic uncertainties. Another clade recovered only L. friderici from the Suriname rivers, validating this nominal species in its type locality. A third no-named clade, characterized by deeper species divergence, recovered five different nominal species interleaved with other undescribed forms previously also recognized as L. cf. friderici, indicating taxonomic errors. The fourth clade only included L. taeniatus. Our results showed a complex scenario involving the morphotype L. cf. friderici and allowed us to address aspects related to evolutionary diversification of this fish group and historical processes involved with, highlighting the importance of revealing hidden biodiversity for the taxonomy and conservationist action plans of these fish. PMID:29497440

What do I do? Developing a taxonomy of chaplaincy activities and interventions for spiritual care in intensive care unit palliative care.

PubMed

Massey, Kevin; Barnes, Marilyn J D; Villines, Dana; Goldstein, Julie D; Pierson, Anna Lee Hisey; Scherer, Cheryl; Vander Laan, Betty; Summerfelt, Wm Thomas

2015-01-01

Chaplains are increasingly seen as key members of interdisciplinary palliative care teams, yet the specific interventions and hoped for outcomes of their work are poorly understood. This project served to develop a standard terminology inventory for the chaplaincy field, to be called the chaplaincy taxonomy. The research team used a mixed methods approach to generate, evaluate and validate items for the taxonomy. We conducted a literature review, retrospective chart review, focus groups, self-observation, experience sampling, concept mapping, and reliability testing. Chaplaincy activities focused primarily on palliative care in an intensive care unit setting in order to capture a broad cross section of chaplaincy activities. Literature and chart review resulted in 438 taxonomy items for testing. Chaplain focus groups generated an additional 100 items and removed 421 items as duplications. Self-Observation, Experience Sampling and Concept Mapping provided validity that the taxonomy items were actual activities that chaplains perform in their spiritual care. Inter-rater reliability for chaplains to identify taxonomy items from vignettes was 0.903. The 100 item chaplaincy taxonomy provides a strong foundation for a normative inventory of chaplaincy activities and outcomes. A deliberative process is proposed to further expand and refine the taxonomy to create a standard terminological inventory for the field of chaplaincy. A standard terminology could improve the ways inter-disciplinary palliative care teams communicate about chaplaincy activities and outcomes.

Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV).

PubMed

Lefkowitz, Elliot J; Dempsey, Donald M; Hendrickson, Robert Curtis; Orton, Richard J; Siddell, Stuart G; Smith, Donald B

2018-01-04

The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa; maintaining a database detailing the currently approved taxonomy; and providing the database, supporting proposals, and other virus-related information from an open-access, public web site. The ICTV web site (http://ictv.global) provides access to the current taxonomy database in online and downloadable formats, and maintains a complete history of virus taxa back to the first release in 1971. The ICTV has also published the ICTV Report on Virus Taxonomy starting in 1971. This Report provides a comprehensive description of all virus taxa covering virus structure, genome structure, biology and phylogenetics. The ninth ICTV report, published in 2012, is available as an open-access online publication from the ICTV web site. The current, 10th report (http://ictv.global/report/), is being published online, and is replacing the previous hard-copy edition with a completely open access, continuously updated publication. No other database or resource exists that provides such a comprehensive, fully annotated compendium of information on virus taxa and taxonomy. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

The Taxonomy of Intervention Intensity

ERIC Educational Resources Information Center

Fuchs, Lynn S.; Fuchs, Douglas; Malone, Amelia S.

2017-01-01

This article describes the Taxonomy of Intervention Intensity, which articulates seven principles for evaluating and building intervention intensity based upon research. The Taxonomy's seven dimensions of intensity are strength, dosage, alignment, attention to transfer, comprehensiveness, behavioral support, and individualization (see Table 1). In…

MO-G-BRE-08: Taxonomy of Corrective Actions in Radiotherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sutlief, S; Brown, D

2014-06-15

Purpose: Various causal taxonomies have been developed for healthcare incidents and for radiation therapy in particular. The causal analysis of incidents leads to corrective actions which can also be organized into a taxonomy. Such a corrective action classification system would provide information about the situational context, the action type, and the leverage of the action in order to detect patterns in the corrective actions frequently employed in radiation therapy. It would also provide practical guidance to the radiation therapy community for determining the appropriateness and potential effectiveness of proposed corrective actions. Materials: A review of causal analysis reports and correctivemore » action plans was conducted using the following sources: US NRC medical event reports, IAEA reports, ROSIS submissions, US Veterans Health Administration reports, and singleincident report sources. The corrective actions presented in the published sources were then mapped onto four corrective action taxonomy prototypes: role-based, safety-context-based, responsibility-based, and hierarchy of hazard control. The resulting corrective action taxonomy was then validated through use of the published sources. Results: The responsibility-based taxonomy and hierarchy of hazard taxonomy provided more intuitive and sensible categories than the role-based taxonomy or the safety-context taxonomy. The most frequent corrective actions were added safety barriers, training, process standardization, and development of a quality improvement program where one was lacking. Conclusion: Published corrective action statements in radiation therapy emphasize what to do more so than whom the recipient is or which process step is affected. The hierarchy of hazard taxonomy provides a suitable framework for radiation therapy and has the advantage of providing insight into the likelihood that a particular corrective action will mitigate the recurrence of the error it was meant to correct. This information would be useful to medical center administration, safety personnel, and regulators who must assess the projected efficacy of corrective actions. Derek Brown is a director of TreatSafely, LLC.« less

Improved knowledge retention among clinical pharmacy students using an anthropology classroom assessment technique.

PubMed

Whitley, Heather P; Parton, Jason M

2014-09-15

To adapt a classroom assessment technique (CAT) from an anthropology course to a diabetes module in a clinical pharmacy skills laboratory and to determine student knowledge retention from baseline. Diabetes item stems, focused on module objectives, replaced anthropology terms. Answer choices, coded to Bloom's Taxonomy, were expanded to include higher-order thinking. Students completed the online 5-item probe 4 times: prelaboratory lecture, postlaboratory, and at 6 months and 12 months after laboratory. Statistical analyses utilized a single factor, repeated measures design using rank transformations of means with a Mann-Whitney-Wilcoxon test. The CAT revealed a significant increase in knowledge from prelaboratory compared to all postlaboratory measurements (p<0.0001). Significant knowledge retention was maintained with basic terms, but declined with complex terms between 6 and 12 months. The anthropology assessment tool was effectively adapted using Bloom's Taxonomy as a guide and, when used repeatedly, demonstrated knowledge retention. Minimal time was devoted to application of the probe making it an easily adaptable CAT.

The role of psychosocial processes in the development and maintenance of chronic pain disorders

PubMed Central

Edwards, Robert R.; Dworkin, Robert H.; Sullivan, Mark D.; Turk, Dennis; Wasan, Ajay D.

2016-01-01

The recently-proposed ACTTION-APS Pain Taxonomy provides an evidence-based, multidimensional, chronic pain classification system. Psychosocial factors play a crucial role within several dimensions of the Taxonomy. In this paper, we discuss the evaluation of psychosocial factors that influence the diagnosis and trajectory of chronic pain disorders. We review studies in individuals with a variety of persistent pain conditions, and describe evidence that psychosocial variables play key roles in conferring risk for the development of pain, in shaping long-term pain-related adjustment, and in modulating pain treatment outcomes. We consider both “general” psychosocial variables such as negative affect, childhood trauma, and social support, as well as “pain-specific” psychosocial variables that include pain-related catastrophizing, self-efficacy for managing pain, and pain-related coping. Collectively, the complexity and profound variability in chronic pain highlights the need to better understand the multidimensional array of interacting forces that determine the trajectory of chronic pain conditions. PMID:27586832

A study of entropy/clarity of genetic sequences using metric spaces and fuzzy sets.

PubMed

Georgiou, D N; Karakasidis, T E; Nieto, Juan J; Torres, A

2010-11-07

The study of genetic sequences is of great importance in biology and medicine. Sequence analysis and taxonomy are two major fields of application of bioinformatics. In the present paper we extend the notion of entropy and clarity to the use of different metrics and apply them in the case of the Fuzzy Polynuclotide Space (FPS). Applications of these notions on selected polynucleotides and complete genomes both in the I(12×k) space, but also using their representation in FPS are presented. Our results show that the values of fuzzy entropy/clarity are indicative of the degree of complexity necessary for the description of the polynucleotides in the FPS, although in the latter case the interpretation is slightly different than in the case of the I(12×k) hypercube. Fuzzy entropy/clarity along with the use of appropriate metrics can contribute to sequence analysis and taxonomy. Copyright © 2010 Elsevier Ltd. All rights reserved.

Molecular diversity of some species belonging to the genus Daphnia O. F. Müller, 1785 (Crustacea: Cladocera) in Turkey.

PubMed

Özdemir, Ebru; Altındağ, Ahmet; Kandemir, İrfan

2017-05-01

Daphnia is a freshwater zooplankton species with controversial taxonomy due to its high morphological variation linked to environmental factors and inter-specific hybridization and polyploidy in some groups. The aim of the present study is to examine molecular diversity of some Daphnia species in Turkey and to establish DNA barcodes of Turkish Daphnia species. Sequence analysis was performed using 540 bp region of cytochrome oxidase subunit I gene of mitochondrial DNA. A total of 34 haplotypes have been identified for Turkey. Daphnia pulex complex was divided into two clades with 16.1% sequence divergence according to molecular taxonomy based on Kimura 2-parameter. The clade which was molecularly diverged from Daphnia pulex with 16.1% sequence divergence was found to show 99% similarity with Daphnia cf. pulicaria (sensu Alonso 1996) instead of Daphnia pulicaria Forbes, 1893. Furthermore, this study has contributed to Turkish zoogeography by demonstrating the distribution of Daphnia species in Turkey.

The diversity of eukaryotic microbiota in the traditional Slovak sheep cheese--bryndza.

PubMed

Laurencík, M; Sulo, P; Sláviková, E; Piecková, E; Seman, M; Ebringer, L

2008-09-30

We investigated the occurrence and diversity of yeasts and filamentous fungi in bryndza an artisanal Slovak soft spreadable cheese prepared from raw sheep milk or from a mixture of sheep and cow milk. Samples collected during four months of the summer production period from two locations (northern and southern parts of central Slovakia) contained 10(5)-10(7) (cfu) yeasts and about 10(2) (cfu) of mold per gram of wet weight. Further characterization by conventional taxonomy and sequence comparison of D1/D2 region from 26S rRNA gene revealed Mucor circinelloides v. Tieghem as the predominant filamentous fungus. A novel Geotrichum sp. together with Kluyveromyces (K. lactis/K. marxianus) was identified as the most abundant yeast species. Occasionally other yeasts, such as Candida inconspicua, Candida silvae, Pichia fermentans and Trichosporon domesticum were found. Conventional taxonomy readily identified isolates to the genus level, but DNA sequence comparison was capable of discriminating them at the species level.

A taxonomy of prospection: introducing an organizational framework for future-oriented cognition.

PubMed

Szpunar, Karl K; Spreng, R Nathan; Schacter, Daniel L

2014-12-30

Prospection--the ability to represent what might happen in the future--is a broad concept that has been used to characterize a wide variety of future-oriented cognitions, including affective forecasting, prospective memory, temporal discounting, episodic simulation, and autobiographical planning. In this article, we propose a taxonomy of prospection to initiate the important and necessary process of teasing apart the various forms of future thinking that constitute the landscape of prospective cognition. The organizational framework that we propose delineates episodic and semantic forms of four modes of future thinking: simulation, prediction, intention, and planning. We show how this framework can be used to draw attention to the ways in which various modes of future thinking interact with one another, generate new questions about prospective cognition, and illuminate our understanding of disorders of future thinking. We conclude by considering basic cognitive processes that give rise to prospective cognitions, cognitive operations and emotional/motivational states relevant to future-oriented cognition, and the possible role of procedural or motor systems in future-oriented behavior.

(GTG)5 microsatellite regions in citrinin-producing Penicillium.

PubMed

Di Conza, José Alejandro; Nepote, Andrea Fabiana; González, Ana María; Lurá, María Cristina

2007-03-01

Morphological and cultural characteristics, as well as biochemical properties, are the main criteria used in fungal taxonomy and in the standard description of fungi species. Sometimes, however, this criterion is difficult to apply due to fungal phenotypic variations. This is particularly true in the genus Penicillium. The aims of this work were to determine (GTG)5 microsatellite sequence in potentially citrinin-producing Penicillium strains and to investigate if this sequence could be useful to characterize such fungi. Penicillium citrinum Thom and Penicillium chrysogenum Thom were isolated from different foods. The identification of the isolates at species level was carried out according to classical taxonomy. The production of citrinin was determined by thin layer chromatography. This study proved that microsatellite regions exist as short repeated sequences in all tested strains. The patterns were very similar for all P. citrinum isolates and it was possible to group them in function of the quantity of citrinin produced. Yet, not similar clusters were obtained when P. chrysogenum isolates were analyzed.

The Distributed Wind Cost Taxonomy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Forsyth, Trudy; Jimenez, Tony; Preus, Robert

To date, there has been no standard method or tool to analyze the installed and operational costs for distributed wind turbine systems. This report describes the development of a classification system, or taxonomy, for distributed wind turbine project costs. The taxonomy establishes a framework to help collect, sort, and compare distributed wind cost data that mirrors how the industry categorizes information. The taxonomy organizes costs so they can be aggregated from installers, developers, vendors, and other sources without losing cost details. Developing a peer-reviewed taxonomy is valuable to industry stakeholders because a common understanding the details of distributed wind turbinemore » costs and balance of station costs is a first step to identifying potential high-value cost reduction opportunities. Addressing cost reduction potential can help increase distributed wind's competitiveness and propel the U.S. distributed wind industry forward. The taxonomy can also be used to perform cost comparisons between technologies and track trends for distributed wind industry costs in the future. As an initial application and piloting of the taxonomy, preliminary cost data were collected for projects of different sizes and from different regions across the contiguous United States. Following the methods described in this report, these data are placed into the established cost categories.« less

Taxonaut: an application software for comparative display of multiple taxonomies with a use case of GBIF Species API

PubMed Central

2016-01-01

Abstract Background The Species API of the Global Biodiversity Information Facility (GBIF) provides public access to taxonomic data aggregated from multiple data sources. Each data source follows its own classification which can be inconsistent with classifications from other sources. Even with a reference classification e.g. the GBIF Backbone taxonomy, a comprehensive method to compare classifications in the data aggregation is essential, especially for non-expert users. New information A Java application was developed to compare multiple taxonomies graphically using classification data acquired from GBIF’s ChecklistBank via the GBIF Species API. It uses a table to display taxonomies where each column represents a taxonomy under comparison, with an aligner column to organise taxa by name. Each cell contains the name of a taxon if the classification in that column contains the name. Each column also has a cell showing the hierarchy of the taxonomy by a folder metaphor where taxa are aligned and synchronised in the aligner column. A set of those comparative tables shows taxa categorised by relationship between taxonomies. The result set is also available as tables in an Excel format file. PMID:27932916

A taxonomy of medical uncertainties in clinical genome sequencing.

PubMed

Han, Paul K J; Umstead, Kendall L; Bernhardt, Barbara A; Green, Robert C; Joffe, Steven; Koenig, Barbara; Krantz, Ian; Waterston, Leo B; Biesecker, Leslie G; Biesecker, Barbara B

2017-08-01

Clinical next-generation sequencing (CNGS) is introducing new opportunities and challenges into the practice of medicine. Simultaneously, these technologies are generating uncertainties of an unprecedented scale that laboratories, clinicians, and patients are required to address and manage. We describe in this report the conceptual design of a new taxonomy of uncertainties around the use of CNGS in health care. Interviews to delineate the dimensions of uncertainty in CNGS were conducted with genomics experts and themes were extracted in order to expand on a previously published three-dimensional taxonomy of medical uncertainty. In parallel, we developed an interactive website to disseminate the CNGS taxonomy to researchers and engage them in its continued refinement. The proposed taxonomy divides uncertainty along three axes-source, issue, and locus-and further discriminates the uncertainties into five layers with multiple domains. Using a hypothetical clinical example, we illustrate how the taxonomy can be applied to findings from CNGS and used to guide stakeholders through interpretation and implementation of variant results. The utility of the proposed taxonomy lies in promoting consistency in describing dimensions of uncertainty in publications and presentations, to facilitate research design and management of the uncertainties inherent in the implementation of CNGS.Genet Med advance online publication 19 January 2017.

A Taxonomy of Medical Uncertainties in Clinical Genome Sequencing

PubMed Central

Han, Paul K. J.; Umstead, Kendall L.; Bernhardt, Barbara A.; Green, Robert C.; Joffe, Steven; Koenig, Barbara; Krantz, Ian; Waterston, Leo B.; Biesecker, Leslie G.; Biesecker, Barbara B.

2017-01-01

Purpose Clinical next generation sequencing (CNGS) is introducing new opportunities and challenges into the practice of medicine. Simultaneously, these technologies are generating uncertainties of unprecedented scale that laboratories, clinicians, and patients are required to address and manage. We describe in this report the conceptual design of a new taxonomy of uncertainties around the use of CNGS in health care. Methods Interviews to delineate the dimensions of uncertainty in CNGS were conducted with genomics experts, and themes were extracted in order to expand upon a previously published three-dimensional taxonomy of medical uncertainty. In parallel we developed an interactive website to disseminate the CNGS taxonomy to researchers and engage them in its continued refinement. Results The proposed taxonomy divides uncertainty along three axes: source, issue, and locus, and further discriminates the uncertainties into five layers with multiple domains. Using a hypothetical clinical example, we illustrate how the taxonomy can be applied to findings from CNGS and used to guide stakeholders through interpretation and implementation of variant results. Conclusion The utility of the proposed taxonomy lies in promoting consistency in describing dimensions of uncertainty in publications and presentations, to facilitate research design and management of the uncertainties inherent in the implementation of CNGS. PMID:28102863

A domains-based taxonomy of supported accommodation for people with severe and persistent mental illness.

PubMed

Siskind, Dan; Harris, Meredith; Pirkis, Jane; Whiteford, Harvey

2013-06-01

A lack of definitional clarity in supported accommodation and the absence of a widely accepted system for classifying supported accommodation models creates barriers to service planning and evaluation. We undertook a systematic review of existing supported accommodation classification systems. Using a structured system for qualitative data analysis, we reviewed the stratification features in these classification systems, identified the key elements of supported accommodation and arranged them into domains and dimensions to create a new taxonomy. The existing classification systems were mapped onto the new taxonomy to verify the domains and dimensions. Existing classification systems used either a service-level characteristic or programmatic approach. We proposed a taxonomy based around four domains: duration of tenure; patient characteristics; housing characteristics; and service characteristics. All of the domains in the taxonomy were drawn from the existing classification structures; however, none of the existing classification structures covered all of the domains in the taxonomy. Existing classification systems are regionally based, limited in scope and lack flexibility. A domains-based taxonomy can allow more accurate description of supported accommodation services, aid in identifying the service elements likely to improve outcomes for specific patient populations, and assist in service planning.

Towards the Development of a Taxonomy for Visualisation of Streamed Geospatial Data

NASA Astrophysics Data System (ADS)

Sibolla, B. H.; Van Zyl, T.; Coetzee, S.

2016-06-01

Geospatial data has very specific characteristics that need to be carefully captured in its visualisation, in order for the user and the viewer to gain knowledge from it. The science of visualisation has gained much traction over the last decade as a response to various visualisation challenges. During the development of an open source based, dynamic two-dimensional visualisation library, that caters for geospatial streaming data, it was found necessary to conduct a review of existing geospatial visualisation taxonomies. The review was done in order to inform the design phase of the library development, such that either an existing taxonomy can be adopted or extended to fit the needs at hand. The major challenge in this case is to develop dynamic two dimensional visualisations that enable human interaction in order to assist the user to understand the data streams that are continuously being updated. This paper reviews the existing geospatial data visualisation taxonomies that have been developed over the years. Based on the review, an adopted taxonomy for visualisation of geospatial streaming data is presented. Example applications of this taxonomy are also provided. The adopted taxonomy will then be used to develop the information model for the visualisation library in a further study.

The 1980-81 AFOSR-HTTM (Heat Transfer and Turbulence Mechanics)-Stanford Conference on Complex Turbulent Flows: Comparison of Computation and Experiment. Volume 2. Taxonomies, Reporters’ Summaries, Evaluation, and Conclusions

DTIC Science & Technology

1981-09-01

247-1 Moffett Field, CA 94035li W. Kordulla "NASA-Ames Research Center Mail Stop 202A-1 "Moffett Field, CA 94035 -. E. Krause Aerodynamiaches Inatitut...University Stanford, CA 94305 Wolfgang Rodi SFB 80 Universitat Karlsruhe Kaiserstrasse 12 D-75 Karlsruhe 1, W. Germany Robert Rogallo NASA-Ames Research Cntr

Operator Workload: Comprehensive Review and Evaluation of Operator Workload Methodologies

DTIC Science & Technology

1989-06-01

chocking for system failures or emergency conditions. It seems fair to characterize the changes In operator functions as more mental or cognitive In nature ...that the operator, the system hardware, and the evMronment all interact in affecting performance and this Interaction can change the nature of the task...a) classifying the nature of the operator tasks and (b) classifying workload assessment techniques. Task taxonomies are useful because some workload

Broad-spectrum antimicrobial epiphytic and endophytic fungi from marine organisms: isolation, bioassay and taxonomy.

PubMed

Zhang, Yi; Mu, Jun; Feng, Yan; Kang, Yue; Zhang, Jia; Gu, Peng-Juan; Wang, Yu; Ma, Li-Fang; Zhu, Yan-Hua

2009-04-17

In the search for new marine derived antibiotics, 43 epi- and endophytic fungal strains were isolated from the surface or the inner tissue of different marine plants and invertebrates. Through preliminary and secondary screening, 10 of them were found to be able to produce broad-spectrum antimicrobial metabolites. By morphological and molecular biological methods, three active strains were characterized to be Penicillium glabrum, Fusarium oxysporum, and Alternaria alternata.

A Taxonomy of Community Living Skills.

ERIC Educational Resources Information Center

Dever, Richard B.

1989-01-01

Described is the "Taxonomy of Community Living Skills," a guide for curriculum developers. Experts (n=59) in mental retardation were surveyed to assess the taxonomy's coherence, appropriateness, completeness, etc. Responses to the model's five domains (personal maintenance and development, homemaking and community life, vocational,…

A Taxonomy of Latent Structure Assumptions for Probability Matrix Decomposition Models.

ERIC Educational Resources Information Center

Meulders, Michel; De Boeck, Paul; Van Mechelen, Iven

2003-01-01

Proposed a taxonomy of latent structure assumptions for probability matrix decomposition (PMD) that includes the original PMD model and a three-way extension of the multiple classification latent class model. Simulation study results show the usefulness of the taxonomy. (SLD)

Microbial taxonomy in the post-genomic era: Rebuilding from scratch?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thompson, Cristiane C.; Amaral, Gilda R.; Campeão, Mariana

2014-12-23

Microbial taxonomy should provide adequate descriptions of bacterial, archaeal, and eukaryotic microbial diversity in ecological, clinical, and industrial environments. We re-evaluated the prokaryote species twice. It is time to revisit polyphasic taxonomy, its principles, and its practice, including its underlying pragmatic species concept. We will be able to realize an old dream of our predecessor taxonomists and build a genomic-based microbial taxonomy, using standardized and automated curation of high-quality complete genome sequences as the new gold standard.

Development of a consensus taxonomy of sedentary behaviors (SIT): report of Delphi Round 1.

PubMed

Chastin, Sebastien Francois Martin; Schwarz, Ulf; Skelton, Dawn A; Skelton, Dawn Ann

2013-01-01

Over the last decade, sedentary behaviors have emerged as a distinctive behavioral paradigm with deleterious effects on health independent of physical activity. The next phase of research is to establish dose response between sedentary behaviors and health outcomes and improve understanding of context and determinants of these behaviors. Establishing a common taxonomy of these behaviors is a necessary step in this process. The Sedentary behavior International Taxonomy project was developed to establish a classification of sedentary behaviors by use of a formal consensus process. The study follows a Delphi process in three Rounds. A preparatory stage informed the development of terms of reference documents. In Round 1, experts were asked to make statements about the taxonomy; 1) its purpose and use ; 2) the domains, categories or facets that should be consider and include; 3) the structure/architecture to arrange and link these domains and facets. In Round 2 experts will be presented with a draft taxonomy emerging from Round 1 and invited to comment and propose alterations. The taxonomy will then be finalised at the outset of this stage. Results of Round 1 are reported here. There is a general consensus that a taxonomy will help advances in research by facilitating systematic and standardised: 1) investigation and analysis; 2) reporting and communication; 3) data pooling, comparison and meta-analysis; 4) development of measurement tools; 4) data descriptions, leading to higher quality in data querying and facilitate discoveries. There is also a consensus that such a taxonomy should be flexible to accommodate diverse purposes of use, and future advances in the field and yet provide a cross-disciplinary common language. A consensual taxonomy structure emerged with nine primary facets (Purpose, Environment, Posture, Social, Measurement, Associated behavior, Status, Time, Type) and the draft structure presented here for Round 2.

Original opinion: the use of Bloom's Taxonomy to teach and assess the skill of the psychiatric formulation during vocational training.

PubMed

de Beer, Wayne A

2017-10-01

This paper proposes the use of the cognitive domain of Bloom's Taxonomy, an educational classification system, to guide the critical thinking required for the composition of the psychiatric formulation during the various stages of specialist training. Bloom's Taxonomy offers a hierarchical, structured approach to clinical reasoning. Use of this method can assist supervisors and trainees to understand better the concepts of and offer a developmental approach to critical reasoning. Application of the Taxonomy, using cognitive 'action words' (verbs) within each of the levels, can promote increasing sophistication in the construction of the psychiatric formulation. Examples of how the Taxonomy can be adapted to design educational resources are suggested in the article.

An Evidence-based Forensic Taxonomy of Windows Phone Dating Apps.

PubMed

Cahyani, Niken Dwi Wahyu; Choo, Kim-Kwang Raymond; Ab Rahman, Nurul Hidayah; Ashman, Helen

2018-05-21

Advances in technologies including development of smartphone features have contributed to the growth of mobile applications, including dating apps. However, online dating services can be misused. To support law enforcement investigations, a forensic taxonomy that provides a systematic classification of forensic artifacts from Windows Phone 8 (WP8) dating apps is presented in this study. The taxonomy has three categories, namely: Apps Categories, Artifacts Categories, and Data Partition Categories. This taxonomy is built based on the findings from a case study of 28 mobile dating apps, using mobile forensic tools. The dating app taxonomy can be used to inform future studies of dating and related apps, such as those from Android and iOS platforms. © 2018 American Academy of Forensic Sciences.

On-line upgrade of program modules using AdaPT

NASA Technical Reports Server (NTRS)

Waldrop, Raymond S.; Volz, Richard A.; Smith, Gary W.; Goldsack, Stephen J.; Holzbach-Valero, A. A.

1993-01-01

One purpose of our research is the investigation of the effectiveness and expressiveness of AdaPT, a set of language extensions to Ada 83, for distributed systems. As a part of that effort, we are now investigating the subject of replacing, e.g. upgrading, software modules while the software system remains in operation. The AdaPT language extensions provide a good basis for this investigation for several reasons: they include the concept of specific, self-contained program modules which can be manipulated; support for program configuration is included in the language; and although the discussion will be in terms of the AdaPT language, the AdaPT to Ada 83 conversion methodology being developed as another part of this project will provide a basis for the application of our findings to Ada 83 and Ada 9X systems. The purpose of this investigation is to explore the basic mechanisms of the replacement process. With this purpose in mind, we will avoid including issues whose presence would obscure these basic mechanisms by introducing additional, unrelated concerns. Thus, while replacement in the presence of real-time deadlines, heterogeneous systems, and unreliable networks is certainly a topic of interest, we will first gain an understanding of the basic processes in the absence of such concerns. The extension of the replacement process to more complex situations can be made later. A previous report established an overview of the module replacement problem, a taxonomy of the various aspects of the replacement process, and a solution to one case in the replacement taxonomy. This report provides solutions to additional cases in the replacement process taxonomy: replacement of partitions with state and replacement of nodes. The solutions presented here establish the basic principles for module replacement. Extension of these solutions to other more complicated cases in the replacement taxonomy is direct, though requiring substantial work beyond the available funding.

Automated Measurement and Verification and Innovative Occupancy Detection Technologies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Price, Phillip; Bruce, Nordman; Piette, Mary Ann

In support of DOE’s sensors and controls research, the goal of this project is to move toward integrated building to grid systems by building on previous work to develop and demonstrate a set of load characterization measurement and evaluation tools that are envisioned to be part of a suite of applications for transactive efficient buildings, built upon data-driven load characterization and prediction models. This will include the ability to include occupancy data in the models, plus data collection and archival methods to include different types of occupancy data with existing networks and a taxonomy for naming these data within amore » Volttron agent platform.« less

The Cartesian Heritage of Bloom's Taxonomy

ERIC Educational Resources Information Center

Bertucio, Brett

2017-01-01

This essay seeks to contribute to the critical reception of "Bloom's Taxonomy of Educational Objectives" by tracing the Taxonomy's underlying philosophical assumptions. Identifying Bloom's work as consistent with the legacy of Cartesian thought, I argue that its hierarchy of behavioral objectives provides a framework for certainty and…

Systematic comparative content analysis of 17 psychosocial work environment questionnaires using a new taxonomy.

PubMed

Kop, Jean-Luc; Althaus, Virginie; Formet-Robert, Nadja; Grosjean, Vincent

2016-04-01

Many questionnaires have been developed to measure how psychosocial characteristics are perceived in a work environment. But the content validity of these questionnaires has rarely been questioned due to the absence of a reference taxonomy for characteristics of work environments. To propose an exhaustive taxonomy of work environment characteristics involved in psychosocial risks and to apply this taxonomy to questionnaires on workplace psychosocial factors. The taxonomy was developed by categorizing factors present in the main theoretical models of the field. Questionnaire items most frequently cited in scientific literature were retained for classification. The taxonomy was structured into four hierarchical levels and comprises 53 categories. The 17 questionnaires analyzed included 927 items: 59 from the "physical environment" category, 116 from the "social environment" category, 236 from the "work activity" category, 255 from the "activity management" category, and 174 from the "organizational context" category. There are major content differences among analyzed questionnaires. This study offers a means for selecting a scale on the basis of content.

Exploring a taxonomy for aggression against women: can it aid conceptual clarity?

PubMed

Cook, Sarah; Parrott, Dominic

2009-01-01

The assessment of aggression against women is demanding primarily because assessment strategies do not share a common language to describe reliably the wide range of forms of aggression women experience. The lack of a common language impairs efforts to describe these experiences, understand causes and consequences of aggression against women, and develop effective intervention and prevention efforts. This review accomplishes two goals. First, it applies a theoretically and empirically based taxonomy to behaviors assessed by existing measurement instruments. Second, it evaluates whether the taxonomy provides a common language for the field. Strengths of the taxonomy include its ability to describe and categorize all forms of aggression found in existing quantitative measures. The taxonomy also classifies numerous examples of aggression discussed in the literature but notably absent from quantitative measures. Although we use existing quantitative measures as a starting place to evaluate the taxonomy, its use is not limited to quantitative methods. Implications for theory, research, and practice are discussed.

The integrative future of taxonomy

PubMed Central

2010-01-01

Background Taxonomy is the biological discipline that identifies, describes, classifies and names extant and extinct species and other taxa. Nowadays, species taxonomy is confronted with the challenge to fully incorporate new theory, methods and data from disciplines that study the origin, limits and evolution of species. Results Integrative taxonomy has been proposed as a framework to bring together these conceptual and methodological developments. Here we review perspectives for an integrative taxonomy that directly bear on what species are, how they can be discovered, and how much diversity is on Earth. Conclusions We conclude that taxonomy needs to be pluralistic to improve species discovery and description, and to develop novel protocols to produce the much-needed inventory of life in a reasonable time. To cope with the large number of candidate species revealed by molecular studies of eukaryotes, we propose a classification scheme for those units that will facilitate the subsequent assembly of data sets for the formal description of new species under the Linnaean system, and will ultimately integrate the activities of taxonomists and molecular biologists. PMID:20500846

Constructing a working taxonomy of functional Ada software components for real-time embedded system applications

NASA Technical Reports Server (NTRS)

Wallace, Robert

1986-01-01

A major impediment to a systematic attack on Ada software reusability is the lack of an effective taxonomy for software component functions. The scope of all possible applications of Ada software is considered too great to allow the practical development of a working taxonomy. Instead, for the purposes herein, the scope of Ada software application is limited to device and subsystem control in real-time embedded systems. A functional approach is taken in constructing the taxonomy tree for identified Ada domain. The use of modular software functions as a starting point fits well with the object oriented programming philosophy of Ada. Examples of the types of functions represented within the working taxonomy are real time kernels, interrupt service routines, synchronization and message passing, data conversion, digital filtering and signal conditioning, and device control. The constructed taxonomy is proposed as a framework from which a need analysis can be performed to reveal voids in current Ada real-time embedded programming efforts for Space Station.

Taxonomy for colorectal cancer screening promotion: Lessons from recent randomized controlled trials.

PubMed

Ritvo, Paul; Myers, Ronald E; Serenity, Mardie; Gupta, Samir; Inadomi, John M; Green, Beverly B; Jerant, Anthony; Tinmouth, Jill; Paszat, Lawrence; Pirbaglou, Meysam; Rabeneck, Linda

2017-08-01

To derive a taxonomy for colorectal cancer screening that advances Randomized Controlled Trials (RCTs) and screening uptake. Detailed publication review, multiple interviews with principal investigators (PIs) and collaboration with PIs as co-authors produced a CRCS intervention taxonomy. Semi-structured interview questions with PIs (Drs. Inadomi, Myers, Green, Gupta, Jerant and Ritvo) yielded details about trial conduct. Interview comparisons led to an iterative process informing serial interviews until a consensus was obtained on final taxonomy structure. These taxonomy headings (Engagement Sponsor, Population Targeted, Alternative Screening Tests, Delivery Methods, and Support for Test Performance (EPADS)) were used to compare studies. Exemplary insights emphasized: 1) direct test delivery to patients; 2) linguistic-ethnic matching of staff to minority subjects; and 3) authorization of navigators to schedule or refer for colonoscopies and/or distribute stool blood tests during screening promotion. PIs of key RCTs (2012-2015) derived a CRCS taxonomy useful in detailed examination of CRCS promotion and design of future RCTs. Copyright © 2017 Elsevier Inc. All rights reserved.

Combined application of the International Classification of Functioning, Disability and Health and the NANDA-International Taxonomy II.

PubMed

Boldt, Christine; Grill, Eva; Bartholomeyczik, Sabine; Brach, Mirjam; Rauch, Alexandra; Eriks-Hoogland, Inge; Stucki, Gerold

2010-08-01

This paper presents a discussion of the conceptual and practical relationships between the International Classification of Functioning, Disability and Health and the NANDA-International Taxonomy II for nursing diagnoses, and their use in nursing practice. The ICF provides a common classification framework for all healthcare professionals, including nurses. Nursing care plans can be broadly based on NANDA-I taxonomies. No published attempt has been made to systematically compare the NANDA-I Taxonomy II to the ICF. The most recently published descriptions of both classifications and a case example presenting the combined use of both classifications. The work was carried out in 2009. There are conceptual commonalities and differences between the ICF and the NANDA-I Taxonomy II. In the case example, the overlap between the ICF categories and NANDA-I nursing diagnoses reflects the fact that the ICF, focusing on functioning and disability, and the NANDA-I Taxonomy II, with its functioning health patterns, are similar in their approaches. The NANDA-I Taxonomy II permits the fulfilment of requirements that are exclusively nursing issues. The application of the ICF is useful for nurses to communicate nursing issues with other healthcare professionals in a common language. For nurses, knowledge shared with other healthcare professionals may contribute to broader understanding of a patient's situation. The ICF and the NANDA-I Taxonomy II should be used in concert by nurses and can complement each other to enhance the quality of clinical team work and nursing practice.

The Evolution of Educational Objectives: Bloom's Taxonomy and beyond

ERIC Educational Resources Information Center

Fallahi, Carolyn R.; LaMonaca, Frank H., Jr.

2009-01-01

It is crucial for teachers to communicate effectively about educational objectives to students, colleagues, and others in education. In 1956, Bloom developed a cognitive learning taxonomy to enhance communication between college examiners. The Bloom taxonomy consists of 6 hierarchical levels of learning (knowledge, comprehension, application,…

Recent taxonomy changes and their impact on biocontrol agents

USDA-ARS?s Scientific Manuscript database

The revolution in DNA sequencing technology has led to and improved understanding of genetics and taxonomy of biocontrol agents. Our lab recently reported the genomes of some important Bacillus bacterial biocontrol agents, which in turn resulted in a change of taxonomy for these commercially importa...

Taxonomy for Assessing Evaluation Competencies in Extension

ERIC Educational Resources Information Center

Rodgers, Michelle S.; Hillaker, Barbara D.; Haas, Bruce E.; Peters, Cheryl

2012-01-01

Evaluation of public service programming is becoming increasingly important with current funding realities. The taxonomy of evaluation competencies compiled by Ghere et al. (2006) provided the starting place for Taxonomy for Assessing Evaluation Competencies in Extension. The Michigan State University Extension case study described here presents a…

An historical framework for psychiatric nosology

PubMed Central

Kendler, K. S.

2009-01-01

This essay, which seeks to provide an historical framework for our efforts to develop a scientific psychiatric nosology, begins by reviewing the classificatory approaches that arose in the early history of biological taxonomy. Initial attempts at species definition used top-down approaches advocated by experts and based on a few essential features of the organism chosen a priori. This approach was subsequently rejected on both conceptual and practical grounds and replaced by bottom-up approaches making use of a much wider array of features. Multiple parallels exist between the beginnings of biological taxonomy and psychiatric nosology. Like biological taxonomy, psychiatric nosology largely began with ‘expert’ classifications, typically influenced by a few essential features, articulated by one or more great 19th-century diagnosticians. Like biology, psychiatry is struggling toward more soundly based bottom-up approaches using diverse illness characteristics. The underemphasized historically contingent nature of our current psychiatric classification is illustrated by recounting the history of how ‘Schneiderian’ symptoms of schizophrenia entered into DSM-III. Given these historical contingencies, it is vital that our psychiatric nosologic enterprise be cumulative. This can be best achieved through a process of epistemic iteration. If we can develop a stable consensus in our theoretical orientation toward psychiatric illness, we can apply this approach, which has one crucial virtue. Regardless of the starting point, if each iteration (or revision) improves the performance of the nosology, the eventual success of the nosologic process, to optimally reflect the complex reality of psychiatric illness, is assured. PMID:19368761

The Endocrine Society guidelines: when the confidence cart goes before the evidence horse.

PubMed

Brito, Juan P; Domecq, Juan P; Murad, Mohammed H; Guyatt, Gordon H; Montori, Victor M

2013-08-01

In 2005, the Endocrine Society (TES) adopted the GRADE system of developing clinical practice guidelines. Grading of Recommendations, Assessment, Development, and Evaluation working group guidance suggests that strong recommendations based on low or very low (L/VL) confidence may often be inappropriate, and has offered a taxonomy of paradigmatic situations in which strong recommendations based on L/VL confidence estimates may be appropriate. We sought to characterize strong recommendations of TES based on L/VL confidence evidence. We identified all strong recommendations based on L/VL confidence evidence published in TES guidelines between 2005 and 2011. We identified those consistent with one of the paradigmatic situations in the taxonomy. Two hundred six of 357 (58%) of the recommendations of TES were strong; of these, 121 (59%) were based on L/VL confidence evidence. Of these 121, 35 (29%) were consistent with one of the paradigmatic situations. The most common situation (13, 11%) was of a strong recommendation against the intervention because of low confidence evidence for benefit and high confidence evidence for harm. The remaining 86 (71%) comprised 43 (36%) "best practice" statements for which sensible alternatives do not exist; 5 (4%) in which recommendations were for "additional research"; 5 (4%) in which greater confidence in the estimates was warranted; and 33 (27%) for which we could not find a compelling explanation for the incongruence. Guideline panels should beware of formulating strong recommendations when confidence in estimates is low. Our taxonomy when such recommendations are appropriate may be helpful.

A Taxonomy of Functions of Dental X-Ray Technologists.

ERIC Educational Resources Information Center

Doty, Charles R.; And Others

The taxonomy of the functions of dental x-ray technologists presented in this report resulted from a dental radiography curriculum development project undertaken at Middlesex County College (MCC) in 1981. After an introductory section citing arguments for creating taxonomies of objectives, the report explains the impetus for the curriculum…

Product Engineering Class in the Software Safety Risk Taxonomy for Building Safety-Critical Systems

NASA Technical Reports Server (NTRS)

Hill, Janice; Victor, Daniel

2008-01-01

When software safety requirements are imposed on legacy safety-critical systems, retrospective safety cases need to be formulated as part of recertifying the systems for further use and risks must be documented and managed to give confidence for reusing the systems. The SEJ Software Development Risk Taxonomy [4] focuses on general software development issues. It does not, however, cover all the safety risks. The Software Safety Risk Taxonomy [8] was developed which provides a construct for eliciting and categorizing software safety risks in a straightforward manner. In this paper, we present extended work on the taxonomy for safety that incorporates the additional issues inherent in the development and maintenance of safety-critical systems with software. An instrument called a Software Safety Risk Taxonomy Based Questionnaire (TBQ) is generated containing questions addressing each safety attribute in the Software Safety Risk Taxonomy. Software safety risks are surfaced using the new TBQ and then analyzed. In this paper we give the definitions for the specialized Product Engineering Class within the Software Safety Risk Taxonomy. At the end of the paper, we present the tool known as the 'Legacy Systems Risk Database Tool' that is used to collect and analyze the data required to show traceability to a particular safety standard

Toward the establishment of design guidelines for effective 3D perspective interfaces

NASA Astrophysics Data System (ADS)

Fitzhugh, Elisabeth; Dixon, Sharon; Aleva, Denise; Smith, Eric; Ghrayeb, Joseph; Douglas, Lisa

2009-05-01

The propagation of information operation technologies, with correspondingly vast amounts of complex network information to be conveyed, significantly impacts operator workload. Information management research is rife with efforts to develop schemes to aid operators to identify, review, organize, and retrieve the wealth of available data. Data may take on such distinct forms as intelligence libraries, logistics databases, operational environment models, or network topologies. Increased use of taxonomies and semantic technologies opens opportunities to employ network visualization as a display mechanism for diverse information aggregations. The broad applicability of network visualizations is still being tested, but in current usage, the complexity of densely populated abstract networks suggests the potential utility of 3D. Employment of 2.5D in network visualization, using classic perceptual cues, creates a 3D experience within a 2D medium. It is anticipated that use of 3D perspective (2.5D) will enhance user ability to visually inspect large, complex, multidimensional networks. Current research for 2.5D visualizations demonstrates that display attributes, including color, shape, size, lighting, atmospheric effects, and shadows, significantly impact operator experience. However, guidelines for utilization of attributes in display design are limited. This paper discusses pilot experimentation intended to identify potential problem areas arising from these cues and determine how best to optimize perceptual cue settings. Development of optimized design guidelines will ensure that future experiments, comparing network displays with other visualizations, are not confounded or impeded by suboptimal attribute characterization. Current experimentation is anticipated to support development of cost-effective, visually effective methods to implement 3D in military applications.

Pathosphere.org: Pathogen Detection and Characterization Through a Web-based, Open-source Informatics Platform

DTIC Science & Technology

2015-12-29

human), Homo sapiens chromosome (human), Mus_musculus ( rodent ), Sus scrofa (pig), mitochondrion genome, and Xenopus laevis (frog) . The taxonomy... Amazon Web Services. PLoS Comput Biol 2011, 7:e1002147. 10. Briese T, Paweska JT, McMullan LK, Hutchison SK, Street C, Palacios G, Khristova ML...human enterovirus C genotypes found in respiratory samples from Peru . J Gen Virol 2013, 94(Pt 1):120–7. 54. Jacob ST, Crozier I, Schieffelin JS

Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov

NASA Technical Reports Server (NTRS)

Venkateswaran, K.; Moser, D. P.; Dollhopf, M. E.; Lies, D. P.; Saffarini, D. A.; MacGregor, B. J.; Ringelberg, D. B.; White, D. C.; Nishijima, M.; Sano, H.;

Synonym-Based Word Frequency Analysis to Support the Development and Presentation of a Public Health Quality Improvement Taxonomy.

PubMed

Pina, Jamie; Massoudi, Barbara L; Chester, Kelley; Koyanagi, Mark

2018-06-07

Researchers and analysts have not completely examined word frequency analysis as an approach to creating a public health quality improvement taxonomy. To develop a taxonomy of public health quality improvement concepts for an online exchange of quality improvement work. We analyzed documents, conducted an expert review, and employed a user-centered design along with a faceted search approach to make online entries searchable for users. To provide the most targeted facets to users, we used word frequency to analyze 334 published public health quality improvement documents to find the most common clusters of word meanings. We then reviewed the highest-weighted concepts and categorized their relationships to quality improvement details in our taxonomy. Next, we mapped meanings to items in our taxonomy and presented them in order of their weighted percentages in the data. Using these methods, we developed and sorted concepts in the faceted search presentation so that online exchange users could access relevant search criteria. We reviewed 50 of the top synonym clusters and identified 12 categories for our taxonomy data. The final categories were as follows: Summary; Planning and Execution Details; Health Impact; Training and Preparation; Information About the Community; Information About the Health Department; Results; Quality Improvement (QI) Staff; Information; Accreditation Details; Collaborations; and Contact Information of the Submitter. Feedback about the elements in the taxonomy and presentation of elements in our search environment from users has been positive. When relevant data are available, the word frequency analysis method may be useful in other taxonomy development efforts for public health.

Bacterial community comparisons by taxonomy-supervised analysis independent of sequence alignment and clustering

PubMed Central

Sul, Woo Jun; Cole, James R.; Jesus, Ederson da C.; Wang, Qiong; Farris, Ryan J.; Fish, Jordan A.; Tiedje, James M.

2011-01-01

High-throughput sequencing of 16S rRNA genes has increased our understanding of microbial community structure, but now even higher-throughput methods to the Illumina scale allow the creation of much larger datasets with more samples and orders-of-magnitude more sequences that swamp current analytic methods. We developed a method capable of handling these larger datasets on the basis of assignment of sequences into an existing taxonomy using a supervised learning approach (taxonomy-supervised analysis). We compared this method with a commonly used clustering approach based on sequence similarity (taxonomy-unsupervised analysis). We sampled 211 different bacterial communities from various habitats and obtained ∼1.3 million 16S rRNA sequences spanning the V4 hypervariable region by pyrosequencing. Both methodologies gave similar ecological conclusions in that β-diversity measures calculated by using these two types of matrices were significantly correlated to each other, as were the ordination configurations and hierarchical clustering dendrograms. In addition, our taxonomy-supervised analyses were also highly correlated with phylogenetic methods, such as UniFrac. The taxonomy-supervised analysis has the advantages that it is not limited by the exhaustive computation required for the alignment and clustering necessary for the taxonomy-unsupervised analysis, is more tolerant of sequencing errors, and allows comparisons when sequences are from different regions of the 16S rRNA gene. With the tremendous expansion in 16S rRNA data acquisition underway, the taxonomy-supervised approach offers the potential to provide more rapid and extensive community comparisons across habitats and samples. PMID:21873204

Auditing as part of the terminology design life cycle.

PubMed

Min, Hua; Perl, Yehoshua; Chen, Yan; Halper, Michael; Geller, James; Wang, Yue

2006-01-01

To develop and test an auditing methodology for detecting errors in medical terminologies satisfying systematic inheritance. This methodology is based on various abstraction taxonomies that provide high-level views of a terminology and highlight potentially erroneous concepts. Our auditing methodology is based on dividing concepts of a terminology into smaller, more manageable units. First, we divide the terminology's concepts into areas according to their relationships/roles. Then each multi-rooted area is further divided into partial-areas (p-areas) that are singly-rooted. Each p-area contains a set of structurally and semantically uniform concepts. Two kinds of abstraction networks, called the area taxonomy and p-area taxonomy, are derived. These taxonomies form the basis for the auditing approach. Taxonomies tend to highlight potentially erroneous concepts in areas and p-areas. Human reviewers can focus their auditing efforts on the limited number of problematic concepts following two hypotheses on the probable concentration of errors. A sample of the area taxonomy and p-area taxonomy for the Biological Process (BP) hierarchy of the National Cancer Institute Thesaurus (NCIT) was derived from the application of our methodology to its concepts. These views led to the detection of a number of different kinds of errors that are reported, and to confirmation of the hypotheses on error concentration in this hierarchy. Our auditing methodology based on area and p-area taxonomies is an efficient tool for detecting errors in terminologies satisfying systematic inheritance of roles, and thus facilitates their maintenance. This methodology concentrates a domain expert's manual review on portions of the concepts with a high likelihood of errors.

Towards an Artificial Space Object Taxonomy

NASA Astrophysics Data System (ADS)

Wilkins, M.; Schumacher, P.; Jah, M.; Pfeffer, A.

2013-09-01

Object recognition is the first step in positively identifying a resident space object (RSO), i.e. assigning an RSO to a category such as GPS satellite or space debris. Object identification is the process of deciding that two RSOs are in fact one and the same. Provided we have appropriately defined a satellite taxonomy that allows us to place a given RSO into a particular class of object without any ambiguity, one can assess the probability of assignment to a particular class by determining how well the object satisfies the unique criteria of belonging to that class. Ultimately, tree-based taxonomies delineate unique signatures by defining the minimum amount of information required to positively identify a RSO. Therefore, taxonomic trees can be used to depict hypotheses in a Bayesian object recognition and identification process. This work describes a new RSO taxonomy along with specific reasoning behind the choice of groupings. An alternative taxonomy was recently presented at the Sixth Conference on Space Debris in Darmstadt, Germany. [1] The best example of a taxonomy that enjoys almost universal scientific acceptance is the classical Linnaean biological taxonomy. A strength of Linnaean taxonomy is that it can be used to organize the different kinds of living organisms, simply and practically. Every species can be given a unique name. This uniqueness and stability are a result of the acceptance by biologists specializing in taxonomy, not merely of the binomial names themselves. Fundamentally, the taxonomy is governed by rules for the use of these names, and these are laid down in formal Nomenclature Codes. We seek to provide a similar formal nomenclature system for RSOs through a defined tree-based taxonomy structure. Each categorization, beginning with the most general or inclusive, at any level is called a taxon. Taxon names are defined by a type, which can be a specimen or a taxon of lower rank, and a diagnosis, a statement intended to supply characters that differentiate the taxon from others with which it is likely to be confused. Each taxon will have a set of uniquely distinguishing features that will allow one to place a given object into a specific group without any ambiguity. When a new object does not fall into a specific taxon that is already defined, the entire tree structure will need to be evaluated to determine if a new taxon should be created. Ultimately, an online learning process to facilitate tree growth would be desirable. One can assess the probability of assignment to a particular taxon by determining how well the object satisfies the unique criteria of belonging to that taxon. Therefore, we can use taxonomic trees in a Bayesian process to assign prior probabilities to each of our object recognition and identification hypotheses. We will show that this taxonomy is robust by demonstrating specific stressing classification examples. We will also demonstrate how to implement this taxonomy in Figaro, an open source probabilistic programming language.

Molecular characterization of Anopheline (Diptera: Culicidae) mosquitoes from eight geographical locations of Sri Lanka.

PubMed

Weeraratne, Thilini C; Surendran, Sinnathambi N; Reimer, Lisa J; Wondji, Charles S; Perera, M Devika B; Walton, Catherine; Parakrama Karunaratne, S H P

2017-06-02

Genus Anopheles is a major mosquito group of interest in Sri Lanka as it includes vectors of malaria and its members exist as species complexes. Taxonomy of the group is mainly based on morphological features, which are not conclusive and can be easily erased while handling the specimens. A combined effort, using morphology and DNA barcoding (using the markers cytochrome c oxidase subunit I (COI) gene and internal transcribed spacer 2 (ITS2) region, was made during the present study to recognize anophelines collected from eight districts of Sri Lanka for the first time. Cytochrome c oxidase subunit I and ITS2 regions of morphologically identified anopheline mosquitoes from Sri Lanka were sequenced. These sequences together with GenBank sequences were used in phylogenetic tree construction and molecular characterization of mosquitoes. According to morphological identification, the field-collected adult mosquitoes belonged to 15 species, i.e., Anopheles aconitus, Anopheles annularis, Anopheles barbirostris, Anopheles culicifacies, Anopheles jamesii, Anopheles karwari, Anopheles maculatus, Anopheles nigerrimus, Anopheles pallidus, Anopheles peditaeniatus, Anopheles pseudojamesi, Anopheles subpictus, Anopheles tessellatus, Anopheles vagus, and Anopheles varuna. However, analysis of 123 COI sequences (445 bp) (16 clades supported by strong bootstrap value in the neighbour joining tree and inter-specific distances of >3%) showed that there are 16 distinct species. Identity of the morphologically identified species, except An. subpictus, was comparable with the DNA barcoding results. COI sequence analysis showed that morphologically identified An. subpictus is composed of two genetic entities: An. subpictus species A and species B (inter-specific K2P distance 0.128). All the four haplotypes of An. culicifacies discovered during the present study belonged to a single species. ITS2 sequences (542 bp) were obtained for all the species except for An. barbirostris, An. subpictus species B, An. tessellatus, and An. varuna. Each of these sequences was represented by a single species-specific haplotype. The present study reflects the importance and feasibility of COI and ITS2 genetic markers in identifying anophelines and their sibling species, and the significance of integrated systematic approach in mosquito taxonomy. Wide distribution of malaria vectors in the country perhaps indicates the potential for re-emergence of malaria in the country.

A Faceted Taxonomy for Rating Student Bibliographies in an Online Information Literacy Game

ERIC Educational Resources Information Center

Leeder, Chris; Markey, Karen; Yakel, Elizabeth

2012-01-01

This study measured the quality of student bibliographies through creation of a faceted taxonomy flexible and fine-grained enough to encompass the variety of online sources cited by today's students. The taxonomy was developed via interviews with faculty, iterative refinement of categories and scoring, and testing on example student…

A Taxonomy of Psychomotor Forms. Occasional Paper No. 35.

ERIC Educational Resources Information Center

Goldberger, Michael

A taxonomy of psychomotor skills provides a classification of all human movement forms. The development of motor skills in this hierarchy begins with the reflexive physical responses of the infant. The stages of growth include basic interactive movement forms, skilled movement forms, and functional and creative movement forms. This taxonomy offers…

Taxonomy of the order Mononegavirales: update 2018.

PubMed

Amarasinghe, Gaya K; Aréchiga Ceballos, Nidia G; Banyard, Ashley C; Basler, Christopher F; Bavari, Sina; Bennett, Andrew J; Blasdell, Kim R; Briese, Thomas; Bukreyev, Alexander; Caì, Yíngyún; Calisher, Charles H; Campos Lawson, Cristine; Chandran, Kartik; Chapman, Colin A; Chiu, Charles Y; Choi, Kang-Seuk; Collins, Peter L; Dietzgen, Ralf G; Dolja, Valerian V; Dolnik, Olga; Domier, Leslie L; Dürrwald, Ralf; Dye, John M; Easton, Andrew J; Ebihara, Hideki; Echevarría, Juan E; Fooks, Anthony R; Formenty, Pierre B H; Fouchier, Ron A M; Freuling, Conrad M; Ghedin, Elodie; Goldberg, Tony L; Hewson, Roger; Horie, Masayuki; Hyndman, Timothy H; Jiāng, Dàohóng; Kityo, Robert; Kobinger, Gary P; Kondō, Hideki; Koonin, Eugene V; Krupovic, Mart; Kurath, Gael; Lamb, Robert A; Lee, Benhur; Leroy, Eric M; Maes, Piet; Maisner, Andrea; Marston, Denise A; Mor, Sunil Kumar; Müller, Thomas; Mühlberger, Elke; Ramírez, Víctor Manuel Neira; Netesov, Sergey V; Ng, Terry Fei Fan; Nowotny, Norbert; Palacios, Gustavo; Patterson, Jean L; Pawęska, Janusz T; Payne, Susan L; Prieto, Karla; Rima, Bertus K; Rota, Paul; Rubbenstroth, Dennis; Schwemmle, Martin; Siddell, Stuart; Smither, Sophie J; Song, Qisheng; Song, Timothy; Stenglein, Mark D; Stone, David M; Takada, Ayato; Tesh, Robert B; Thomazelli, Luciano Matsumiya; Tomonaga, Keizō; Tordo, Noël; Towner, Jonathan S; Vasilakis, Nikos; Vázquez-Morón, Sonia; Verdugo, Claudio; Volchkov, Viktor E; Wahl, Victoria; Walker, Peter J; Wang, David; Wang, Lin-Fa; Wellehan, James F X; Wiley, Michael R; Whitfield, Anna E; Wolf, Yuri I; Yè, Gōngyín; Zhāng, Yǒng-Zhèn; Kuhn, Jens H

2018-04-11

In 2018, the order Mononegavirales was expanded by inclusion of 1 new genus and 12 novel species. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV) and summarizes additional taxonomic proposals that may affect the order in the near future.

Analyzing Written Comments by Performance Raters.

ERIC Educational Resources Information Center

Littlefield, John; And Others

A four-level taxonomy is proposed to define the usefulness of rater written comments for supporting letters of recommendation. The taxonomy is used to classify comments on 220 rating forms by 25 raters from two surgery departments regarding performance by third-year medical students. Written comments were classified by the following taxonomy: (1)…

Manifest Variable Granger Causality Models for Developmental Research: A Taxonomy

ERIC Educational Resources Information Center

von Eye, Alexander; Wiedermann, Wolfgang

2015-01-01

Granger models are popular when it comes to testing hypotheses that relate series of measures causally to each other. In this article, we propose a taxonomy of Granger causality models. The taxonomy results from crossing the four variables Order of Lag, Type of (Contemporaneous) Effect, Direction of Effect, and Segment of Dependent Series…

Self-Awareness and Personal Growth: Theory and Application of Bloom's Taxonomy

ERIC Educational Resources Information Center

Ugur, Hasan; Constantinescu, Petru-Madalin; Stevens, Michael J.

2015-01-01

Problem Statement: In this article, we summarize a group-based, self-development curriculum based on humanistic principles, framed by contemporary self-determination theory (SDT), and designed in accordance with Bloom's Taxonomy. The processes of awareness and integration are common to SDT and Bloom's Taxonomy, and to our knowledge, have not been…

Understanding the Advising Learning Process Using Learning Taxonomies

ERIC Educational Resources Information Center

Muehleck, Jeanette K.; Smith, Cathleen L.; Allen, Janine M.

2014-01-01

To better understand the learning that transpires in advising, we used Anderson et al.'s (2001) revision of Bloom's (1956) taxonomy and Krathwohl, Bloom, and Masia's (1964) affective taxonomy to analyze eight student-reported advising outcomes from Smith and Allen (2014). Using the cognitive processes and knowledge domains of Anderson et al.'s…

Climbing Bloom's Taxonomy Pyramid: Lessons from a Graduate Histology Course

ERIC Educational Resources Information Center

Zaidi, Nikki B.; Hwang, Charles; Scott, Sara; Stallard, Stefanie; Purkiss, Joel; Hortsch, Michael

2017-01-01

Bloom's taxonomy was adopted to create a subject-specific scoring tool for histology multiple-choice questions (MCQs). This Bloom's Taxonomy Histology Tool (BTHT) was used to analyze teacher- and student-generated quiz and examination questions from a graduate level histology course. Multiple-choice questions using histological images were…

A Taxonomy of Fallacies in System Safety Arguments

NASA Technical Reports Server (NTRS)

Greenwell, William S.; Knight, John C.; Holloway, C. Michael; Pease, Jacob J.

2006-01-01

Safety cases are gaining acceptance as assurance vehicles for safety-related systems. A safety case documents the evidence and argument that a system is safe to operate; however, logical fallacies in the underlying argument may undermine a system s safety claims. Removing these fallacies is essential to reduce the risk of safety-related system failure. We present a taxonomy of common fallacies in safety arguments that is intended to assist safety professionals in avoiding and detecting fallacious reasoning in the arguments they develop and review. The taxonomy derives from a survey of general argument fallacies and a separate survey of fallacies in real-world safety arguments. Our taxonomy is specific to safety argumentation, and it is targeted at professionals who work with safety arguments but may lack formal training in logic or argumentation. We discuss the rationale for the selection and categorization of fallacies in the taxonomy. In addition to its applications to the development and review of safety cases, our taxonomy could also support the analysis of system failures and promote the development of more robust safety case patterns.

Systematic comparative content analysis of 17 psychosocial work environment questionnaires using a new taxonomy

PubMed Central

2016-01-01

Background Many questionnaires have been developed to measure how psychosocial characteristics are perceived in a work environment. But the content validity of these questionnaires has rarely been questioned due to the absence of a reference taxonomy for characteristics of work environments. Objectives To propose an exhaustive taxonomy of work environment characteristics involved in psychosocial risks and to apply this taxonomy to questionnaires on workplace psychosocial factors. Methods The taxonomy was developed by categorizing factors present in the main theoretical models of the field. Questionnaire items most frequently cited in scientific literature were retained for classification. Results The taxonomy was structured into four hierarchical levels and comprises 53 categories. The 17 questionnaires analyzed included 927 items: 59 from the “physical environment” category, 116 from the “social environment” category, 236 from the “work activity” category, 255 from the “activity management” category, and 174 from the “organizational context” category. Conclusions There are major content differences among analyzed questionnaires. This study offers a means for selecting a scale on the basis of content. PMID:27367232

Toward unification of taxonomy databases in a distributed computer environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kitakami, Hajime; Tateno, Yoshio; Gojobori, Takashi

1994-12-31

All the taxonomy databases constructed with the DNA databases of the international DNA data banks are powerful electronic dictionaries which aid in biological research by computer. The taxonomy databases are, however not consistently unified with a relational format. If we can achieve consistent unification of the taxonomy databases, it will be useful in comparing many research results, and investigating future research directions from existent research results. In particular, it will be useful in comparing relationships between phylogenetic trees inferred from molecular data and those constructed from morphological data. The goal of the present study is to unify the existent taxonomymore » databases and eliminate inconsistencies (errors) that are present in them. Inconsistencies occur particularly in the restructuring of the existent taxonomy databases, since classification rules for constructing the taxonomy have rapidly changed with biological advancements. A repair system is needed to remove inconsistencies in each data bank and mismatches among data banks. This paper describes a new methodology for removing both inconsistencies and mismatches from the databases on a distributed computer environment. The methodology is implemented in a relational database management system, SYBASE.« less

An Empirical Taxonomy of Hospital Governing Board Roles

PubMed Central

Lee, Shoou-Yih D; Alexander, Jeffrey A; Wang, Virginia; Margolin, Frances S; Combes, John R

2008-01-01

Objective To develop a taxonomy of governing board roles in U.S. hospitals. Data Sources 2005 AHA Hospital Governance Survey, 2004 AHA Annual Survey of Hospitals, and Area Resource File. Study Design A governing board taxonomy was developed using cluster analysis. Results were validated and reviewed by industry experts. Differences in hospital and environmental characteristics across clusters were examined. Data Extraction Methods One-thousand three-hundred thirty-four hospitals with complete information on the study variables were included in the analysis. Principal Findings Five distinct clusters of hospital governing boards were identified. Statistical tests showed that the five clusters had high internal reliability and high internal validity. Statistically significant differences in hospital and environmental conditions were found among clusters. Conclusions The developed taxonomy provides policy makers, health care executives, and researchers a useful way to describe and understand hospital governing board roles. The taxonomy may also facilitate valid and systematic assessment of governance performance. Further, the taxonomy could be used as a framework for governing boards themselves to identify areas for improvement and direction for change. PMID:18355260

[Planning With Nanda, Noc, Nic Taxonomies In Neurologic Rehabilitation. A clinical study].

PubMed

Iori, Alessandra; Foracchia, Marco; Gradellini, Cinzia

2015-01-01

Nursing classifications identify a specific professional responsibility, increase nursing visibility, according with nursing evolution of these last years. To evaluate care planning with NANDA taxonomy in neurologic rehabilitation context. Care plan managing with NANDA taxonomy, regarding diagnosis of constipation and impaired skin integrity, using a computerized tool for systematically observation, organized in check list. Registered data with taxonomy planning are higher in quantitative and qualitative terms. For most of patients (87%) one diagnosis has been opened, both diagnosis for 60% of them. Nursing care plan with NANDA taxonomy can be considered a valid methodology of care for neurologic patient, this since it requests a deep and complete registration of first assessment a systematically registration of each monitoring, it increases visibility of nursing job, and it underlines specific autonomy and responsibility in prevention and management of problems.

Development of a Consensus Taxonomy of Sedentary Behaviors (SIT): Report of Delphi Round 1

PubMed Central

Chastin, Sebastien Francois Martin; Schwarz, Ulf; Skelton, Dawn Ann

2013-01-01

Background Over the last decade, sedentary behaviors have emerged as a distinctive behavioral paradigm with deleterious effects on health independent of physical activity. The next phase of research is to establish dose response between sedentary behaviors and health outcomes and improve understanding of context and determinants of these behaviors. Establishing a common taxonomy of these behaviors is a necessary step in this process. Aim The Sedentary behavior International Taxonomy project was developed to establish a classification of sedentary behaviors by use of a formal consensus process. Methods The study follows a Delphi process in three Rounds. A preparatory stage informed the development of terms of reference documents. In Round 1, experts were asked to make statements about the taxonomy; 1) its purpose and use ; 2) the domains, categories or facets that should be consider and include; 3) the structure/architecture to arrange and link these domains and facets. In Round 2 experts will be presented with a draft taxonomy emerging from Round 1 and invited to comment and propose alterations. The taxonomy will then be finalised at the outset of this stage. Results Results of Round 1 are reported here. There is a general consensus that a taxonomy will help advances in research by facilitating systematic and standardised: 1) investigation and analysis; 2) reporting and communication; 3) data pooling, comparison and meta-analysis; 4) development of measurement tools; 4) data descriptions, leading to higher quality in data querying and facilitate discoveries. There is also a consensus that such a taxonomy should be flexible to accommodate diverse purposes of use, and future advances in the field and yet provide a cross-disciplinary common language. A consensual taxonomy structure emerged with nine primary facets (Purpose, Environment, Posture, Social, Measurement, Associated behavior, Status, Time, Type) and the draft structure presented here for Round 2. PMID:24312653

A value-based taxonomy of improvement approaches in healthcare.

PubMed

Colldén, Christian; Gremyr, Ida; Hellström, Andreas; Sporraeus, Daniella

2017-06-19

Purpose The concept of value is becoming increasingly fashionable in healthcare and various improvement approaches (IAs) have been introduced with the aim of increasing value. The purpose of this paper is to construct a taxonomy that supports the management of parallel IAs in healthcare. Design/methodology/approach Based on previous research, this paper proposes a taxonomy that includes the dimensions of view on value and organizational focus; three contemporary IAs - lean, value-based healthcare, and patient-centered care - are related to the taxonomy. An illustrative qualitative case study in the context of psychiatric (psychosis) care is then presented that contains data from 23 interviews and focuses on the value concept, IAs, and the proposed taxonomy. Findings Respondents recognized the dimensions of the proposed taxonomy and indicated its usefulness as support for choosing and combining different IAs into a coherent management model, and for facilitating dialog about IAs. The findings also suggested that the view of value as "health outcomes" is widespread, but healthcare professionals are less likely than managers to also view value as a process. Originality/value The conceptual contribution of this paper is to delineate some important characteristics of IAs in relation to the emerging "value era". It also highlights the coexistence of different IAs in healthcare management practice. A taxonomy is proposed that can help managers choose, adapt, and combine IAs in local management models.

Barrier scattering with complex-valued quantum trajectories: Taxonomy and analysis of isochrones

DOE Office of Scientific and Technical Information (OSTI.GOV)

David, Julianne K.; Wyatt, Robert E.

2008-03-07

To facilitate the search for isochrones when using complex-valued trajectory methods for quantum barrier scattering calculations, the structure and shape of isochrones in the complex plane were studied. Isochrone segments were categorized based on their distinguishing features, which are shared by each situation studied: High and low energy wave packets, scattering from both thick and thin Gaussian and Eckart barriers of varying height. The characteristic shape of the isochrone is a trifurcated system: Trajectories that transmit the barrier are launched from the lower branch (T), while the middle and upper branches form the segments for reflected trajectories (F and B).more » In addition, a model is presented for the curved section of the lower branch (from which transmitted trajectories are launched), and important features of the complex extension of the initial wave packet are identified.« less

Task-Based Navigation of a Taxonomy Interface to a Digital Repository

ERIC Educational Resources Information Center

Khoo, Christopher S. G.; Wang, Zhonghong; Chaudhry, Abdus Sattar

2012-01-01

Introduction: This is a study of hierarchical navigation; how users browse a taxonomy-based interface to an organizational repository to locate information resources. The study is part of a project to develop a taxonomy for an library and information science department to organize resources and support user browsing in a digital repository.…

Psychological Benefits of Leisure Participation: A Taxonomy of Leisure Activities Based on Their Need-Gratifying Properties.

ERIC Educational Resources Information Center

Tinsley, Howard E. A.; Eldredge, Barbara D.

1995-01-01

Proposes a needs-based taxonomy of leisure activities. Study participants (n=3,771) indicated the extent to which leisure activities met different psychological needs. Results support theories that leisure experiences affect individuals' physical and mental health. Provides a taxonomy of 12 leisure activity clusters so as to allow greater…

Unpacking the Revised Bloom's Taxonomy: Developing Case-Based Learning Activities

ERIC Educational Resources Information Center

Nkhoma, Mathews Zanda; Lam, Tri Khai; Sriratanaviriyakul, Narumon; Richardson, Joan; Kam, Booi; Lau, Kwok Hung

2017-01-01

Purpose: The purpose of this paper is to propose the use of case studies in teaching an undergraduate course of Internet for Business in class, based on the revised Bloom's taxonomy. The study provides the empirical evidence about the effect of case-based teaching method integrated the revised Bloom's taxonomy on students' incremental learning,…

The Basic/Essential Skills Taxonomy. Second Edition--Revised.

ERIC Educational Resources Information Center

Snyder, Lester M., Jr.

This revision of the "Basic/Essential Skills Taxonomy" exhibits changes based on use of the original taxonomy in the field. It features more precise definitions of the levels of key words and phrases, the deletion of some science items that ranged above basic skills, the combination of the language arts sections from the original two parts, and…

Studying the Value of Library and Information Services: A Taxonomy of Users Assessments.

ERIC Educational Resources Information Center

Kantor, Paul B.; Saracevic, Tefko

1995-01-01

Describes the development of a taxonomy of the value of library services based on users' assessments from five large research libraries. Highlights include empirical and derived taxonomy, replicability of the study, reasons for using the library, how library services are related to time and money, and a theory of value. (LRW)

A Proposal for a Taxonomy for Vulnerabilities in Supervisory Control and Data Acquisition (SCADA) Systems

DTIC Science & Technology

2014-09-01

executable that is setuid root.4 fingerd The Morris worm exploited a buffer overflow in the fingerd program to gain unauthorized access to computer...in other taxonomies. There are still holes ; in fact, none of the vulnerabilities that Bishop discussed have a clear place in this taxonomy until a

EPA Web Taxonomy

EPA Pesticide Factsheets

EPA's Web Taxonomy is a faceted hierarchical vocabulary used to tag web pages with terms from a controlled vocabulary. Tagging enables search and discovery of EPA's Web based information assests. EPA's Web Taxonomy is being provided in Simple Knowledge Organization System (SKOS) format. SKOS is a standard for sharing and linking knowledge organization systems that promises to make Federal terminology resources more interoperable.

Reexamining organizational configurations: an update, validation, and expansion of the taxonomy of health networks and systems.

PubMed

Dubbs, Nicole L; Bazzoli, Gloria J; Shortell, Stephen M; Kralovec, Peter D

2004-02-01

To (a) assess how the original cluster categories of hospital-led health networks and systems have changed over time; (b) identify any new patterns of cluster configurations; and (c) demonstrate how additional data can be used to refine and enhance the taxonomy measures. DATA SOURCES; 1994 and 1998 American Hospital Association (AHA) Annual Survey of Hospitals. As in the original taxonomy, separate cluster solutions are identified for health networks and health systems by applying three strategic/structural dimensions (differentiation, integration, and centralization) to three components of the health service/product continuum (hospital services, physician arrangements, and provider-based insurance activities). Factor, cluster, and discriminant analyses are used to analyze the 1998 data. Descriptive and comparative methods are used to analyze the updated 1998 taxonomy relative to the original 1994 version. The 1998 cluster categories are similar to the original taxonomy, however, they reveal some new organizational configurations. For the health networks, centralization of product/service lines is occurring more selectively than in the past. For the health systems, participation has grown in and dispersed across a more diverse set of decentralized organizational forms. For both networks and systems, the definition of centralization has changed over time. In its updated form, the taxonomy continues to provide policymakers and practitioners with a descriptive and contextual framework against which to assess organizational programs and policies. There is a need to continue to revisit the taxonomy from time to time because of the persistent evolution of the U.S. health care industry and the consequent shifting of organizational configurations in this arena. There is also value in continuing to move the taxonomy in the direction of refinement/expansion as new opportunities become available.

What is a medical decision? A taxonomy based on physician statements in hospital encounters: a qualitative study

PubMed Central

Ofstad, Eirik H; Frich, Jan C; Schei, Edvin; Frankel, Richard M; Gulbrandsen, Pål

2016-01-01

Objective The medical literature lacks a comprehensive taxonomy of decisions made by physicians in medical encounters. Such a taxonomy might be useful in understanding the physician-centred, patient-centred and shared decision-making in clinical settings. We aimed to identify and classify all decisions emerging in conversations between patients and physicians. Design Qualitative study of video recorded patient–physician encounters. Participants and setting 380 patients in consultations with 59 physicians from 17 clinical specialties and three different settings (emergency room, ward round, outpatient clinic) in a Norwegian teaching hospital. A randomised sample of 30 encounters from internal medicine was used to identify and classify decisions, a maximum variation sample of 20 encounters was used for reliability assessments, and the remaining encounters were analysed to test for applicability across specialties. Results On the basis of physician statements in our material, we developed a taxonomy of clinical decisions—the Decision Identification and Classification Taxonomy for Use in Medicine (DICTUM). We categorised decisions into 10 mutually exclusive categories: gathering additional information, evaluating test results, defining problem, drug-related, therapeutic procedure-related, legal and insurance-related, contact-related, advice and precaution, treatment goal, and deferment. Four-coder inter-rater reliability using Krippendorff's α was 0.79. Conclusions DICTUM represents a precise, detailed and comprehensive taxonomy of medical decisions communicated within patient–physician encounters. Compared to previous normative frameworks, the taxonomy is descriptive, substantially broader and offers new categories to the variety of clinical decisions. The taxonomy could prove helpful in studies on the quality of medical work, use of time and resources, and understanding of why, when and how patients are or are not involved in decisions. PMID:26868946

Auditing as Part of the Terminology Design Life Cycle

PubMed Central

Min, Hua; Perl, Yehoshua; Chen, Yan; Halper, Michael; Geller, James; Wang, Yue

2006-01-01

Objective To develop and test an auditing methodology for detecting errors in medical terminologies satisfying systematic inheritance. This methodology is based on various abstraction taxonomies that provide high-level views of a terminology and highlight potentially erroneous concepts. Design Our auditing methodology is based on dividing concepts of a terminology into smaller, more manageable units. First, we divide the terminology’s concepts into areas according to their relationships/roles. Then each multi-rooted area is further divided into partial-areas (p-areas) that are singly-rooted. Each p-area contains a set of structurally and semantically uniform concepts. Two kinds of abstraction networks, called the area taxonomy and p-area taxonomy, are derived. These taxonomies form the basis for the auditing approach. Taxonomies tend to highlight potentially erroneous concepts in areas and p-areas. Human reviewers can focus their auditing efforts on the limited number of problematic concepts following two hypotheses on the probable concentration of errors. Results A sample of the area taxonomy and p-area taxonomy for the Biological Process (BP) hierarchy of the National Cancer Institute Thesaurus (NCIT) was derived from the application of our methodology to its concepts. These views led to the detection of a number of different kinds of errors that are reported, and to confirmation of the hypotheses on error concentration in this hierarchy. Conclusion Our auditing methodology based on area and p-area taxonomies is an efficient tool for detecting errors in terminologies satisfying systematic inheritance of roles, and thus facilitates their maintenance. This methodology concentrates a domain expert’s manual review on portions of the concepts with a high likelihood of errors. PMID:16929044

Introduction to the Special Issue: Precarious Solidarity-Preferential Access in Canadian Health Care.

PubMed

Reid, Lynette

2017-06-01

Systems of universal health coverage may aspire to provide care based on need and not ability to pay; the complexities of this aspiration (conceptual, practical, and ethical) call for normative analysis. This special issue arises in the wake of a judicial inquiry into preferential access in the Canadian province of Alberta, the Vertes Commission. I describe this inquiry and set out a taxonomy of forms of differential and preferential access. Papers in this special issue focus on the conceptual specification of health system boundaries (the concept of medical need) and on the normative questions raised by complex models of funding and delivery of care, where patients, providers, and services cross system boundaries.

[Nursing diagnosis "impaired walking" in elderly patients: integrative literature review].

PubMed

Marques-Vieira, Cristina Maria Alves; de Sousa, Luís Manuel Mota; de Matos Machado Carias, João Filipe; Caldeira, Sílvia Maria Alves

2015-03-01

The impaired walking nursing diagnosis has been included in NANDA International classification taxonomy in 1998, and this review aims to identify the defining characteristics and related factors in elderly patients in recent literature. Integrative literature review based on the following guiding question: Are there more defining characteristics and factors related to the nursing diagnosis impaired walking than those included in NANDA International classification taxonomy in elderly patients? Search conducted in 2007-2013 on international and Portuguese databases. Sample composed of 15 papers. Among the 6 defining characteristics classified at NANDA International, 3 were identified in the search results, but 13 were not included in the classification. Regarding the 14 related factors that are classified, 9 were identified in the sample and 12 were not included in the NANDA International taxonomy. This review allowed the identification of new elements not included in NANDA International Taxonomy and may contribute to the development of taxonomy and nursing knowledge.

Taxonomic triage and the poverty of phylogeny.

PubMed Central

Wheeler, Quentin D

2004-01-01

Revisionary taxonomy is frequently dismissed as merely descriptive, which belies its strong intellectual content and hypothesis-driven nature. Funding for taxonomy is inadequate and largely diverted to studies of phylogeny that neither improve classifications nor nomenclature. Phylogenetic classifications are optimal for storing and predicting information, but phylogeny divorced from taxonomy is ephemeral and erodes the accuracy and information content of the language of biology. Taxonomic revisions and monographs are efficient, high-throughput species hypothesis-testing devices that are ideal for the World Wide Web. Taxonomic knowledge remains essential to credible biological research and is made urgent by the biodiversity crisis. Theoretical and technological advances and threats of mass species extinctions indicate that this is the time for a renaissance in taxonomy. Clarity of vision and courage of purpose are needed from individual taxonomists and natural history museums to bring about this evolution of taxonomy into the information age. PMID:15253345

A psychologically-based taxonomy of misdirection

PubMed Central

Kuhn, Gustav; Caffaratti, Hugo A.; Teszka, Robert; Rensink, Ronald A.

2014-01-01

Magicians use misdirection to prevent you from realizing the methods used to create a magical effect, thereby allowing you to experience an apparently impossible event. Magicians have acquired much knowledge about misdirection, and have suggested several taxonomies of misdirection. These describe many of the fundamental principles in misdirection, focusing on how misdirection is achieved by magicians. In this article we review the strengths and weaknesses of past taxonomies, and argue that a more natural way of making sense of misdirection is to focus on the perceptual and cognitive mechanisms involved. Our psychologically-based taxonomy has three basic categories, corresponding to the types of psychological mechanisms affected: perception, memory, and reasoning. Each of these categories is then divided into subcategories based on the mechanisms that control these effects. This new taxonomy can help organize magicians' knowledge of misdirection in a meaningful way, and facilitate the dialog between magicians and scientists. PMID:25538648

Evaluation of radiographic interpretation competence of veterinary students in Finland.

PubMed

Koskinen, Heli I; Snellman, Marjatta

2009-01-01

In the evaluation of the clinical competence of veterinary students, many different definitions and methods are approved. Due to the increasing discussion of the quality of outcomes produced by newly graduated veterinarians, methods for the evaluation of clinical competencies should also be evaluated. In this study, this was done by comparing two qualitative evaluation schemes: the well-known structure of observed learning outcome (SOLO) taxonomy and a modification of this taxonomy. A case-based final radiologic examination was selected and the investigation was performed by classifying students' outcomes. These classes were finally put next to original (quantitative) scores and the statistical calculations were initiated. Significant correlations between taxonomies (0.53) and the modified taxonomy and original scores (0.66) were found and some qualitative similarities between evaluation methods were observed. In addition, some supplements were recommended for the structure of evaluation schemes, especially for the structure of the modified SOLO taxonomy.

Introducing annamarie jagose.

PubMed

McCallum, T

2001-01-01

SUMMARY Annamarie Jagose's fiction can be loosely divided into the early short stories and the later novels. The stories are generally feminist and lesbian in content and characters, and contain many traditional story elements. The novels, In Translation and Lulu,are more complex works. In these texts, Jagose is interested in "queering" identity, both heterosexual and homosexual, and in questioning the effectiveness of these traditional taxonomies. Both the stories and novels feature an exquisite control of language, a wry humour, and a deft understanding of human relationships.

Young Investigator Program (8.5): Preventing Complex Failures of Human Interactive Systems with Erroneous Behavior Generation and Robust Human Task Behavior Patterns

DTIC Science & Technology

2017-11-13

behavior . The International Journal of Human-Computer Studies , 108, 105-121. https://doi.org/10.1016/j.ijhcs.2017.06.006 A second journal article...documenting the erroneous behavior generation approach and the case study analyses is currently being written. Planned submission is Spring 2017. RPPR...Belvoir, 2010. [3] A task-based taxonomy of erroneous human behavior . International Journal of Human-Computer Studies , 108:105–121, 2017. [4] M. L

Essential Steps in Characterizing Bacteriophages: Biology, Taxonomy, and Genome Analysis.

PubMed

Aziz, Ramy Karam; Ackermann, Hans-Wolfgang; Petty, Nicola K; Kropinski, Andrew M

2018-01-01

Because of the rise in antimicrobial resistance there has been a significant increase in interest in phages for therapeutic use. Furthermore, the cost of sequencing phage genomes has decreased to the point where it is being used as a teaching tool for genomics. Unfortunately, the quality of the descriptions of the phage and its annotation frequently are substandard. The following chapter is designed to help people working on phages, particularly those new to the field, to accurately describe their newly isolated viruses.

[Malassezia folliculitis in an immunocompromised patient].

PubMed

Mota, R; Reifenberger, J; Homey, B; Bruch-Gerharz, D

2011-10-01

Malassezia folliculitis (synonym: Pityrosporum folliculitis) is a polymorphic dermatomycosis characterized by the development of small papules and pustules. In severe cases, molluscoid comedonal papules are typical. The disease occurs mainly in sebum-rich areas of the face, back and chest, frequently affecting patients under immunosuppressive therapy. We report a case of Malassezia folliculitis observed in a heart transplant recipient who was successfully treated with itraconazole. Moreover, we summarize the taxonomy of the genus Malassezia as well as diagnostic and therapeutic measures of the related folliculitis.

Development, Application and Assessment of a Taxonomy for Characterizing International Environmental Problems

DTIC Science & Technology

1990-01-01

Population at risk 3579 NOTES. No one in the U.S. is effected ( health effects ) by a food shortage due to a drought 8. Land area at risk 1 3 5 Q 9 NOTES: Amount...adequately captures the characteristics most people are concerned with--human health , ecological effects , and welfare--for these problems. Because of...reasons as in India: Pure Food (10) is included because of the effects of pesticides, while Animal Habitat (9) and Stock of Wildlife (23) are included

A Preliminary Bloom's Taxonomy Assessment of End-of-Chapter Problems in Business School Textbooks

ERIC Educational Resources Information Center

Marshall, Jennings B.; Carson, Charles M.

2008-01-01

This article examines textbook problems used in a sampling of some of the most common core courses found in schools of business to ascertain what level of learning, as defined by Bloom's Taxonomy, is required to provide a correct answer. A set of working definitions based on Bloom's Taxonomy (Bloom & Krathwohl, 1956) was developed for the six…

Student Perceptions Regarding the Usefulness of Explicit Discussion of "Structure of the Observed Learning Outcome" Taxonomy

ERIC Educational Resources Information Center

Prakash, E. S.; Narayan, K. A.; Sethuraman, K. R.

2010-01-01

One method of grading responses of the descriptive type is by using Structure of Observed Learning Outcomes (SOLO) taxonomy. The basis of this study was the expectation that if students were oriented to SOLO taxonomy, it would provide them an opportunity to understand some of the factors that teachers consider while grading descriptive responses…

A Taxonomy for Postsecondary Education Programs for Students with Intellectual and Developmental Disabilities. Policy Research Brief. Volume 23, Number 1

ERIC Educational Resources Information Center

McEathron, Mary; Beuhring, Trisha; Maynard, Amelia; Mavis, Ann

2013-01-01

This "Policy Research Brief" presents the current state of the Taxonomy for Postsecondary Education Programs for Students with Intellectual and Developmental Disabilities, along with examples of how it can be used. The purpose of the taxonomy is to provide a basis for comparing the features of the growing number of postsecondary…

Taxonomy of Reading Skills and Materials for Youths and Adults. A System of Prescribing for Individual Skill Deficiencies.

ERIC Educational Resources Information Center

Giuliano, Helen Solana; And Others

This Taxonomy was designed to assist the instructor or reading specialist in the identification and location of specific instructional materials that can be used for remediation of skill deficiencies. The Taxonomy was developed by the White Plains Adult Education Center, and a description of the Center's program and method of integrating the…

Application of the ultrametric distance to portfolio taxonomy. Critical approach and comparison with other methods

NASA Astrophysics Data System (ADS)

Skórnik-Pokarowska, Urszula; Orłowski, Arkadiusz

2004-12-01

We calculate the ultrametric distance between the pairs of stocks that belong to the same portfolio. The ultrametric distance allows us to distinguish groups of shares that are related. In this way, we can construct a portfolio taxonomy that can be used for constructing an efficient portfolio. We also construct a portfolio taxonomy based not only on stock prices but also on economic indices such as liquidity ratio, debt ratio and sales profitability ratio. We show that a good investment strategy can be obtained by applying to the portfolio chosen by the taxonomy method the so-called Constant Rebalanced Portfolio.

Establishing a Framework for a Natural Area Taxonomy.

PubMed

Ebach, Malte C; Michaux, Bernard

2017-09-01

The identification of areas of endemism is essential in building an area classification, but plays little role in how natural areas are discovered. Rather area monophyly, derived from cladistics, is essential in the discovery of natural area classifications or area taxonomy. We propose Area Taxonomy to be a new sub-discipline of historical biogeography, one that can be revised and debated, and which has its own area nomenclature. Separately to area taxonomy, we outline how natural areas may be discovered by transcribing the concepts of homology and monophyly from biological systematics to historical biogeography, in the form of area homologues, area homologies and area monophyly.

Taxonomies of networks from community structure

PubMed Central

Reid, Stephen; Porter, Mason A.; Mucha, Peter J.; Fricker, Mark D.; Jones, Nick S.

2014-01-01

The study of networks has become a substantial interdisciplinary endeavor that encompasses myriad disciplines in the natural, social, and information sciences. Here we introduce a framework for constructing taxonomies of networks based on their structural similarities. These networks can arise from any of numerous sources: they can be empirical or synthetic, they can arise from multiple realizations of a single process (either empirical or synthetic), they can represent entirely different systems in different disciplines, etc. Because mesoscopic properties of networks are hypothesized to be important for network function, we base our comparisons on summaries of network community structures. Although we use a specific method for uncovering network communities, much of the introduced framework is independent of that choice. After introducing the framework, we apply it to construct a taxonomy for 746 networks and demonstrate that our approach usefully identifies similar networks. We also construct taxonomies within individual categories of networks, and we thereby expose nontrivial structure. For example, we create taxonomies for similarity networks constructed from both political voting data and financial data. We also construct network taxonomies to compare the social structures of 100 Facebook networks and the growth structures produced by different types of fungi. PMID:23030977

The contributions of library and information services to hospitals and academic health sciences centers: a preliminary taxonomy

PubMed Central

Abels, Eileen G.; Cogdill, Keith W.; Zach, Lisl

2002-01-01

Objectives: This article presents a taxonomy of the contributions of library and information services (LIS) in hospitals and academic health sciences centers. The taxonomy emerges from a study with three objectives: to articulate the value of LIS for hospitals and academic health sciences centers in terms of contributions to organizational missions and goals, to identify measures and measurable surrogates associated with each LIS contribution, and to document best practices for communicating the value of LIS to institutional administrators. Methods: The preliminary taxonomy of LIS contributions in hospitals and academic health sciences centers is based on a review of the literature, twelve semi-structured interviews with LIS directors and institutional administrators, and a focus group of administrators from five academic, teaching, and nonteaching hospitals. Results: Derived from the balanced scorecard approach, the taxonomy of LIS contributions is organized on the basis of five mission-level concepts and fifteen organizational goals. LIS contributions are included only if they have measurable surrogates. Conclusions: The taxonomy of LIS contributions offers a framework for the collection of both quantitative and qualitative data in support of communicating the value of LIS in hospitals and academic health sciences centers. PMID:12113510

Viral taxonomy needs a spring clean; its exploration era is over.

PubMed

Gibbs, Adrian J

2013-08-09

The International Committee on Taxonomy of Viruses has recently changed its approved definition of a viral species, and also discontinued work on its database of virus descriptions. These events indicate that the exploration era of viral taxonomy has ended; over the past century the principles of viral taxonomy have been established, the tools for phylogenetic inference invented, and the ultimate discriminatory data required for taxonomy, namely gene sequences, are now readily available. Further changes would make viral taxonomy more informative. First, the status of a 'taxonomic species' with an italicized name should only be given to viruses that are specifically linked with a single 'type genomic sequence' like those in the NCBI Reference Sequence Database. Secondly all approved taxa should be predominately monophyletic, and uninformative higher taxa disendorsed. These are 'quality assurance' measures and would improve the value of viral nomenclature to its users. The ICTV should also promote the use of a public database, such as Wikipedia, to replace the ICTV database as a store of the primary metadata of individual viruses, and should publish abstracts of the ICTV Reports in that database, so that they are 'Open Access'.

Taxonomies of networks from community structure

NASA Astrophysics Data System (ADS)

Onnela, Jukka-Pekka; Fenn, Daniel J.; Reid, Stephen; Porter, Mason A.; Mucha, Peter J.; Fricker, Mark D.; Jones, Nick S.

2012-09-01

The study of networks has become a substantial interdisciplinary endeavor that encompasses myriad disciplines in the natural, social, and information sciences. Here we introduce a framework for constructing taxonomies of networks based on their structural similarities. These networks can arise from any of numerous sources: They can be empirical or synthetic, they can arise from multiple realizations of a single process (either empirical or synthetic), they can represent entirely different systems in different disciplines, etc. Because mesoscopic properties of networks are hypothesized to be important for network function, we base our comparisons on summaries of network community structures. Although we use a specific method for uncovering network communities, much of the introduced framework is independent of that choice. After introducing the framework, we apply it to construct a taxonomy for 746 networks and demonstrate that our approach usefully identifies similar networks. We also construct taxonomies within individual categories of networks, and we thereby expose nontrivial structure. For example, we create taxonomies for similarity networks constructed from both political voting data and financial data. We also construct network taxonomies to compare the social structures of 100 Facebook networks and the growth structures produced by different types of fungi.

Genetic and Morphological Analyses Demonstrate That Schizolecis guntheri (Siluriformes: Loricariidae) Is Likely to Be a Species Complex

PubMed Central

Souza, Camila S.; Costa-Silva, Guilherme J.; Roxo, Fábio F.; Foresti, Fausto; Oliveira, Claudio

2018-01-01

Schizolecis is a monotypic genus of Siluriformes widely distributed throughout isolated coastal drainages of southeastern Brazil. Previous studies have shown that fish groups found in isolated river basins tend to differentiate over time in the absence of gene flow, resulting in allopatric speciation. In this study, we used partial sequences of the mitochondrial gene COI with the analysis of the General Mixed Yule Coalescent model (GMYC) and the Automatic Barcode Gap Discovery (ABGD) for single locus species delimitation, and a Principal Component Analysis (PCA) of external morphology to test the hypothesis that Schizolecis guntheri is a complex of species. We analyzed 94 samples of S. guntheri for GMYC and ABGD, and 82 samples for PCA from 22 coastal rivers draining to the Atlantic in southeastern Brazil from the Paraná State to the north of the Rio de Janeiro State. As a result, the GMYC model and the ABGD delimited five operational taxonomy units (OTUs – a nomenclature referred to in the present study of the possible new species delimited for the genetic analysis), a much higher number compared to the traditional alfa taxonomy that only recognizes S. guntheri across the isolated coastal rivers of Brazil. Furthermore, the PCA analysis suggests that S. guntheri is highly variable in aspects of external body proportions, including dorsal-fin spine length, pectoral-fin spine length, pelvic-fin spine length, lower caudal-fin spine length, caudal peduncle depth, anal width and mandibular ramus length. However, no exclusive character was found among the isolated populations that could be used to describe a new species of Schizolecis. Therefore, we can conclude, based on our results of PCA contrasting with the results of GMYC and ABGD, that S. guntheri represents a complex of species. PMID:29552028

Changing Names with Changed Address: Integrated Taxonomy and Species Delimitation in the Holarctic Colymbetes paykulli Group (Coleoptera: Dytiscidae)

PubMed Central

Drotz, Marcus K.; Brodin, Tomas; Nilsson, Anders N.

2015-01-01

Species delimitation of geographically isolated forms is a long-standing problem in less studied insect groups. Often taxonomic decisions are based directly on morphologic variation, and lack a discussion regarding sample size and the efficiency of migration barriers or dispersal/migration capacity of the studied species. These problems are here exemplified in a water beetle complex from the Bering Sea region that separates North America from Eurasia. Only a few sampled specimens occur from this particular area and they are mostly found in museum and private collections. Here we utilize the theory of integrated taxonomy to discuss the speciation of the Holarctic Colymbetes paykulli water beetle complex, which historically has included up to five species of which today only two are recognized. Three delimitation methods are used; landmark based morphometry of body shape, variation in reticulation patterns of the pronotum exo-skeleton and sequence variation of the partial mitochondrial gene Cyt b. Our conclusion is that the Palearctic and Nearctic populations of C. paykulli are given the status of separate species, based on the fact that all methods showed significant separation between populations. As a consequence the name of the Palearctic species is C. paykulli Erichson and the Nearctic species should be known as C. longulus LeConte. There is no clear support for delineation between Palearctic and Nearctic populations of C. dahuricus based on mtDNA. However, significant difference in size and reticulation patterns from the two regions is shown. The combined conclusion is that the C. dahuricus complex needs a more thorough investigation to fully disentangle its taxonomic status. Therefore it is here still regarded as a Holarctic species. This study highlights the importance to study several diagnosable characters that has the potential to discriminate evolutionary lineage during speciation. PMID:26619278

Genetic and Morphological Analyses Demonstrate That Schizolecis guntheri (Siluriformes: Loricariidae) Is Likely to Be a Species Complex.

PubMed

Souza, Camila S; Costa-Silva, Guilherme J; Roxo, Fábio F; Foresti, Fausto; Oliveira, Claudio

2018-01-01

Schizolecis is a monotypic genus of Siluriformes widely distributed throughout isolated coastal drainages of southeastern Brazil. Previous studies have shown that fish groups found in isolated river basins tend to differentiate over time in the absence of gene flow, resulting in allopatric speciation. In this study, we used partial sequences of the mitochondrial gene COI with the analysis of the General Mixed Yule Coalescent model (GMYC) and the Automatic Barcode Gap Discovery (ABGD) for single locus species delimitation, and a Principal Component Analysis (PCA) of external morphology to test the hypothesis that Schizolecis guntheri is a complex of species. We analyzed 94 samples of S. guntheri for GMYC and ABGD, and 82 samples for PCA from 22 coastal rivers draining to the Atlantic in southeastern Brazil from the Paraná State to the north of the Rio de Janeiro State. As a result, the GMYC model and the ABGD delimited five operational taxonomy units (OTUs - a nomenclature referred to in the present study of the possible new species delimited for the genetic analysis), a much higher number compared to the traditional alfa taxonomy that only recognizes S. guntheri across the isolated coastal rivers of Brazil. Furthermore, the PCA analysis suggests that S. guntheri is highly variable in aspects of external body proportions, including dorsal-fin spine length, pectoral-fin spine length, pelvic-fin spine length, lower caudal-fin spine length, caudal peduncle depth, anal width and mandibular ramus length. However, no exclusive character was found among the isolated populations that could be used to describe a new species of Schizolecis . Therefore, we can conclude, based on our results of PCA contrasting with the results of GMYC and ABGD, that S. guntheri represents a complex of species.

Novel approaches for the taxonomic and metabolic characterization of lactobacilli: Integration of 16S rRNA gene sequencing with MALDI-TOF MS and 1H-NMR

PubMed Central

Parolin, Carola; Giordani, Barbara; Compri, Monica; Cevenini, Roberto; Vitali, Beatrice

2017-01-01

Lactobacilli represent a wide range of bacterial species with several implications for the human host. They play a crucial role in maintaining the ecological equilibrium of different biological niches and are essential for fermented food production and probiotic formulation. Despite the consensus about the ‘health-promoting’ significance of Lactobacillus genus, its genotypic and phenotypic characterization still poses several difficulties. The aim of this study was to assess the integration of different approaches, genotypic (16S rRNA gene sequencing), proteomic (MALDI-TOF MS) and metabolomic (1H-NMR), for the taxonomic and metabolic characterization of Lactobacillus species. For this purpose we analyzed 40 strains of various origin (intestinal, vaginal, food, probiotics), belonging to different species. The high discriminatory power of MALDI-TOF for species identification was underlined by the excellent agreement with the genotypic analysis. Indeed, MALDI-TOF allowed to correctly identify 39 out of 40 Lactobacillus strains at the species level, with an overall concordance of 97.5%. In the perspective to simplify the MALDI TOF sample preparation, especially for routine practice, we demonstrated the perfect agreement of the colony-picking from agar plates with the protein extraction protocol. 1H-NMR analysis, applied to both culture supernatants and bacterial lysates, identified a panel of metabolites whose variations in concentration were associated with the taxonomy, but also revealed a high intra-species variability that did not allow a species-level identification. Therefore, despite not suitable for mere taxonomic purposes, metabolomics can be useful to correlate particular biological activities with taxonomy and to understand the mechanisms related to the antimicrobial effect shown by some Lactobacillus species. PMID:28207855

Improved Knowledge Retention Among Clinical Pharmacy Students Using an Anthropology Classroom Assessment Technique

PubMed Central

Parton, Jason M.

2014-01-01

Objective. To adapt a classroom assessment technique (CAT) from an anthropology course to a diabetes module in a clinical pharmacy skills laboratory and to determine student knowledge retention from baseline. Design. Diabetes item stems, focused on module objectives, replaced anthropology terms. Answer choices, coded to Bloom’s Taxonomy, were expanded to include higher-order thinking. Students completed the online 5-item probe 4 times: prelaboratory lecture, postlaboratory, and at 6 months and 12 months after laboratory. Statistical analyses utilized a single factor, repeated measures design using rank transformations of means with a Mann-Whitney-Wilcoxon test. Assessment. The CAT revealed a significant increase in knowledge from prelaboratory compared to all postlaboratory measurements (p<0.0001). Significant knowledge retention was maintained with basic terms, but declined with complex terms between 6 and 12 months. Conclusion. The anthropology assessment tool was effectively adapted using Bloom’s Taxonomy as a guide and, when used repeatedly, demonstrated knowledge retention. Minimal time was devoted to application of the probe making it an easily adaptable CAT. PMID:25258445

Uncovering the diversity in the Amazophrynella minuta complex: integrative taxonomy reveals a new species of Amazophrynella (Anura, Bufonidae) from southern Peru

PubMed Central

Rojas, Rommel R.; Chaparro, Juan C.; Carvalho, Vinícius Tadeu De; Ávila, Robson W.; Farias, Izeni Pires; Hrbek, Tomas; Gordo, Marcelo

2016-01-01

Abstract A new species of the genus Amazophrynella (Anura, Bufonidae) is described from the departments of Madre de Dios, Cusco and Junin in Peru. An integrative taxonomy approach is used. A morphological diagnosis, morphometrics comparisons, description of the advertisement call, and the phylogenetic relationships of the new species are provided. Amazophrynella javierbustamantei sp. n. differs from other species of Amazophrynella by: intermediate body-size (snout-vent length 14.9 mm in males, n = 26 and 19.6 mm in females, n = 20), tuberculate skin texture of body, greatest hand length of the Amazophrynella spp. (3.6 mm in males, n = 26 and 4.6 mm in females, n = 20), venter coloration yellowish, tiny rounded black points covering the venter, and thirteen molecular autapomorphies in the 16S RNA gene. Its distribution varies from 215 to 708 m a.s.l. This discovery highlights the importance of the remnant forest in preserving the biodiversity in Peru, and increase in seven the species formally described in the genus Amazophrynella. PMID:27047239

Towards a phylogenetic classification of Leptothecata (Cnidaria, Hydrozoa)

PubMed Central

Maronna, Maximiliano M.; Miranda, Thaís P.; Peña Cantero, Álvaro L.; Barbeitos, Marcos S.; Marques, Antonio C.

2016-01-01

Leptothecata are hydrozoans whose hydranths are covered by perisarc and gonophores and whose medusae bear gonads on their radial canals. They develop complex polypoid colonies and exhibit considerable morphological variation among species with respect to growth, defensive structures and mode of development. For instance, several lineages within this order have lost the medusa stage. Depending on the author, traditional taxonomy in hydrozoans may be either polyp- or medusa-oriented. Therefore, the absence of the latter stage in some lineages may lead to very different classification schemes. Molecular data have proved useful in elucidating this taxonomic challenge. We analyzed a super matrix of new and published rRNA gene sequences (16S, 18S and 28S), employing newly proposed methods to measure branch support and improve phylogenetic signal. Our analysis recovered new clades not recognized by traditional taxonomy and corroborated some recently proposed taxa. We offer a thorough taxonomic revision of the Leptothecata, erecting new orders, suborders, infraorders and families. We also discuss the origination and diversification dynamics of the group from a macroevolutionary perspective. PMID:26821567

Scalable metagenomic taxonomy classification using a reference genome database

PubMed Central

Ames, Sasha K.; Hysom, David A.; Gardner, Shea N.; Lloyd, G. Scott; Gokhale, Maya B.; Allen, Jonathan E.

2013-01-01

Motivation: Deep metagenomic sequencing of biological samples has the potential to recover otherwise difficult-to-detect microorganisms and accurately characterize biological samples with limited prior knowledge of sample contents. Existing metagenomic taxonomic classification algorithms, however, do not scale well to analyze large metagenomic datasets, and balancing classification accuracy with computational efficiency presents a fundamental challenge. Results: A method is presented to shift computational costs to an off-line computation by creating a taxonomy/genome index that supports scalable metagenomic classification. Scalable performance is demonstrated on real and simulated data to show accurate classification in the presence of novel organisms on samples that include viruses, prokaryotes, fungi and protists. Taxonomic classification of the previously published 150 giga-base Tyrolean Iceman dataset was found to take <20 h on a single node 40 core large memory machine and provide new insights on the metagenomic contents of the sample. Availability: Software was implemented in C++ and is freely available at http://sourceforge.net/projects/lmat Contact: allen99@llnl.gov Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23828782

A taxonomy of prospection: Introducing an organizational framework for future-oriented cognition

PubMed Central

Szpunar, Karl K.; Spreng, R. Nathan; Schacter, Daniel L.

2014-01-01

Prospection—the ability to represent what might happen in the future—is a broad concept that has been used to characterize a wide variety of future-oriented cognitions, including affective forecasting, prospective memory, temporal discounting, episodic simulation, and autobiographical planning. In this article, we propose a taxonomy of prospection to initiate the important and necessary process of teasing apart the various forms of future thinking that constitute the landscape of prospective cognition. The organizational framework that we propose delineates episodic and semantic forms of four modes of future thinking: simulation, prediction, intention, and planning. We show how this framework can be used to draw attention to the ways in which various modes of future thinking interact with one another, generate new questions about prospective cognition, and illuminate our understanding of disorders of future thinking. We conclude by considering basic cognitive processes that give rise to prospective cognitions, cognitive operations and emotional/motivational states relevant to future-oriented cognition, and the possible role of procedural or motor systems in future-oriented behavior. PMID:25416592

CELLPEDIA: a repository for human cell information for cell studies and differentiation analyses.

PubMed

Hatano, Akiko; Chiba, Hirokazu; Moesa, Harry Amri; Taniguchi, Takeaki; Nagaie, Satoshi; Yamanegi, Koji; Takai-Igarashi, Takako; Tanaka, Hiroshi; Fujibuchi, Wataru

2011-01-01

CELLPEDIA is a repository database for current knowledge about human cells. It contains various types of information, such as cell morphologies, gene expression and literature references. The major role of CELLPEDIA is to provide a digital dictionary of human cells for the biomedical field, including support for the characterization of artificially generated cells in regenerative medicine. CELLPEDIA features (i) its own cell classification scheme, in which whole human cells are classified by their physical locations in addition to conventional taxonomy; and (ii) cell differentiation pathways compiled from biomedical textbooks and journal papers. Currently, human differentiated cells and stem cells are classified into 2260 and 66 cell taxonomy keys, respectively, from which 934 parent-child relationships reported in cell differentiation or transdifferentiation pathways are retrievable. As far as we know, this is the first attempt to develop a digital cell bank to function as a public resource for the accumulation of current knowledge about human cells. The CELLPEDIA homepage is freely accessible except for the data submission pages that require authentication (please send a password request to cell-info@cbrc.jp). Database URL: http://cellpedia.cbrc.jp/

The phylogeny and systematics of the Nassariidae revisited (Gastropoda, Buccinoidea).

PubMed

Galindo, Lee Ann; Puillandre, Nicolas; Utge, José; Lozouet, Pierre; Bouchet, Philippe

2016-06-01

Nassariidae are a group of scavenging, predominantly marine, snails that are diversified on soft bottoms as well as on rocky shores, and are the subject of numerous research papers in ecology, ecotoxicology or paleontology. A weak and/or apparently continuous variation in shell characters has resulted in an intimidating taxonomy, with complex synonymy lists. Over 1320 extant nominal species have been described, of which 442 are currently regarded as valid. Above species level, the state of the art is equally hazy, with four subfamilies and twelve genera currently accepted, and many other names in the graveyard of synonymy. A molecular analysis based on three mitochondrial (COI, 16S, 12S) and two nuclear (28S, H3) markers was conducted. Our dataset includes 218 putative nassariid species, comprising 9 of the 12 valid genera, and 25 nominal genera represented by their type species. The monophyly of the Nassariidae as classically construed is not confirmed. Species of Antillophos, Engoniophos, Phos, Nassaria, Tomlinia and Anentome (formerly considered Buccinidae) are included inside the Nassariidae clade. Within the Nassariinae, the tree unexpectedly demonstrates that species from the Atlantic and the Indo-Pacific form different clades which represent several independent diversification events. Through an integrative approach, the reconstruction of ancestral states was addressed for eight characters supposedly informative for taxonomy. Using numerous fossil calibration points, Nassariidae appear to have originated 120 MYA ago in Atlantic temperate waters during the Lower Cretaceous. Our results have a profound impact on nassariid taxonomy, especially with regard to the validity of subfamily- and genus-level names. Copyright © 2016 Elsevier Inc. All rights reserved.

Taxonomy of oxalotrophic Methylobacterium strains

NASA Astrophysics Data System (ADS)

Sahin, Nurettin; Kato, Yuko; Yilmaz, Ferah

2008-10-01

Most of the oxalotrophic bacteria are facultative methylotrophs and play important ecological roles in soil fertility and cycling of elements. This study gives a detailed picture of the taxonomy and diversity of these bacteria and provides new information about the taxonomical variability within the genus Methylobacterium. Twelve mesophilic, pink-pigmented, and facultatively methylotrophic oxalate-oxidizing strains were included in this work that had been previously isolated from the soil and some plant tissues by the potassium oxalate enrichment method. The isolates were characterized using biochemical tests, cellular lipid profiles, spectral characteristics of carotenoid pigments, G+C content of the DNA, and 16S rDNA sequencing. The taxonomic similarities among the strains were analyzed using the simple matching ( S SM) and Jaccard ( S J) coefficients, and the UPGMA clustering algorithm. The phylogenetic position of the strains was inferred by the neighbor-joining method on the basis of the 16S rDNA sequences. All isolates were Gram-negative, facultatively methylotrophic, oxidase and catalase positive, and required no growth factors. Based on the results of numerical taxonomy, the strains formed four closely related clusters sharing ≥85% similarity. Analysis of the 16S rDNA sequences demonstrated that oxalotrophic, pink-pigmented, and facultatively methylotrophic strains could be identified as members of the genus Methylobacterium. Except for M. variabile and M. aquaticum, all of the Methylobacterium type strains tested had the ability of oxalate utilization. Our results indicate that the capability of oxalate utilization seems to be an uncommon trait and could be used as a valuable taxonomic criterion for differentiation of Methylobacterium species.

Taxonomy of oxalotrophic Methylobacterium strains.

PubMed

Sahin, Nurettin; Kato, Yuko; Yilmaz, Ferah

2008-10-01

Most of the oxalotrophic bacteria are facultative methylotrophs and play important ecological roles in soil fertility and cycling of elements. This study gives a detailed picture of the taxonomy and diversity of these bacteria and provides new information about the taxonomical variability within the genus Methylobacterium. Twelve mesophilic, pink-pigmented, and facultatively methylotrophic oxalate-oxidizing strains were included in this work that had been previously isolated from the soil and some plant tissues by the potassium oxalate enrichment method. The isolates were characterized using biochemical tests, cellular lipid profiles, spectral characteristics of carotenoid pigments, G+C content of the DNA, and 16S rDNA sequencing. The taxonomic similarities among the strains were analyzed using the simple matching (S (SM)) and Jaccard (S (J)) coefficients, and the UPGMA clustering algorithm. The phylogenetic position of the strains was inferred by the neighbor-joining method on the basis of the 16S rDNA sequences. All isolates were Gram-negative, facultatively methylotrophic, oxidase and catalase positive, and required no growth factors. Based on the results of numerical taxonomy, the strains formed four closely related clusters sharing > or =85% similarity. Analysis of the 16S rDNA sequences demonstrated that oxalotrophic, pink-pigmented, and facultatively methylotrophic strains could be identified as members of the genus Methylobacterium. Except for M. variabile and M. aquaticum, all of the Methylobacterium type strains tested had the ability of oxalate utilization. Our results indicate that the capability of oxalate utilization seems to be an uncommon trait and could be used as a valuable taxonomic criterion for differentiation of Methylobacterium species.

Using narrative text and coded data to develop hazard scenarios for occupational injury interventions

PubMed Central

Lincoln, A; Sorock, G; Courtney, T; Wellman, H; Smith, G; Amoroso, P

2004-01-01

Objective: To determine whether narrative text in safety reports contains sufficient information regarding contributing factors and precipitating mechanisms to prioritize occupational back injury prevention strategies. Design, setting, subjects, and main outcome measures: Nine essential data elements were identified in narratives and coded sections of safety reports for each of 94 cases of back injuries to United States Army truck drivers reported to the United States Army Safety Center between 1987 and 1997. The essential elements of each case were used to reconstruct standardized event sequences. A taxonomy of the event sequences was then developed to identify common hazard scenarios and opportunities for primary interventions. Results: Coded data typically only identified five data elements (broad activity, task, event/exposure, nature of injury, and outcomes) while narratives provided additional elements (contributing factor, precipitating mechanism, primary source) essential for developing our taxonomy. Three hazard scenarios were associated with back injuries among Army truck drivers accounting for 83% of cases: struck by/against events during motor vehicle crashes; falls resulting from slips/trips or loss of balance; and overexertion from lifting activities. Conclusions: Coded data from safety investigations lacked sufficient information to thoroughly characterize the injury event. However, the combination of existing narrative text (similar to that collected by many injury surveillance systems) and coded data enabled us to develop a more complete taxonomy of injury event characteristics and identify common hazard scenarios. This study demonstrates that narrative text can provide the additional information on contributing factors and precipitating mechanisms needed to target prevention strategies. PMID:15314055

Evaluation of the level of difficulty of patient cases for veterinary problem-solving examination: a preliminary comparison of three taxonomies of learning.

PubMed

Koskinen, Heli

2007-01-01

An important issue that has received insufficient attention in the use of problem-based learning in the medical curriculum is the mode of assessing the level of difficulty of patient cases. In the present study, the level of difficulty of case-based questions in a veterinary degree final examination in reproduction was evaluated. First, cognitive taxonomies were evaluated to clarify whether qualitative methods such as Bloom's taxonomy, the Structure of the Observed Learning Outcome (SOLO) taxonomy, and the Amsterdam Clinical Challenge Scale (ACCS) differed from each other as evaluation tools for problem-based cases. Using these taxonomies, 30 case-based questions from the final examination in reproduction in the Helsinki veterinary program were initially evaluated to determine which one was best suited to the evaluation of the difficulty of cases. In follow-up, the same cases were also evaluated by an experienced veterinary instructor in reproduction, with the aim of gaining insight into using these approaches to evaluating difficulty. It would appear, from this preliminary assessment, that the SOLO taxonomy may be the most suitable for evaluating the difficulty of patient cases, since the instructor's quality rating resembled more closely the SOLO than the Bloom taxonomy or the ACCS. It is to be emphasized that the purpose of this study was to provide a preliminary evaluation of possible approaches that might be used to assess patient-case difficulty. Resolving all issues will require a greater number of evaluations of all components.

[Quality of psychological strain in police work--development of a taxonomy of sources of stress].

PubMed

Reinecke, Stefan; Runde, Bernd; Bastians, Frauke; Weiss, Udo; Heuft, Gereon; Bär, Olaf

2007-01-01

Police officers frequently face traumatic stressors of different origins and thus bear an increased risk of developing a post-traumatic stress disorder. The most mentally burdening situations range from shootings, death of fellow officers, dealing with dead bodies in general, the effects of shift work, time pressure or discontent with management due to mobbing. Part of the present study examines the quality of stress in police work with the goal of developing a taxonomy of the origins of stress. A stratified sample of 109 police officers participated in the study. They were interviewed about stressful situations in their work life. In the interviews participants generated incidents describing stressful or straining situations. These incidents were used to develop a taxonomy of stressful situations in everyday police work. A further 22 interviews with officers of the federal police were carried out to examine the transferability of the developed taxonomy to other occupational groups. The taxonomy distinguishes between five sources of strain. Strain can arise from (1.) the task itself, (2.) the organization and structure of work, (3.) the temporal conditions and (4.) the social conditions. The fifth category describes the source of strain based on other conditions. The results also show that the taxonomy is transferable to other occupational groups. This taxonomy leads to the systematisation of the differences among the stress phenomena which occur in police work. The results can help in the development of practical prevention, counselling and therapeutic programs.

Decisional needs assessment of patients with complex care needs in primary care: a participatory systematic mixed studies review protocol

PubMed Central

Pluye, Pierre; Légaré, France; Haggerty, Jeannie; Gore, Genevieve C; Sherif, Reem El; Poitras, Marie-Ève; Beaulieu, Marie-Claude; Beaulieu, Marie-Dominique; Bush, Paula L; Couturier, Yves; Débarges, Béatrice; Gagnon, Justin; Giguère, Anik; Grad, Roland; Granikov, Vera; Goulet, Serge; Hudon, Catherine; Kremer, Bernardo; Kröger, Edeltraut; Kudrina, Irina; Lebouché, Bertrand; Loignon, Christine; Lussier, Marie-Thérèse; Martello, Cristiano; Nguyen, Quynh; Pratt, Rebekah; Rihoux, Benoit; Rosenberg, Ellen; Samson, Isabelle; Senn, Nicolas; Li Tang, David; Tsujimoto, Masashi; Vedel, Isabelle; Ventelou, Bruno; Wensing, Michel; Bigras, Magali

2017-01-01

Introduction Patients with complex care needs (PCCNs) often suffer from combinations of multiple chronic conditions, mental health problems, drug interactions and social vulnerability, which can lead to healthcare services overuse, underuse or misuse. Typically, PCCNs face interactional issues and unmet decisional needs regarding possible options in a cascade of interrelated decisions involving different stakeholders (themselves, their families, their caregivers, their healthcare practitioners). Gaps in knowledge, values clarification and social support in situations where options need to be deliberated hamper effective decision support interventions. This review aims to (1) assess decisional needs of PCCNs from the perspective of stakeholders, (2) build a taxonomy of these decisional needs and (3) prioritise decisional needs with knowledge users (clinicians, patients and managers). Methods and analysis This review will be based on the interprofessional shared decision making (IP-SDM) model and the Ottawa Decision Support Framework. Applying a participatory research approach, we will identify potentially relevant studies through a comprehensive literature search; select relevant ones using eligibility criteria inspired from our previous scoping review on PCCNs; appraise quality using the Mixed Methods Appraisal Tool; conduct a three-step synthesis (sequential exploratory mixed methods design) to build taxonomy of key decisional needs; and integrate these results with those of a parallel PCCNs’ qualitative decisional need assessment (semistructured interviews and focus group with stakeholders). Ethics and dissemination This systematic review, together with the qualitative study (approved by the Centre Intégré Universitaire de Santé et Service Sociaux du Saguenay-Lac-Saint-Jean ethical committee), will produce a working taxonomy of key decisional needs (ontological contribution), to inform the subsequent user-centred design of a support tool for addressing PCCNs’ decisional needs (practical contribution). We will adapt the IP-SDM model, normally dealing with a single decision, for PCCNs who experience cascade of decisions involving different stakeholders (theoretical contribution). Knowledge users will facilitate dissemination of the results in the Canadian primary care network. PROSPERO registration number CRD42015020558. PMID:29133314

Decisional needs assessment of patients with complex care needs in primary care: a participatory systematic mixed studies review protocol.

PubMed

Bujold, Mathieu; Pluye, Pierre; Légaré, France; Haggerty, Jeannie; Gore, Genevieve C; Sherif, Reem El; Poitras, Marie-Eve; Beaulieu, Marie-Claude; Beaulieu, Marie-Dominique; Bush, Paula L; Couturier, Yves; Débarges, Beatrice; Gagnon, Justin; Giguère, Anik; Grad, Roland; Granikov, Vera; Goulet, Serge; Hudon, Catherine; Kremer, Bernardo; Kröger, Edeltraut; Kudrina, Irina; Lebouché, Bertrand; Loignon, Christine; Lussier, Marie-Therese; Martello, Cristiano; Nguyen, Quynh; Pratt, Rebekah; Rihoux, Benoit; Rosenberg, Ellen; Samson, Isabelle; Senn, Nicolas; Li Tang, David; Tsujimoto, Masashi; Vedel, Isabelle; Ventelou, Bruno; Wensing, Michel

2017-11-12

Patients with complex care needs (PCCNs) often suffer from combinations of multiple chronic conditions, mental health problems, drug interactions and social vulnerability, which can lead to healthcare services overuse, underuse or misuse. Typically, PCCNs face interactional issues and unmet decisional needs regarding possible options in a cascade of interrelated decisions involving different stakeholders (themselves, their families, their caregivers, their healthcare practitioners). Gaps in knowledge, values clarification and social support in situations where options need to be deliberated hamper effective decision support interventions. This review aims to (1) assess decisional needs of PCCNs from the perspective of stakeholders, (2) build a taxonomy of these decisional needs and (3) prioritise decisional needs with knowledge users (clinicians, patients and managers). This review will be based on the interprofessional shared decision making (IP-SDM) model and the Ottawa Decision Support Framework. Applying a participatory research approach, we will identify potentially relevant studies through a comprehensive literature search; select relevant ones using eligibility criteria inspired from our previous scoping review on PCCNs; appraise quality using the Mixed Methods Appraisal Tool; conduct a three-step synthesis (sequential exploratory mixed methods design) to build taxonomy of key decisional needs; and integrate these results with those of a parallel PCCNs' qualitative decisional need assessment (semistructured interviews and focus group with stakeholders). This systematic review, together with the qualitative study (approved by the Centre Intégré Universitaire de Santé et Service Sociaux du Saguenay-Lac-Saint-Jean ethical committee), will produce a working taxonomy of key decisional needs (ontological contribution), to inform the subsequent user-centred design of a support tool for addressing PCCNs' decisional needs (practical contribution). We will adapt the IP-SDM model, normally dealing with a single decision, for PCCNs who experience cascade of decisions involving different stakeholders (theoretical contribution). Knowledge users will facilitate dissemination of the results in the Canadian primary care network. CRD42015020558. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

A rehabilitation intervention to promote physical recovery following intensive care: a detailed description of construct development, rationale and content together with proposed taxonomy to capture processes in a randomised controlled trial.

PubMed

Ramsay, Pam; Salisbury, Lisa G; Merriweather, Judith L; Huby, Guro; Rattray, Janice E; Hull, Alastair M; Brett, Stephen J; Mackenzie, Simon J; Murray, Gordon D; Forbes, John F; Walsh, Timothy Simon

2014-01-29

Increasing numbers of patients are surviving critical illness, but survival may be associated with a constellation of physical and psychological sequelae that can cause ongoing disability and reduced health-related quality of life. Limited evidence currently exists to guide the optimum structure, timing, and content of rehabilitation programmes. There is a need to both develop and evaluate interventions to support and expedite recovery during the post-ICU discharge period. This paper describes the construct development for a complex rehabilitation intervention intended to promote physical recovery following critical illness. The intervention is currently being evaluated in a randomised trial (ISRCTN09412438; funder Chief Scientists Office, Scotland). The intervention was developed using the Medical Research Council (MRC) framework for developing complex healthcare interventions. We ensured representation from a wide variety of stakeholders including content experts from multiple specialties, methodologists, and patient representation. The intervention construct was initially based on literature review, local observational and audit work, qualitative studies with ICU survivors, and brainstorming activities. Iterative refinement was aided by the publication of a National Institute for Health and Care Excellence guideline (No. 83), publicly available patient stories (Healthtalkonline), a stakeholder event in collaboration with the James Lind Alliance, and local piloting. Modelling and further work involved a feasibility trial and development of a novel generic rehabilitation assistant (GRA) role. Several rounds of external peer review during successive funding applications also contributed to development. The final construct for the complex intervention involved a dedicated GRA trained to pre-defined competencies across multiple rehabilitation domains (physiotherapy, dietetics, occupational therapy, and speech/language therapy), with specific training in post-critical illness issues. The intervention was from ICU discharge to 3 months post-discharge, including inpatient and post-hospital discharge elements. Clear strategies to provide information to patients/families were included. A detailed taxonomy was developed to define and describe the processes undertaken, and capture them during the trial. The detailed process measure description, together with a range of patient, health service, and economic outcomes were successfully mapped on to the modified CONSORT recommendations for reporting non-pharmacologic trial interventions. The MRC complex intervention framework was an effective guide to developing a novel post-ICU rehabilitation intervention. Combining a clearly defined new healthcare role with a detailed taxonomy of process and activity enabled the intervention to be clearly described for the purpose of trial delivery and reporting. These data will be useful when interpreting the results of the randomised trial, will increase internal and external trial validity, and help others implement the intervention if the intervention proves clinically and cost effective.

A rehabilitation intervention to promote physical recovery following intensive care: a detailed description of construct development, rationale and content together with proposed taxonomy to capture processes in a randomised controlled trial

PubMed Central

2014-01-01

Background Increasing numbers of patients are surviving critical illness, but survival may be associated with a constellation of physical and psychological sequelae that can cause ongoing disability and reduced health-related quality of life. Limited evidence currently exists to guide the optimum structure, timing, and content of rehabilitation programmes. There is a need to both develop and evaluate interventions to support and expedite recovery during the post-ICU discharge period. This paper describes the construct development for a complex rehabilitation intervention intended to promote physical recovery following critical illness. The intervention is currently being evaluated in a randomised trial (ISRCTN09412438; funder Chief Scientists Office, Scotland). Methods The intervention was developed using the Medical Research Council (MRC) framework for developing complex healthcare interventions. We ensured representation from a wide variety of stakeholders including content experts from multiple specialties, methodologists, and patient representation. The intervention construct was initially based on literature review, local observational and audit work, qualitative studies with ICU survivors, and brainstorming activities. Iterative refinement was aided by the publication of a National Institute for Health and Care Excellence guideline (No. 83), publicly available patient stories (Healthtalkonline), a stakeholder event in collaboration with the James Lind Alliance, and local piloting. Modelling and further work involved a feasibility trial and development of a novel generic rehabilitation assistant (GRA) role. Several rounds of external peer review during successive funding applications also contributed to development. Results The final construct for the complex intervention involved a dedicated GRA trained to pre-defined competencies across multiple rehabilitation domains (physiotherapy, dietetics, occupational therapy, and speech/language therapy), with specific training in post-critical illness issues. The intervention was from ICU discharge to 3 months post-discharge, including inpatient and post-hospital discharge elements. Clear strategies to provide information to patients/families were included. A detailed taxonomy was developed to define and describe the processes undertaken, and capture them during the trial. The detailed process measure description, together with a range of patient, health service, and economic outcomes were successfully mapped on to the modified CONSORT recommendations for reporting non-pharmacologic trial interventions. Conclusions The MRC complex intervention framework was an effective guide to developing a novel post-ICU rehabilitation intervention. Combining a clearly defined new healthcare role with a detailed taxonomy of process and activity enabled the intervention to be clearly described for the purpose of trial delivery and reporting. These data will be useful when interpreting the results of the randomised trial, will increase internal and external trial validity, and help others implement the intervention if the intervention proves clinically and cost effective. PMID:24476530

Application of Behavior Change Techniques in a Personalized Nutrition Electronic Health Intervention Study: Protocol for the Web-Based Food4Me Randomized Controlled Trial

PubMed Central

Macready, Anna L; Fallaize, Rosalind; Butler, Laurie T; Ellis, Judi A; Kuznesof, Sharron; Frewer, Lynn J; Celis-Morales, Carlos; Livingstone, Katherine M; Araújo-Soares, Vera; Fischer, Arnout RH; Stewart-Knox, Barbara J; Mathers, John C

2018-01-01

Background To determine the efficacy of behavior change techniques applied in dietary and physical activity intervention studies, it is first necessary to record and describe techniques that have been used during such interventions. Published frameworks used in dietary and smoking cessation interventions undergo continuous development, and most are not adapted for Web-based delivery. The Food4Me study (N=1607) provided the opportunity to use existing frameworks to describe standardized Web-based techniques employed in a large-scale, internet-based intervention to change dietary behavior and physical activity. Objective The aims of this study were (1) to describe techniques embedded in the Food4Me study design and explain the selection rationale and (2) to demonstrate the use of behavior change technique taxonomies, develop standard operating procedures for training, and identify strengths and limitations of the Food4Me framework that will inform its use in future studies. Methods The 6-month randomized controlled trial took place simultaneously in seven European countries, with participants receiving one of four levels of personalized advice (generalized, intake-based, intake+phenotype–based, and intake+phenotype+gene–based). A three-phase approach was taken: (1) existing taxonomies were reviewed and techniques were identified a priori for possible inclusion in the Food4Me study, (2) a standard operating procedure was developed to maintain consistency in the use of methods and techniques across research centers, and (3) the Food4Me behavior change technique framework was reviewed and updated post intervention. An analysis of excluded techniques was also conducted. Results Of 46 techniques identified a priori as being applicable to Food4Me, 17 were embedded in the intervention design; 11 were from a dietary taxonomy, and 6 from a smoking cessation taxonomy. In addition, the four-category smoking cessation framework structure was adopted for clarity of communication. Smoking cessation texts were adapted for dietary use where necessary. A posteriori, a further 9 techniques were included. Examination of excluded items highlighted the distinction between techniques considered appropriate for face-to-face versus internet-based delivery. Conclusions The use of existing taxonomies facilitated the description and standardization of techniques used in Food4Me. We recommend that for complex studies of this nature, technique analysis should be conducted a priori to develop standardized procedures and training and reviewed a posteriori to audit the techniques actually adopted. The present framework description makes a valuable contribution to future systematic reviews and meta-analyses that explore technique efficacy and underlying psychological constructs. This was a novel application of the behavior change taxonomies and was the first internet-based personalized nutrition intervention to use such a framework remotely. Trial Registration ClinicalTrials.gov NCT01530139; https://clinicaltrials.gov/ct2/show/NCT01530139 (Archived by WebCite at http://www.webcitation.org/6y8XYUft1) PMID:29631993

Taxonomy and species boundaries in the coral genus Favia Milne Edwards and Haime, 1857 (Cnidaria: Scleractinia) from Thailand revealed by morphological and genetic data

NASA Astrophysics Data System (ADS)

Kongjandtre, N.; Ridgway, T.; Cook, L. G.; Huelsken, T.; Budd, A. F.; Hoegh-Guldberg, O.

2012-06-01

While Faviidae is a widely and uniformly distributed coral family throughout the Indo-Pacific, the extensive phenotypic plasticity of colony surface and corallite features often confounds the use of macromorphological characters in species identification, and contributes to conflict between traditional classification and molecular analyses of the group. Recent advances in morphological and molecular techniques now provide a suite of methods to re-address coral taxonomy in complex groups, such as that represented by the Faviidae. This study combines morphologic measurements including "3D coordinates landmarks" data with phylogenetic assessments of nuclear (ITS) and mitochondrial (COI-trnM) DNA to assess species boundaries in nine species of Faviidae with para-septothecal walls from Thailand. Strong concordance was found between morphological features and a priori groupings based on both morphospecies and genetically defined groups (ITS and COI-trnM). Favia truncatus was the most well-defined species based on morphological analyses, and it was also shown to be monophyletic using phylogenetic analyses. Besides F. truncatus, the only other species that was found to be monophyletic in analyses of both genes was F. cf. helianthoides, but its skeletal morphology overlapped with the F. favus species complex (comprised of F. favus, F. speciosa, F. matthaii and F. rotumana). Although not genetically monophyletic, the F. favus species complex and F. pallida were fairly well delineated morphologically. Morphospecies within the F. favus species complex are therefore possibly a result of genetic drift and/or stable polymorphisms driven by divergent selection. These results represent a first step toward a taxonomic revision of the Indo-Pacific Favia, which will integrate morphological methods with the study of type material, genetic information, reproductive data, and tests of phenotypic plasticity—given that multiple lines of evidence are needed to resolve ambiguous species and assign species names.

The Blooming Anatomy Tool (BAT): A Discipline-Specific Rubric for Utilizing Bloom's Taxonomy in the Design and Evaluation of Assessments in the Anatomical Sciences

ERIC Educational Resources Information Center

Thompson, Andrew R.; O'Loughlin, Valerie D.

2015-01-01

Bloom's taxonomy is a resource commonly used to assess the cognitive level associated with course assignments and examination questions. Although widely utilized in educational research, Bloom's taxonomy has received limited attention as an analytical tool in the anatomical sciences. Building on previous research, the Blooming Anatomy Tool (BAT)…

The Examination of Alignment between National Assessment and English Curriculum Objectives Using Revised Bloom's Taxonomy

ERIC Educational Resources Information Center

Kozikoglu, Ishak

2018-01-01

Bloom's taxonomy for the classification of the objectives in cognitive domain was developed in mid 1950s and this taxonomy was revised by a group with Anderson and Krathwohl by making some changes and revisions. The purpose of this research was to evaluate the objectives of 8th grade English curriculum and TEOG exam questions (national assessment…

The Domain of Cognition: An Alternative to Bloom's Cognitive Domain within the Framework of an Information Processing Model.

ERIC Educational Resources Information Center

Stahl, Robert J.; Murphy, Gary T.

Weaknesses in the structure, levels, and sequence of Bloom's taxonomy of cognitive domains emphasize the need for both a new model of how individual learners process information and a new taxonomy of the different levels of memory, thinking, and learning. Both the model and the taxonomy should be consistent with current research findings. The…

A Critical Analysis of Bloom's Taxonomy in Teaching Creative and Critical Thinking Skills in Malaysia through English Literature

ERIC Educational Resources Information Center

Rahman, Shukran Abdul; Manaf, Nor Faridah Abdul

2017-01-01

Purpose: The study aims to (1) review the literature that analyses the relevance of Bloom's Taxonomy of Educational Objectives in the teaching of creative and critical thinking among students in Malaysia, and (2) identify missing aspects in Bloom's Taxonomy vis a vis the indigenous context, important to promote creative and critical thinking among…

"Communicate to vaccinate": the development of a taxonomy of communication interventions to improve routine childhood vaccination.

PubMed

Willis, Natalie; Hill, Sophie; Kaufman, Jessica; Lewin, Simon; Kis-Rigo, John; De Castro Freire, Sara Bensaude; Bosch-Capblanch, Xavier; Glenton, Claire; Lin, Vivian; Robinson, Priscilla; Wiysonge, Charles S

2013-05-11

Vaccination is a cost-effective public health measure and is central to the Millennium Development Goal of reducing child mortality. However, childhood vaccination coverage remains sub-optimal in many settings. While communication is a key feature of vaccination programmes, we are not aware of any comprehensive approach to organising the broad range of communication interventions that can be delivered to parents and communities to improve vaccination coverage. Developing a classification system (taxonomy) organised into conceptually similar categories will aid in: understanding the relationships between different types of communication interventions; facilitating conceptual mapping of these interventions; clarifying the key purposes and features of interventions to aid implementation and evaluation; and identifying areas where evidence is strong and where there are gaps. This paper reports on the development of the 'Communicate to vaccinate' taxonomy. The taxonomy was developed in two stages. Stage 1 included: 1) forming an advisory group; 2) searching for descriptions of interventions in trials (CENTRAL database) and general health literature (Medline); 3) developing a sampling strategy; 4) screening the search results; 5) developing a data extraction form; and 6) extracting intervention data. Stage 2 included: 1) grouping the interventions according to purpose; 2) holding deliberative forums in English and French with key vaccination stakeholders to gather feedback; 3) conducting a targeted search of grey literature to supplement the taxonomy; 4) finalising the taxonomy based on the input provided. The taxonomy includes seven main categories of communication interventions: inform or educate, remind or recall, teach skills, provide support, facilitate decision making, enable communication and enhance community ownership. These categories are broken down into 43 intervention types across three target groups: parents or soon-to-be-parents; communities, community members or volunteers; and health care providers. Our taxonomy illuminates and organises this field and identifies the range of available communication interventions to increase routine childhood vaccination uptake. We have utilised a variety of data sources, capturing information from rigorous evaluations such as randomised trials as well as experiences and knowledge of practitioners and vaccination stakeholders. The taxonomy reflects current public health practice and can guide the future development of vaccination programmes.

“Communicate to vaccinate”: the development of a taxonomy of communication interventions to improve routine childhood vaccination

PubMed Central

2013-01-01

Background Vaccination is a cost-effective public health measure and is central to the Millennium Development Goal of reducing child mortality. However, childhood vaccination coverage remains sub-optimal in many settings. While communication is a key feature of vaccination programmes, we are not aware of any comprehensive approach to organising the broad range of communication interventions that can be delivered to parents and communities to improve vaccination coverage. Developing a classification system (taxonomy) organised into conceptually similar categories will aid in: understanding the relationships between different types of communication interventions; facilitating conceptual mapping of these interventions; clarifying the key purposes and features of interventions to aid implementation and evaluation; and identifying areas where evidence is strong and where there are gaps. This paper reports on the development of the ‘Communicate to vaccinate’ taxonomy. Methods The taxonomy was developed in two stages. Stage 1 included: 1) forming an advisory group; 2) searching for descriptions of interventions in trials (CENTRAL database) and general health literature (Medline); 3) developing a sampling strategy; 4) screening the search results; 5) developing a data extraction form; and 6) extracting intervention data. Stage 2 included: 1) grouping the interventions according to purpose; 2) holding deliberative forums in English and French with key vaccination stakeholders to gather feedback; 3) conducting a targeted search of grey literature to supplement the taxonomy; 4) finalising the taxonomy based on the input provided. Results The taxonomy includes seven main categories of communication interventions: inform or educate, remind or recall, teach skills, provide support, facilitate decision making, enable communication and enhance community ownership. These categories are broken down into 43 intervention types across three target groups: parents or soon-to-be-parents; communities, community members or volunteers; and health care providers. Conclusions Our taxonomy illuminates and organises this field and identifies the range of available communication interventions to increase routine childhood vaccination uptake. We have utilised a variety of data sources, capturing information from rigorous evaluations such as randomised trials as well as experiences and knowledge of practitioners and vaccination stakeholders. The taxonomy reflects current public health practice and can guide the future development of vaccination programmes. PMID:23663327

Use of physically-based models and Soil Taxonomy to identify soil moisture classes: Problems and proposals

NASA Astrophysics Data System (ADS)

Bonfante, A.; Basile, A.; de Mascellis, R.; Manna, P.; Terribile, F.

2009-04-01

Soil classification according to Soil Taxonomy include, as fundamental feature, the estimation of soil moisture regime. The term soil moisture regime refers to the "presence or absence either of ground water or of water held at a tension of less than 1500 kPa in the soil or in specific horizons during periods of the year". In the classification procedure, defining of the soil moisture control section is the primary step in order to obtain the soil moisture regimes classification. Currently, the estimation of soil moisture regimes is carried out through simple calculation schemes, such as Newhall and Billaux models, and only in few cases some authors suggest the use of different more complex models (i.e., EPIC) In fact, in the Soil Taxonomy, the definition of the soil moisture control section is based on the wetting front position in two different conditions: the upper boundary is the depth to which a dry soil will be moistened by 2.5 cm of water within 24 hours and the lower boundary is the depth to which a dry soil will be moistened by 7.5 cm of water within 48 hours. Newhall, Billaux and EPIC models don't use physical laws to describe soil water flows, but they use a simple bucket-like scheme where the soil is divided into several compartments and water moves, instantly, only downward when the field capacity is achieved. On the other side, a large number of one-dimensional hydrological simulation models (SWAP, Cropsyst, Hydrus, MACRO, etc..) are available, tested and successfully used. The flow is simulated according to pressure head gradients through the numerical solution of the Richard's equation. These simulation models can be fruitful used to improve the study of soil moisture regimes. The aims of this work are: (i) analysis of the soil moisture control section concept by a physically based model (SWAP); (ii) comparison of the classification obtained in five different Italian pedoclimatic conditions (Mantova and Lodi in northern Italy; Salerno, Benevento and Caserta in southern Italy) applying the classical models (Newhall e Billaux) and the physically-based models (CropSyst e SWAP), The results have shown that the Soil Taxonomy scheme for the definition of the soil moisture regime is unrealistic for the considered Mediterranean soil hydrological conditions. In fact, the same classifications arise irrespective of the soil type. In this respect some suggestions on how modified the section control boundaries were formulated. Keywords: Soil moisture regimes, Newhall, Swap, Soil Taxonomy

Sample data processing in an additive and reproducible taxonomic workflow by using character data persistently linked to preserved individual specimens

PubMed Central

Kilian, Norbert; Henning, Tilo; Plitzner, Patrick; Müller, Andreas; Güntsch, Anton; Stöver, Ben C.; Müller, Kai F.; Berendsohn, Walter G.; Borsch, Thomas

2015-01-01

We present the model and implementation of a workflow that blazes a trail in systematic biology for the re-usability of character data (data on any kind of characters of pheno- and genotypes of organisms) and their additivity from specimen to taxon level. We take into account that any taxon characterization is based on a limited set of sampled individuals and characters, and that consequently any new individual and any new character may affect the recognition of biological entities and/or the subsequent delimitation and characterization of a taxon. Taxon concepts thus frequently change during the knowledge generation process in systematic biology. Structured character data are therefore not only needed for the knowledge generation process but also for easily adapting characterizations of taxa. We aim to facilitate the construction and reproducibility of taxon characterizations from structured character data of changing sample sets by establishing a stable and unambiguous association between each sampled individual and the data processed from it. Our workflow implementation uses the European Distributed Institute of Taxonomy Platform, a comprehensive taxonomic data management and publication environment to: (i) establish a reproducible connection between sampled individuals and all samples derived from them; (ii) stably link sample-based character data with the metadata of the respective samples; (iii) record and store structured specimen-based character data in formats allowing data exchange; (iv) reversibly assign sample metadata and character datasets to taxa in an editable classification and display them and (v) organize data exchange via standard exchange formats and enable the link between the character datasets and samples in research collections, ensuring high visibility and instant re-usability of the data. The workflow implemented will contribute to organizing the interface between phylogenetic analysis and revisionary taxonomic or monographic work. Database URL: http://campanula.e-taxonomy.net/ PMID:26424081

The globally distributed genus Alexandrium: multifaceted roles in marine ecosystems and impacts on human health

PubMed Central

Alpermann, Tilman J.; Cembella, Allan D.; Collos, Yves; Masseret, Estelle; Montresor, Marina

2011-01-01

The dinoflagellate genus Alexandrium is one of the major harmful algal bloom (HAB) genera with respect to the diversity, magnitude and consequences of blooms. The ability of Alexandrium to colonize multiple habitats and to persist over large regions through time is testimony to the adaptability and resilience of this group of species. Three different families of toxins, as well as an as yet incompletely characterized suite of allelochemicals are produced among Alexandrium species. Nutritional strategies are equally diverse, including the ability to utilize a range of inorganic and organic nutrient sources, and feeding by ingestion of other organisms. Many Alexandrium species have complex life histories that include sexuality and often, but not always, cyst formation, which is characteristic of a meroplanktonic life strategy and offers considerable ecological advantages. Due to the public health and ecosystem impacts of Alexandrium blooms, the genus has been extensively studied, and there exists a broad knowledge base that ranges from taxonomy and phylogeny through genomics and toxin biosynthesis to bloom dynamics and modeling. Here we present a review of the genus Alexandrium, focusing on the major toxic and otherwise harmful species. PMID:22308102

The globally distributed genus Alexandrium: multifaceted roles in marine ecosystems and impacts on human health.

PubMed

Anderson, Donald M; Alpermann, Tilman J; Cembella, Allan D; Collos, Yves; Masseret, Estelle; Montresor, Marina

2012-02-01

The dinoflagellate genus Alexandrium is one of the major harmful algal bloom (HAB) genera with respect to the diversity, magnitude and consequences of blooms. The ability of Alexandrium to colonize multiple habitats and to persist over large regions through time is testimony to the adaptability and resilience of this group of species. Three different families of toxins, as well as an as yet incompletely characterized suite of allelochemicals are produced among Alexandrium species. Nutritional strategies are equally diverse, including the ability to utilize a range of inorganic and organic nutrient sources, and feeding by ingestion of other organisms. Many Alexandrium species have complex life histories that include sexuality and often, but not always, cyst formation, which is characteristic of a meroplanktonic life strategy and offers considerable ecological advantages. Due to the public health and ecosystem impacts of Alexandrium blooms, the genus has been extensively studied, and there exists a broad knowledge base that ranges from taxonomy and phylogeny through genomics and toxin biosynthesis to bloom dynamics and modeling. Here we present a review of the genus Alexandrium, focusing on the major toxic and otherwise harmful species.

Semantic Web meets Integrative Biology: a survey.

PubMed

Chen, Huajun; Yu, Tong; Chen, Jake Y

2013-01-01

Integrative Biology (IB) uses experimental or computational quantitative technologies to characterize biological systems at the molecular, cellular, tissue and population levels. IB typically involves the integration of the data, knowledge and capabilities across disciplinary boundaries in order to solve complex problems. We identify a series of bioinformatics problems posed by interdisciplinary integration: (i) data integration that interconnects structured data across related biomedical domains; (ii) ontology integration that brings jargons, terminologies and taxonomies from various disciplines into a unified network of ontologies; (iii) knowledge integration that integrates disparate knowledge elements from multiple sources; (iv) service integration that build applications out of services provided by different vendors. We argue that IB can benefit significantly from the integration solutions enabled by Semantic Web (SW) technologies. The SW enables scientists to share content beyond the boundaries of applications and websites, resulting into a web of data that is meaningful and understandable to any computers. In this review, we provide insight into how SW technologies can be used to build open, standardized and interoperable solutions for interdisciplinary integration on a global basis. We present a rich set of case studies in system biology, integrative neuroscience, bio-pharmaceutics and translational medicine, to highlight the technical features and benefits of SW applications in IB.

Biology, taxonomy, and IPM strategies of Bactrocera tau Walker and complex species (Diptera; Tephritidae) in Asia: a comprehensive review.

PubMed

Jaleel, Waqar; Lu, Lihua; He, Yurong

2018-06-02

Bactrocera flies are the serious pests of fruit, vegetables, and nuts over the world. Bactrocera tau Walker is an economically important pest of agricultural crops. In Asia, approximately 30-40% losses of agricultural products are caused by B. tau infestation every year. In Asia, the B. tau contains a complex of sibling species that called the tau complex. However, the basic studies of B. tau and complex species are very important for integrated management. A comprehensive review of the B. tau and complex species has not been provided elsewhere. So, considering the importance of B. tau and complex species, this study provides the published information on ecology, nomenclature, identification tools, geographical distribution, potential invasion, and IPM tactics of B. tau and complex species, which would be more informative for publication facilitating related to integrated pest management (IPM) strategies of B. tau and complex species. In IPM of B. tau and complex species, the phytochemical and biological controls have not been applied successfully in Asia; there is an urgent need to study and applications of these two mentioned control techniques against the B. tau and complex species in Asia.

Aspergillus flavus: human pathogen, allergen and mycotoxin producer.

PubMed

Hedayati, M T; Pasqualotto, A C; Warn, P A; Bowyer, P; Denning, D W

2007-06-01

Aspergillus infections have grown in importance in the last years. However, most of the studies have focused on Aspergillus fumigatus, the most prevalent species in the genus. In certain locales and hospitals, Aspergillus flavus is more common in air than A. fumigatus, for unclear reasons. After A. fumigatus, A. flavus is the second leading cause of invasive aspergillosis and it is the most common cause of superficial infection. Experimental invasive infections in mice show A. flavus to be 100-fold more virulent than A. fumigatus in terms of inoculum required. Particularly common clinical syndromes associated with A. flavus include chronic granulomatous sinusitis, keratitis, cutaneous aspergillosis, wound infections and osteomyelitis following trauma and inoculation. Outbreaks associated with A. flavus appear to be associated with single or closely related strains, in contrast to those associated with A. fumigatus. In addition, A. flavus produces aflatoxins, the most toxic and potent hepatocarcinogenic natural compounds ever characterized. Accurate species identification within Aspergillus flavus complex remains difficult due to overlapping morphological and biochemical characteristics, and much taxonomic and population genetics work is necessary to better understand the species and related species. The flavus complex currently includes 23 species or varieties, including two sexual species, Petromyces alliaceus and P. albertensis. The genome of the highly related Aspergillus oryzae is completed and available; that of A. flavus in the final stages of annotation. Our understanding of A. flavus lags far behind that of A. fumigatus. Studies of the genomics, taxonomy, population genetics, pathogenicity, allergenicity and antifungal susceptibility of A. flavus are all required.

A taxonomy and discussion of software attack technologies

NASA Astrophysics Data System (ADS)

Banks, Sheila B.; Stytz, Martin R.

2005-03-01

Software is a complex thing. It is not an engineering artifact that springs forth from a design by simply following software coding rules; creativity and the human element are at the heart of the process. Software development is part science, part art, and part craft. Design, architecture, and coding are equally important activities and in each of these activities, errors may be introduced that lead to security vulnerabilities. Therefore, inevitably, errors enter into the code. Some of these errors are discovered during testing; however, some are not. The best way to find security errors, whether they are introduced as part of the architecture development effort or coding effort, is to automate the security testing process to the maximum extent possible and add this class of tools to the tools available, which aids in the compilation process, testing, test analysis, and software distribution. Recent technological advances, improvements in computer-generated forces (CGFs), and results in research in information assurance and software protection indicate that we can build a semi-intelligent software security testing tool. However, before we can undertake the security testing automation effort, we must understand the scope of the required testing, the security failures that need to be uncovered during testing, and the characteristics of the failures. Therefore, we undertook the research reported in the paper, which is the development of a taxonomy and a discussion of software attacks generated from the point of view of the security tester with the goal of using the taxonomy to guide the development of the knowledge base for the automated security testing tool. The representation for attacks and threat cases yielded by this research captures the strategies, tactics, and other considerations that come into play during the planning and execution of attacks upon application software. The paper is organized as follows. Section one contains an introduction to our research and a discussion of the motivation for our work. Section two contains a presents our taxonomy of software attacks and a discussion of the strategies employed and general weaknesses exploited for each attack. Section three contains a summary and suggestions for further research.

Assessing Quality of Data Standards: Framework and Illustration Using XBRL GAAP Taxonomy

NASA Astrophysics Data System (ADS)

Zhu, Hongwei; Wu, Harris

The primary purpose of data standards or metadata schemas is to improve the interoperability of data created by multiple standard users. Given the high cost of developing data standards, it is desirable to assess the quality of data standards. We develop a set of metrics and a framework for assessing data standard quality. The metrics include completeness and relevancy. Standard quality can also be indirectly measured by assessing interoperability of data instances. We evaluate the framework using data from the financial sector: the XBRL (eXtensible Business Reporting Language) GAAP (Generally Accepted Accounting Principles) taxonomy and US Securities and Exchange Commission (SEC) filings produced using the taxonomy by approximately 500 companies. The results show that the framework is useful and effective. Our analysis also reveals quality issues of the GAAP taxonomy and provides useful feedback to taxonomy users. The SEC has mandated that all publicly listed companies must submit their filings using XBRL. Our findings are timely and have practical implications that will ultimately help improve the quality of financial data.

The "wild shot": photography for more biology in natural history collections, not for replacing vouchers.

PubMed

Garrouste, Romain

2017-05-24

Recently a correspondence in Zootaxa (Ceríaco et al., 2016) with more than 450 signatories including taxonomists, curators and other taxonomy users from all continents has received wide attention and has stimulated extensive discussion (a true buzz) around the possible interpretations of the Code (ICZN) about photography in taxonomy (Researchgate website link). This short note was necessary to recall the necessity of preserved specimens as vouchers for taxonomy, in response to photography-based taxonomy (PBT) as defended by Pape et al. (2016), and in a broad sense, for all the life sciences. This had been widely discussed and argued by Dubois & Nemésio (2007) who concluded on the importance of vouchers in taxonomy. But if the subject of these papers and discussions are about photography as the only way to document a new species, none of them discussed really what photography could represent in enhancing knowledge in natural sciences based on collections of specimens including type series and in association with other media (video and sound).

Algal taxonomy: a road to nowhere?

PubMed

De Clerck, Olivier; Guiry, Michael D; Leliaert, Frederik; Samyn, Yves; Verbruggen, Heroen

2013-04-01

The widespread view of taxonomy as an essentially retrogressive and outmoded science unable to cope with the current biodiversity crisis stimulated us to analyze the current status of cataloguing global algal diversity. Contrary to this largely pessimistic belief, species description rates of algae through time and trends in the number of active taxonomists, as revealed by the web resource AlgaeBase, show a much more positive picture. More species than ever before are being described by a large community of algal taxonomists. The lack of any decline in the rate at which new species and genera are described, however, is indicative of the large proportion of undiscovered diversity and bears heavily on any prediction of global algal species diversity and the time needed to catalogue it. The saturation of accumulation curves of higher taxa (family, order, and classes) on the other hand suggest that at these taxonomic levels most diversity has been discovered. This reasonably positive picture does not imply that algal taxonomy does not face serious challenges in the near future. The observed levels of cryptic diversity in algae, combined with the shift in methods used to characterize them, have resulted in a rampant uncertainty about the status of many older species. As a consequence, there is a tendency in phycology to move gradually away from traditional names to a more informal system whereby clade-, specimen- or strain-based identifiers are used to communicate biological information. Whether these informal names for species-level clades represent a temporary situation stimulated by the lag between species discovery and formal description, or an incipient alternative or parallel taxonomy, will be largely determined by how well we manage to integrate historical collections into modern taxonomic research. Additionally, there is a pressing need for a consensus about the organizational framework to manage the information about algal species names. An eventual strategy should preferably come out of an international working group that includes the various databases as well as the various phycological societies. In this strategy, phycologists should link up to major international initiatives that are currently being developed, such as the compulsory registration of taxonomic and nomenclatural acts and the introduction of Life Science Identifiers. © 2012 Phycological Society of America.

Bloom's taxonomy of cognitive learning objectives.

PubMed

Adams, Nancy E

2015-07-01

Information professionals who train or instruct others can use Bloom's taxonomy to write learning objectives that describe the skills and abilities that they desire their learners to master and demonstrate. Bloom's taxonomy differentiates between cognitive skill levels and calls attention to learning objectives that require higher levels of cognitive skills and, therefore, lead to deeper learning and transfer of knowledge and skills to a greater variety of tasks and contexts.

Taxonomy Working Group Final Report

NASA Technical Reports Server (NTRS)

Parsons, Vickie S.; Beil, Robert J.; Terrone, Mark; Barth, Timothy S.; Panontin, Tina L.; Wales, Roxana; Rackley, Michael W.; Milne, James S.; McPherson, John W.; Dutra, Jayne E.;

Eye on the Gemba: Using Student-Created Videos and the Revised Bloom's Taxonomy to Teach Lean Management

ERIC Educational Resources Information Center

Marley, Kathryn A.

2014-01-01

Developing exercises that lead students to use higher order thinking skills is a challenge for faculty in any discipline. An excellent way to approach this problem is to use the Revised Bloom's Taxonomy as a guide. In the taxonomy, the highest level of learning is to create. The author describes an assignment that builds on the use of…

Ecogenomics and Taxonomy of Cyanobacteria Phylum

PubMed Central

Walter, Juline M.; Coutinho, Felipe H.; Dutilh, Bas E.; Swings, Jean; Thompson, Fabiano L.; Thompson, Cristiane C.

2017-01-01

Cyanobacteria are major contributors to global biogeochemical cycles. The genetic diversity among Cyanobacteria enables them to thrive across many habitats, although only a few studies have analyzed the association of phylogenomic clades to specific environmental niches. In this study, we adopted an ecogenomics strategy with the aim to delineate ecological niche preferences of Cyanobacteria and integrate them to the genomic taxonomy of these bacteria. First, an appropriate phylogenomic framework was established using a set of genomic taxonomy signatures (including a tree based on conserved gene sequences, genome-to-genome distance, and average amino acid identity) to analyse ninety-nine publicly available cyanobacterial genomes. Next, the relative abundances of these genomes were determined throughout diverse global marine and freshwater ecosystems, using metagenomic data sets. The whole-genome-based taxonomy of the ninety-nine genomes allowed us to identify 57 (of which 28 are new genera) and 87 (of which 32 are new species) different cyanobacterial genera and species, respectively. The ecogenomic analysis allowed the distinction of three major ecological groups of Cyanobacteria (named as i. Low Temperature; ii. Low Temperature Copiotroph; and iii. High Temperature Oligotroph) that were coherently linked to the genomic taxonomy. This work establishes a new taxonomic framework for Cyanobacteria in the light of genomic taxonomy and ecogenomic approaches. PMID:29184540

Are Patient and Carer Experiences Mirrored in the Practice Reviews of Self-management Support (Prisms) Provider Taxonomy?

PubMed Central

Kenealy, Timothy; Kuluski, Kerry; McKillop, Ann; Parsons, John; Wong-Cornall, Cecilia

2017-01-01

Introduction: Patient self-management support is central to care for long term conditions and for integrated care. Patients and their carers are the final arbiter of whether support for self-management has been effective. A new taxonomy lists 14 categories of provider activities that support patient self-management (Practical Reviews in Self-Management Support, PRISMS). We asked whether we could recognise these provider activities in narratives from patients and carers. We sought to extend the theoretical framework of the taxonomy to include the view from patient and carers. Methods: We interviewed 28 patients and family carers in a case study of primary health care in New Zealand in 2015 to determine which components of the taxonomy were visible. We drew on interviews with clinicians and organisation persons to explain case study context. Results: We found, within patient and carer data, evidence of all 14 components of provider self-management support. The overarching dimensions of the taxonomy helped reveal an intensity and consistency of provider behaviour that was not apparent considering the individual components. Conclusions: Patient and carer data mapped to provider activities. The taxonomy was not explicit on provider relationships and engagement with, or separate support needs of, patients and carers. PMID:28970749

Towards an international taxonomy of integrated primary care: a Delphi consensus approach.

PubMed

Valentijn, Pim P; Vrijhoef, Hubertus J M; Ruwaard, Dirk; Boesveld, Inge; Arends, Rosa Y; Bruijnzeels, Marc A

2015-05-22

Developing integrated service models in a primary care setting is considered an essential strategy for establishing a sustainable and affordable health care system. The Rainbow Model of Integrated Care (RMIC) describes the theoretical foundations of integrated primary care. The aim of this study is to refine the RMIC by developing a consensus-based taxonomy of key features. First, the appropriateness of previously identified key features was retested by conducting an international Delphi study that was built on the results of a previous national Delphi study. Second, categorisation of the features among the RMIC integrated care domains was assessed in a second international Delphi study. Finally, a taxonomy was constructed by the researchers based on the results of the three Delphi studies. The final taxonomy consists of 21 key features distributed over eight integration domains which are organised into three main categories: scope (person-focused vs. population-based), type (clinical, professional, organisational and system) and enablers (functional vs. normative) of an integrated primary care service model. The taxonomy provides a crucial differentiation that clarifies and supports implementation, policy formulation and research regarding the organisation of integrated primary care. Further research is needed to develop instruments based on the taxonomy that can reveal the realm of integrated primary care in practice.

Ecogenomics and Taxonomy of Cyanobacteria Phylum.

PubMed

Walter, Juline M; Coutinho, Felipe H; Dutilh, Bas E; Swings, Jean; Thompson, Fabiano L; Thompson, Cristiane C

2017-01-01

Cyanobacteria are major contributors to global biogeochemical cycles. The genetic diversity among Cyanobacteria enables them to thrive across many habitats, although only a few studies have analyzed the association of phylogenomic clades to specific environmental niches. In this study, we adopted an ecogenomics strategy with the aim to delineate ecological niche preferences of Cyanobacteria and integrate them to the genomic taxonomy of these bacteria. First, an appropriate phylogenomic framework was established using a set of genomic taxonomy signatures (including a tree based on conserved gene sequences, genome-to-genome distance, and average amino acid identity) to analyse ninety-nine publicly available cyanobacterial genomes. Next, the relative abundances of these genomes were determined throughout diverse global marine and freshwater ecosystems, using metagenomic data sets. The whole-genome-based taxonomy of the ninety-nine genomes allowed us to identify 57 (of which 28 are new genera) and 87 (of which 32 are new species) different cyanobacterial genera and species, respectively. The ecogenomic analysis allowed the distinction of three major ecological groups of Cyanobacteria (named as i. Low Temperature; ii. Low Temperature Copiotroph; and iii. High Temperature Oligotroph) that were coherently linked to the genomic taxonomy. This work establishes a new taxonomic framework for Cyanobacteria in the light of genomic taxonomy and ecogenomic approaches.

An Analysis of the Most Commonly Tested Topics and Their Taxonomy From Recent Self-Assessment Examinations.

PubMed

Krueger, Chad A; Moroze, Sean; Murtha, Andrew S; Rivera, Jessica C

The purpose of this study is to determine the most commonly tested topics and the question taxonomy of the American Academy of Orthopaedic Surgeons Self-Assessment Examinations (SAE) from 2009 through 2014. All SAEs were analyzed from 2009 through 2014. The SAEs were separated by subject and the questions of each SAE were analyzed for topic, taxonomic classification, and question type. A total of 2107 questions were reviewed from 10 different subjects. In all, 6 of the 9 subjects had roughly 1/3 of their questions composed of the 3 most commonly tested topics. Each subject had at least 1 trauma-related question within its top 5 most commonly tested topics. Almost half (47%) of all questions were of taxonomy 1 classification and 29% were taxonomy 3. The Basic Science SAEs had the greatest percentage of taxonomy 1 questions of any subject (83%) whereas Trauma contained the highest percentage of taxonomy 3 questions (47%). Certain topics within each subject are consistently tested more often than other topics. In general, the 3 most commonly tested topics comprise about one-third of total questions and orthopedic surgeons should be very familiar with these topics in order to best prepare for standardized examinations. Published by Elsevier Inc.

Developing a method for specifying the components of behavior change interventions in practice: the example of smoking cessation.

PubMed

Lorencatto, Fabiana; West, Robert; Seymour, Natalie; Michie, Susan

2013-06-01

There is a difference between interventions as planned and as delivered in practice. Unless we know what was actually delivered, we cannot understand "what worked" in effective interventions. This study aimed to (a) assess whether an established taxonomy of 53 smoking cessation behavior change techniques (BCTs) may be applied or adapted as a method for reliably specifying the content of smoking cessation behavioral support consultations and (b) develop an effective method for training researchers and practitioners in the reliable application of the taxonomy. Fifteen transcripts of audio-recorded consultations delivered by England's Stop Smoking Services were coded into component BCTs using the taxonomy. Interrater reliability and potential adaptations to the taxonomy to improve coding were discussed following 3 coding waves. A coding training manual was developed through expert consensus and piloted on 10 trainees, assessing coding reliability and self-perceived competence before and after training. An average of 33 BCTs from the taxonomy were identified at least once across sessions and coding waves. Consultations contained on average 12 BCTs (range = 8-31). Average interrater reliability was high (88% agreement). The taxonomy was adapted to simplify coding by merging co-occurring BCTs and refining BCT definitions. Coding reliability and self-perceived competence significantly improved posttraining for all trainees. It is possible to apply a taxonomy to reliably identify and classify BCTs in smoking cessation behavioral support delivered in practice, and train inexperienced coders to do so reliably. This method can be used to investigate variability in provision of behavioral support across services, monitor fidelity of delivery, and identify training needs.

Towards a unified taxonomy of health indicators: academic health centers and communities working together to improve population health.

PubMed

Aguilar-Gaxiola, Sergio; Ahmed, Syed; Franco, Zeno; Kissack, Anne; Gabriel, Davera; Hurd, Thelma; Ziegahn, Linda; Bates, Nancy J; Calhoun, Karen; Carter-Edwards, Lori; Corbie-Smith, Giselle; Eder, Milton Mickey; Ferrans, Carol; Hacker, Karen; Rumala, Bernice B; Strelnick, A Hal; Wallerstein, Nina

2014-04-01

The Clinical and Translational Science Awards (CTSA) program represents a significant public investment. To realize its major goal of improving the public's health and reducing health disparities, the CTSA Consortium's Community Engagement Key Function Committee has undertaken the challenge of developing a taxonomy of community health indicators. The objective is to initiate a unified approach for monitoring progress in improving population health outcomes. Such outcomes include, importantly, the interests and priorities of community stakeholders, plus the multiple, overlapping interests of universities and of the public health and health care professions involved in the development and use of local health care indicators.The emerging taxonomy of community health indicators that the authors propose supports alignment of CTSA activities and facilitates comparative effectiveness research across CTSAs, thereby improving the health of communities and reducing health disparities. The proposed taxonomy starts at the broadest level, determinants of health; subsequently moves to more finite categories of community health indicators; and, finally, addresses specific quantifiable measures. To illustrate the taxonomy's application, the authors have synthesized 21 health indicator projects from the literature and categorized them into international, national, or local/special jurisdictions. They furthered categorized the projects within the taxonomy by ranking indicators with the greatest representation among projects and by ranking the frequency of specific measures. They intend for the taxonomy to provide common metrics for measuring changes to population health and, thus, extend the utility of the CTSA Community Engagement Logic Model. The input of community partners will ultimately improve population health.

Building a taxonomy of integrated palliative care initiatives: results from a focus group

PubMed Central

Ewert, Benjamin; Hodiamont, Farina; van Wijngaarden, Jeroen; Payne, Sheila; Groot, Marieke; Hasselaar, Jeroen; Menten, Johann; Radbruch, Lukas

2016-01-01

Background Empirical evidence suggests that integrated palliative care (IPC) increases the quality of care for palliative patients and supports professional caregivers. Existing IPC initiatives in Europe vary in their design and are hardly comparable. InSuP-C, a European Union research project, aimed to build a taxonomy of IPC initiatives applicable across diseases, healthcare sectors and systems. Methods The taxonomy of IPC initiatives was developed in cooperation with an international and multidisciplinary focus group of 18 experts. Subsequently, a consensus meeting of 10 experts revised a preliminary taxonomy and adopted the final classification system. Results Consisting of eight categories, with two to four items each, the taxonomy covers the process and structure of IPC initiatives. If two items in at least one category apply to an initiative, a minimum level of integration is assumed to have been reached. Categories range from the type of initiative (items: pathway, model or guideline) to patients’ key contact (items: non-pc specialist, pc specialist, general practitioner). Experts recommended the inclusion of two new categories: level of care (items: primary, secondary or tertiary) indicating at which stage palliative care is integrated and primary focus of intervention describing IPC givers’ different roles (items: treating function, advising/consulting or training) in the care process. Conclusions Empirical studies are required to investigate how the taxonomy is used in practice and whether it covers the reality of patients in need of palliative care. The InSuP-C project will test this taxonomy empirically in selected initiatives using IPC. PMID:26647043

Development, dissemination, and applications of a new terminological resource, the Q-Code taxonomy for professional aspects of general practice/family medicine.

PubMed

Jamoulle, Marc; Resnick, Melissa; Grosjean, Julien; Ittoo, Ashwin; Cardillo, Elena; Vander Stichele, Robert; Darmoni, Stefan; Vanmeerbeek, Marc

2018-12-01

While documentation of clinical aspects of General Practice/Family Medicine (GP/FM) is assured by the International Classification of Primary Care (ICPC), there is no taxonomy for the professional aspects (context and management) of GP/FM. To present the development, dissemination, applications, and resulting face validity of the Q-Codes taxonomy specifically designed to describe contextual features of GP/FM, proposed as an extension to the ICPC. The Q-Codes taxonomy was developed from Lamberts' seminal idea for indexing contextual content (1987) by a multi-disciplinary team of knowledge engineers, linguists and general practitioners, through a qualitative and iterative analysis of 1702 abstracts from six GP/FM conferences using Atlas.ti software. A total of 182 concepts, called Q-Codes, representing professional aspects of GP/FM were identified and organized in a taxonomy. Dissemination: The taxonomy is published as an online terminological resource, using semantic web techniques and web ontology language (OWL) ( http://www.hetop.eu/Q ). Each Q-Code is identified with a unique resource identifier (URI), and provided with preferred terms, and scope notes in ten languages (Portuguese, Spanish, English, French, Dutch, Korean, Vietnamese, Turkish, Georgian, German) and search filters for MEDLINE and web searches. This taxonomy has already been used to support queries in bibliographic databases (e.g., MEDLINE), to facilitate indexing of grey literature in GP/FM as congress abstracts, master theses, websites and as an educational tool in vocational teaching, Conclusions: The rapidly growing list of practical applications provides face-validity for the usefulness of this freely available new terminological resource.

Sine systemate chaos? A versatile tool for earthworm taxonomy: non-destructive imaging of freshly fixed and museum specimens using micro-computed tomography.

PubMed

Fernández, Rosa; Kvist, Sebastian; Lenihan, Jennifer; Giribet, Gonzalo; Ziegler, Alexander

2014-01-01

In spite of the high relevance of lumbricid earthworms ('Oligochaeta': Lumbricidae) for soil structure and functioning, the taxonomy of this group of terrestrial invertebrates remains in a quasi-chaotic state. Earthworm taxonomy traditionally relies on the interpretation of external and internal morphological characters, but the acquisition of these data is often hampered by tedious dissections or restricted access to valuable and rare museum specimens. The present state of affairs, in conjunction with the difficulty of establishing primary homologies for multiple morphological features, has led to an almost unrivaled instability in the taxonomy and systematics of certain earthworm groups, including Lumbricidae. As a potential remedy, we apply for the first time a non-destructive imaging technique to lumbricids and explore the future application of this approach to earthworm taxonomy. High-resolution micro-computed tomography (μCT) scanning of freshly fixed and museum specimens was carried out using two cosmopolitan species, Aporrectodea caliginosa and A. trapezoides. By combining two-dimensional and three-dimensional dataset visualization techniques, we demonstrate that the morphological features commonly used in earthworm taxonomy can now be analyzed without the need for dissection, whether freshly fixed or museum specimens collected more than 60 years ago are studied. Our analyses show that μCT in combination with soft tissue staining can be successfully applied to lumbricid earthworms. An extension of the approach to other families is poised to strengthen earthworm taxonomy by providing a versatile tool to resolve the taxonomic chaos currently present in this ecologically important, but taxonomically neglected group of terrestrial invertebrates.

Sine Systemate Chaos? A Versatile Tool for Earthworm Taxonomy: Non-Destructive Imaging of Freshly Fixed and Museum Specimens Using Micro-Computed Tomography

PubMed Central

Fernández, Rosa; Kvist, Sebastian; Lenihan, Jennifer; Giribet, Gonzalo; Ziegler, Alexander

2014-01-01

In spite of the high relevance of lumbricid earthworms (‘Oligochaeta’: Lumbricidae) for soil structure and functioning, the taxonomy of this group of terrestrial invertebrates remains in a quasi-chaotic state. Earthworm taxonomy traditionally relies on the interpretation of external and internal morphological characters, but the acquisition of these data is often hampered by tedious dissections or restricted access to valuable and rare museum specimens. The present state of affairs, in conjunction with the difficulty of establishing primary homologies for multiple morphological features, has led to an almost unrivaled instability in the taxonomy and systematics of certain earthworm groups, including Lumbricidae. As a potential remedy, we apply for the first time a non-destructive imaging technique to lumbricids and explore the future application of this approach to earthworm taxonomy. High-resolution micro-computed tomography (μCT) scanning of freshly fixed and museum specimens was carried out using two cosmopolitan species, Aporrectodea caliginosa and A. trapezoides. By combining two-dimensional and three-dimensional dataset visualization techniques, we demonstrate that the morphological features commonly used in earthworm taxonomy can now be analyzed without the need for dissection, whether freshly fixed or museum specimens collected more than 60 years ago are studied. Our analyses show that μCT in combination with soft tissue staining can be successfully applied to lumbricid earthworms. An extension of the approach to other families is poised to strengthen earthworm taxonomy by providing a versatile tool to resolve the taxonomic chaos currently present in this ecologically important, but taxonomically neglected group of terrestrial invertebrates. PMID:24837238

The structure of observed learning outcome (SOLO) taxonomy: a model to promote dental students' learning.

PubMed

Lucander, H; Bondemark, L; Brown, G; Knutsson, K

2010-08-01

Selective memorising of isolated facts or reproducing what is thought to be required - the surface approach to learning - is not the desired outcome for a dental student or a dentist in practice. The preferred outcome is a deep approach as defined by an intention to seek understanding, develop expertise and relate information and knowledge into a coherent whole. The aim of this study was to investigate whether the structure of observed learning outcome (SOLO) taxonomy could be used as a model to assist and promote the dental students to develop a deep approach to learning assessed as learning outcomes in a summative assessment. Thirty-two students, participating in course eight in 2007 at the Faculty of Odontology at Malmö University, were introduced to the SOLO taxonomy and constituted the test group. The control group consisted of 35 students participating in course eight in 2006. The effect of the introduction was measured by evaluating responses to a question in the summative assessment by using the SOLO taxonomy. The evaluators consisted of two teachers who performed the assessment of learning outcomes independently and separately on the coded material. The SOLO taxonomy as a model for learning was found to improve the quality of learning. Compared to the control group significantly more strings and structured relations between these strings were present in the test group after the SOLO taxonomy had been introduced (P < 0.01, one tailed test for both results). The SOLO taxonomy is recommended as a model for promoting and developing a deeper approach to learning in dentistry.

What is a medical decision? A taxonomy based on physician statements in hospital encounters: a qualitative study.

PubMed

Ofstad, Eirik H; Frich, Jan C; Schei, Edvin; Frankel, Richard M; Gulbrandsen, Pål

2016-02-11

The medical literature lacks a comprehensive taxonomy of decisions made by physicians in medical encounters. Such a taxonomy might be useful in understanding the physician-centred, patient-centred and shared decision-making in clinical settings. We aimed to identify and classify all decisions emerging in conversations between patients and physicians. Qualitative study of video recorded patient-physician encounters. 380 patients in consultations with 59 physicians from 17 clinical specialties and three different settings (emergency room, ward round, outpatient clinic) in a Norwegian teaching hospital. A randomised sample of 30 encounters from internal medicine was used to identify and classify decisions, a maximum variation sample of 20 encounters was used for reliability assessments, and the remaining encounters were analysed to test for applicability across specialties. On the basis of physician statements in our material, we developed a taxonomy of clinical decisions--the Decision Identification and Classification Taxonomy for Use in Medicine (DICTUM). We categorised decisions into 10 mutually exclusive categories: gathering additional information, evaluating test results, defining problem, drug-related, therapeutic procedure-related, legal and insurance-related, contact-related, advice and precaution, treatment goal, and deferment. Four-coder inter-rater reliability using Krippendorff's α was 0.79. DICTUM represents a precise, detailed and comprehensive taxonomy of medical decisions communicated within patient-physician encounters. Compared to previous normative frameworks, the taxonomy is descriptive, substantially broader and offers new categories to the variety of clinical decisions. The taxonomy could prove helpful in studies on the quality of medical work, use of time and resources, and understanding of why, when and how patients are or are not involved in decisions. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

The comprehensive 'Communicate to Vaccinate' taxonomy of communication interventions for childhood vaccination in routine and campaign contexts.

PubMed

Kaufman, Jessica; Ames, Heather; Bosch-Capblanch, Xavier; Cartier, Yuri; Cliff, Julie; Glenton, Claire; Lewin, Simon; Muloliwa, Artur Manuel; Oku, Afiong; Oyo-Ita, Angela; Rada, Gabriel; Hill, Sophie

2017-05-10

Communication can be used to generate demand for vaccination or address vaccine hesitancy, and is crucial to successful childhood vaccination programmes. Research efforts have primarily focused on communication for routine vaccination. However, vaccination campaigns, particularly in low- or middle-income countries (LMICs), also use communication in diverse ways. Without a comprehensive framework integrating communication interventions from routine and campaign contexts, it is not possible to conceptualise the full range of possible vaccination communication interventions. Therefore, vaccine programme managers may be unaware of potential communication options and researchers may not focus on building evidence for interventions used in practice. In this paper, we broaden the scope of our existing taxonomy of communication interventions for routine vaccination to include communication used in campaigns, and integrate these into a comprehensive taxonomy of vaccination communication interventions. Building on our taxonomy of communication for routine vaccination, we identified communication interventions used in vaccination campaigns through a targeted literature search; observation of vaccination activities in Cameroon, Mozambique and Nigeria; and stakeholder consultations. We added these interventions to descriptions of routine vaccination communication and categorised the interventions according to their intended purposes, building from an earlier taxonomy of communication related to routine vaccination. The comprehensive taxonomy groups communication used in campaigns and routine childhood vaccination into seven purpose categories: 'Inform or Educate'; 'Remind or Recall'; 'Enhance Community Ownership'; 'Teach Skills'; 'Provide Support'; 'Facilitate Decision Making' and 'Enable Communication'. Consultations with LMIC stakeholders and experts informed the taxonomy's definitions and structure and established its potential uses. This taxonomy provides a standardised way to think and speak about vaccination communication. It is categorised by purpose to help conceptualise communication interventions as potential solutions to address needs or problems. It can be utilised by programme planners, implementers, researchers and funders to see the range of communication interventions used in practice, facilitate evidence synthesis and identify evidence gaps.

The ACTTION-American Pain Society Pain Taxonomy (AAPT): an evidence-based and multidimensional approach to classifying chronic pain conditions.

PubMed

Fillingim, Roger B; Bruehl, Stephen; Dworkin, Robert H; Dworkin, Samuel F; Loeser, John D; Turk, Dennis C; Widerstrom-Noga, Eva; Arnold, Lesley; Bennett, Robert; Edwards, Robert R; Freeman, Roy; Gewandter, Jennifer; Hertz, Sharon; Hochberg, Marc; Krane, Elliot; Mantyh, Patrick W; Markman, John; Neogi, Tuhina; Ohrbach, Richard; Paice, Judith A; Porreca, Frank; Rappaport, Bob A; Smith, Shannon M; Smith, Thomas J; Sullivan, Mark D; Verne, G Nicholas; Wasan, Ajay D; Wesselmann, Ursula

2014-03-01

Current approaches to classification of chronic pain conditions suffer from the absence of a systematically implemented and evidence-based taxonomy. Moreover, existing diagnostic approaches typically fail to incorporate available knowledge regarding the biopsychosocial mechanisms contributing to pain conditions. To address these gaps, the Analgesic, Anesthetic, and Addiction Clinical Trial Translations Innovations Opportunities and Networks (ACTTION) public-private partnership with the U.S. Food and Drug Administration and the American Pain Society (APS) have joined together to develop an evidence-based chronic pain classification system called the ACTTION-APS Pain Taxonomy. This paper describes the outcome of an ACTTION-APS consensus meeting, at which experts agreed on a structure for this new taxonomy of chronic pain conditions. Several major issues around which discussion revolved are presented and summarized, and the structure of the taxonomy is presented. ACTTION-APS Pain Taxonomy will include the following dimensions: 1) core diagnostic criteria; 2) common features; 3) common medical comorbidities; 4) neurobiological, psychosocial, and functional consequences; and 5) putative neurobiological and psychosocial mechanisms, risk factors, and protective factors. In coming months, expert working groups will apply this taxonomy to clusters of chronic pain conditions, thereby developing a set of diagnostic criteria that have been consistently and systematically implemented across nearly all common chronic pain conditions. It is anticipated that the availability of this evidence-based and mechanistic approach to pain classification will be of substantial benefit to chronic pain research and treatment. The ACTTION-APS Pain Taxonomy is an evidence-based chronic pain classification system designed to classify chronic pain along the following dimensions: 1) core diagnostic criteria; 2) common features; 3) common medical comorbidities; 4) neurobiological, psychosocial, and functional consequences; and 5) putative neurobiological and psychosocial mechanisms, risk factors, and protective factors. Copyright © 2014 American Pain Society. Published by Elsevier Inc. All rights reserved.

Developing the FARSEEING Taxonomy of Technologies: Classification and description of technology use (including ICT) in falls prevention studies.

PubMed

Boulton, Elisabeth; Hawley-Hague, Helen; Vereijken, Beatrix; Clifford, Amanda; Guldemond, Nick; Pfeiffer, Klaus; Hall, Alex; Chesani, Federico; Mellone, Sabato; Bourke, Alan; Todd, Chris

2016-06-01

Recent Cochrane reviews on falls and fall prevention have shown that it is possible to prevent falls in older adults living in the community and in care facilities. Technologies aimed at fall detection, assessment, prediction and prevention are emerging, yet there has been no consistency in describing or reporting on interventions using technologies. With the growth of eHealth and data driven interventions, a common language and classification is required. The FARSEEING Taxonomy of Technologies was developed as a tool for those in the field of biomedical informatics to classify and characterise components of studies and interventions. The Taxonomy Development Group (TDG) comprised experts from across Europe. Through face-to-face meetings and contributions via email, five domains were developed, modified and agreed: Approach; Base; Components of outcome measures; Descriptors of technologies; and Evaluation. Each domain included sub-domains and categories with accompanying definitions. The classification system was tested against published papers and further amendments undertaken, including development of an online tool. Six papers were classified by the TDG with levels of consensus recorded. Testing the taxonomy with papers highlighted difficulties in definitions across international healthcare systems, together with differences of TDG members' backgrounds. Definitions were clarified and amended accordingly, but some difficulties remained. The taxonomy and manual were large documents leading to a lengthy classification process. The development of the online application enabled a much simpler classification process, as categories and definitions appeared only when relevant. Overall consensus for the classified papers was 70.66%. Consensus scores increased as modifications were made to the taxonomy. The FARSEEING Taxonomy of Technologies presents a common language, which should now be adopted in the field of biomedical informatics. In developing the taxonomy as an online tool, it has become possible to continue to develop and modify the classification system to incorporate new technologies and interventions. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

The necessity of DNA taxonomy to reveal cryptic diversity and spatial distribution of meiofauna, with a focus on Nemertea.

PubMed

Leasi, Francesca; Norenburg, Jon L

2014-01-01

Meiofauna represent one of the most abundant and diverse communities in marine benthic ecosystems. However, an accurate assessment of diversity at the level of species has been and remains challenging for these microscopic organisms. Therefore, for many taxa, especially the soft body forms such as nemerteans, which often lack clear diagnostic morphological traits, DNA taxonomy is an effective means to assess species diversity. Morphological taxonomy of Nemertea is well documented as complicated by scarcity of unambiguous character states and compromised by diagnoses of a majority of species (and higher clades) being inadequate or based on ambiguous characters and character states. Therefore, recent studies have advocated for the primacy of molecular tools to solve the taxonomy of this group. DNA taxonomy uncovers possible hidden cryptic species, provides a coherent means to systematize taxa in definite clades, and also reveals possible biogeographic patterns. Here, we analyze diversity of nemertean species by considering the barcode region of the mitochondrial gene Cytochrome Oxidase subunit I (COI) and different species delineation approaches in order to infer evolutionarily significant units. In the aim to uncover actual diversity of meiofaunal nemerteans across different sites in Central America, COI sequences were obtained for specimens assigned here to the genera Cephalothrix, Ototyphlonemertes, and Tetrastemma-like worms, each commonly encountered in our sampling. Additional genetic, taxonomic, and geographic data of other specimens belonging to these genera were added from GenBank. Results are consistent across different DNA taxonomy approaches, and revealed (i) the presence of several hidden cryptic species and (ii) numerous potential misidentifications due to traditional taxonomy. (iii) We additionally test a possible biogeographic pattern of taxonomic units revealed by this study, and, except for a few cases, the putative species seem not to be widely distributed, in contrast to what traditional taxonomy would suggest for the recognized morphotypes.

Contrasting Evolutionary Paths Among Indo-Pacific Pomacentrus Species Promoted by Extensive Pericentric Inversions and Genome Organization of Repetitive Sequences.

PubMed

Getlekha, Nuntaporn; Cioffi, Marcelo de Bello; Maneechot, Nuntiya; Bertollo, Luiz Antônio Carlos; Supiwong, Weerayuth; Tanomtong, Alongklod; Molina, Wagner Franco

2018-02-01

Pomacentrus (damselfishes) is one of the most characteristic groups of fishes in the Indo-Pacific coral reef. Its 77 described species exhibit a complex taxonomy with cryptic lineages across their extensive distribution. Periods of evolutionary divergences between them are very variable, and the cytogenetic events that followed their evolutionary diversification are largely unknown. In this respect, analyses of chromosomal divergence, within a phylogenetic perspective, are particularly informative regarding karyoevolutionary trends. As such, we conducted conventional cytogenetic and cytogenomic analyses in four Pomacentrus species (Pomacentrus similis, Pomacentrus auriventris, Pomacentrus moluccensis, and Pomacentrus cuneatus), through the mapping of repetitive DNA classes and transposable elements, including 18S rDNA, 5S rDNA, (CA) 15 , (GA) 15 , (CAA) 10 , Rex6, and U2 snDNA as markers. P. auriventris and P. similis, belonging to the Pomacentrus coelestis complex, have indistinguishable karyotypes (2n = 48; NF = 48), with a peculiar syntenic organization of ribosomal genes. On the other hand, P. moluccensis and P. cuneatus, belonging to another clade, exhibit very different karyotypes (2n = 48, NF = 86 and 92, respectively), with a large number of bi-armed chromosomes, where multiple pericentric inversions played a significant role in their karyotype organization. In this sense, different chromosomal pathways followed the phyletic diversification in the Pomacentrus genus, making possible the characterization of two well-contrasting species groups regarding their karyotype features. Despite this, pericentric inversions act as an effective postzygotic barrier in many organisms, which appear to be also the case for P. moluccensis and P. cuneatus; the extensive chromosomal similarities in the two species of P. coelestis complex suggest minor participation of chromosomal postzygotic barriers in the phyletic diversification of these species.

Ecoepidemiology of Cryptococcus gattii in Developing Countries

PubMed Central

Hagen, Ferry; Pinheiro, Rosangela L.; Muro, Marisol D.; Meis, Jacques F.; Queiroz-Telles, Flávio

2017-01-01

Cryptococcosis is a systemic infection caused by species of the encapsulated yeast Cryptococcus. The disease may occur in immunocompromised and immunocompetent hosts and is acquired by the inhalation of infectious propagules present in the environment. Cryptococcus is distributed in a plethora of ecological niches, such as soil, pigeon droppings, and tree hollows, and each year new reservoirs are discovered, which helps researchers to better understand the epidemiology of the disease. In this review, we describe the ecoepidemiology of the C. gattii species complex focusing on clinical cases and ecological reservoirs in developing countries from different continents. We also discuss some important aspects related to the antifungal susceptibility of different species within the C. gattii species complex and bring new insights on the revised Cryptococcus taxonomy. PMID:29371578

Christmas tree worms of Indo-Pacific coral reefs: untangling the Spirobranchus corniculatus (Grube, 1862) complex

NASA Astrophysics Data System (ADS)

Willette, Demian A.; Iñiguez, Abril R.; Kupriyanova, Elena K.; Starger, Craig J.; Varman, Tristan; Toha, Abdul Hamid; Maralit, Benedict A.; Barber, Paul H.

2015-09-01

Christmas tree worm is the common name of a group of colorful serpulid polychaetes from the genus Spirobranchus that are symbionts of hermatypic corals. As is increasingly common with reef-associated organisms, Spirobranchus is arranged as a complex of species with overlapping geographic ranges. Current species delimitations based largely on opercular morphology are problematic because of high intraspecific variation. Here, a multi-gene phylogeny of the Spirobranchus corniculatus complex, which tentatively includes S. corniculatus, S. cruciger, and S. gaymardi, sampled from the Coral Triangle, Australia, and Fiji, was reconstructed to test whether the complex includes three genetically distinct lineages identifiable by their opercula. Maximum-likelihood analyses of nuclear and mitochondrial markers revealed a single, monophyletic clade for the S. corniculatus complex. Furthermore, the genetic and morphological variation observed is not geographically based, indicating that the former S. corniculatus complex of three morphospecies is a single, morphologically variable species across the Central Indo-Pacific. Resolving the taxonomy of S. corniculatus presents novel opportunities to utilize this tentative bio-indicator species for monitoring reef health.

A topographic feature taxonomy for a U.S. national topographic mapping ontology

USGS Publications Warehouse

Varanka, Dalia E.

2013-01-01

Using legacy feature lists from the U.S. National Topographic Mapping Program of the twentieth century, a taxonomy of features is presented for purposes of developing a national topographic feature ontology for geographic mapping and analysis. After reviewing published taxonomic classifications, six basic classes are suggested; terrain, surface water, ecological regimes, built-up areas, divisions, and events. Aspects of ontology development are suggested as the taxonomy is described.

Taxonomy of the family Arenaviridae and the order Bunyavirales: update 2018.

PubMed

Maes, Piet; Alkhovsky, Sergey V; Bào, Yīmíng; Beer, Martin; Birkhead, Monica; Briese, Thomas; Buchmeier, Michael J; Calisher, Charles H; Charrel, Rémi N; Choi, Il Ryong; Clegg, Christopher S; de la Torre, Juan Carlos; Delwart, Eric; DeRisi, Joseph L; Di Bello, Patrick L; Di Serio, Francesco; Digiaro, Michele; Dolja, Valerian V; Drosten, Christian; Druciarek, Tobiasz Z; Du, Jiang; Ebihara, Hideki; Elbeaino, Toufic; Gergerich, Rose C; Gillis, Amethyst N; Gonzalez, Jean-Paul J; Haenni, Anne-Lise; Hepojoki, Jussi; Hetzel, Udo; Hồ, Thiện; Hóng, Ní; Jain, Rakesh K; Jansen van Vuren, Petrus; Jin, Qi; Jonson, Miranda Gilda; Junglen, Sandra; Keller, Karen E; Kemp, Alan; Kipar, Anja; Kondov, Nikola O; Koonin, Eugene V; Kormelink, Richard; Korzyukov, Yegor; Krupovic, Mart; Lambert, Amy J; Laney, Alma G; LeBreton, Matthew; Lukashevich, Igor S; Marklewitz, Marco; Markotter, Wanda; Martelli, Giovanni P; Martin, Robert R; Mielke-Ehret, Nicole; Mühlbach, Hans-Peter; Navarro, Beatriz; Ng, Terry Fei Fan; Nunes, Márcio Roberto Teixeira; Palacios, Gustavo; Pawęska, Janusz T; Peters, Clarence J; Plyusnin, Alexander; Radoshitzky, Sheli R; Romanowski, Víctor; Salmenperä, Pertteli; Salvato, Maria S; Sanfaçon, Hélène; Sasaya, Takahide; Schmaljohn, Connie; Schneider, Bradley S; Shirako, Yukio; Siddell, Stuart; Sironen, Tarja A; Stenglein, Mark D; Storm, Nadia; Sudini, Harikishan; Tesh, Robert B; Tzanetakis, Ioannis E; Uppala, Mangala; Vapalahti, Olli; Vasilakis, Nikos; Walker, Peter J; Wáng, Guópíng; Wáng, Lìpíng; Wáng, Yànxiăng; Wèi, Tàiyún; Wiley, Michael R; Wolf, Yuri I; Wolfe, Nathan D; Wú, Zhìqiáng; Xú, Wénxìng; Yang, Li; Yāng, Zuòkūn; Yeh, Shyi-Dong; Zhāng, Yǒng-Zhèn; Zhèng, Yàzhōu; Zhou, Xueping; Zhū, Chénxī; Zirkel, Florian; Kuhn, Jens H

2018-04-21

In 2018, the family Arenaviridae was expanded by inclusion of 1 new genus and 5 novel species. At the same time, the recently established order Bunyavirales was expanded by 3 species. This article presents the updated taxonomy of the family Arenaviridae and the order Bunyavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV) and summarizes additional taxonomic proposals that may affect the order in the near future.

Taxonomy of the order Mononegavirales: update 2016.

PubMed

Afonso, Claudio L; Amarasinghe, Gaya K; Bányai, Krisztián; Bào, Yīmíng; Basler, Christopher F; Bavari, Sina; Bejerman, Nicolás; Blasdell, Kim R; Briand, François-Xavier; Briese, Thomas; Bukreyev, Alexander; Calisher, Charles H; Chandran, Kartik; Chéng, Jiāsēn; Clawson, Anna N; Collins, Peter L; Dietzgen, Ralf G; Dolnik, Olga; Domier, Leslie L; Dürrwald, Ralf; Dye, John M; Easton, Andrew J; Ebihara, Hideki; Farkas, Szilvia L; Freitas-Astúa, Juliana; Formenty, Pierre; Fouchier, Ron A M; Fù, Yànpíng; Ghedin, Elodie; Goodin, Michael M; Hewson, Roger; Horie, Masayuki; Hyndman, Timothy H; Jiāng, Dàohóng; Kitajima, Elliot W; Kobinger, Gary P; Kondo, Hideki; Kurath, Gael; Lamb, Robert A; Lenardon, Sergio; Leroy, Eric M; Li, Ci-Xiu; Lin, Xian-Dan; Liú, Lìjiāng; Longdon, Ben; Marton, Szilvia; Maisner, Andrea; Mühlberger, Elke; Netesov, Sergey V; Nowotny, Norbert; Patterson, Jean L; Payne, Susan L; Paweska, Janusz T; Randall, Rick E; Rima, Bertus K; Rota, Paul; Rubbenstroth, Dennis; Schwemmle, Martin; Shi, Mang; Smither, Sophie J; Stenglein, Mark D; Stone, David M; Takada, Ayato; Terregino, Calogero; Tesh, Robert B; Tian, Jun-Hua; Tomonaga, Keizo; Tordo, Noël; Towner, Jonathan S; Vasilakis, Nikos; Verbeek, Martin; Volchkov, Viktor E; Wahl-Jensen, Victoria; Walsh, John A; Walker, Peter J; Wang, David; Wang, Lin-Fa; Wetzel, Thierry; Whitfield, Anna E; Xiè, Ji Tāo; Yuen, Kwok-Yung; Zhang, Yong-Zhen; Kuhn, Jens H

2016-08-01

In 2016, the order Mononegavirales was emended through the addition of two new families (Mymonaviridae and Sunviridae), the elevation of the paramyxoviral subfamily Pneumovirinae to family status (Pneumoviridae), the addition of five free-floating genera (Anphevirus, Arlivirus, Chengtivirus, Crustavirus, and Wastrivirus), and several other changes at the genus and species levels. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).

Taxonomy of the order Mononegavirales: update 2016

USGS Publications Warehouse

Afonso, C.L.; Kurath, Gael; 82 Additional Authors,

2016-01-01

In 2016, the order Mononegavirales was emended through the addition of two new families (Mymonaviridae and Sunviridae), the elevation of the paramyxoviral subfamily Pneumovirinae to family status (Pneumoviridae), the addition of five free-floating genera (Anphevirus, Arlivirus, Chengtivirus, Crustavirus, and Wastrivirus), and several other changes at the genus and species levels. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).

Coral Taxonomy. Results and Recommendations of a Regional Unesco (COMAR)/UNEP Workshop with Advanced Training (Phuket Marine Biological Centre, Thailand, February 10-26, 1984). Unesco Reports in Marine Science No. 33.

ERIC Educational Resources Information Center

United Nations Educational, Scientific, and Cultural Organization, Paris (France). Div. of Marine Sciences.

This document reports on a workshop on coral species present in Thailand and on the status of coral taxonomy in central Indo-Pacific countries. The report discusses workshop aims, summarizes field and laboratory studies, provides a tentative checklist of hermatypic coral species from Thailand, assesses the status of coral taxonomy in participating…

Taxonomy of the order Mononegavirales: update 2016

DOE Office of Scientific and Technical Information (OSTI.GOV)

Afonso, Claudio L.; Amarasinghe, Gaya K.; Bányai, Krisztián

2016-05-23

In 2016, the order Mononegavirales was emended through the addition of two new families (Mymonaviridae and Sunviridae), the elevation of the paramyxoviral subfamily Pneumovirinae to family status (Pneumoviridae), the addition of five free-floating genera (Anphevirus, Arlivirus, Chengtivirus, Crustavirus, and Wastrivirus), and several other changes at the genus and species levels. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).

TAXONOMY OF THE ORDER MONONEGAVIRALES: UPDATE 2016

PubMed Central

Afonso, Claudio L.; Amarasinghe, Gaya K.; Bányai, Krisztián; Bào, Yīmíng; Basler, Christopher F.; Bavari, Sina; Bejerman, Nicolás; Blasdell, Kim R.; Briand, François-Xavier; Briese, Thomas; Bukreyev, Alexander; Calisher, Charles H.; Chandran, Kartik; Chéng, Jiāsēn; Clawson, Anna N.; Collins, Peter L.; Dietzgen, Ralf G.; Dolnik, Olga; Domier, Leslie L.; Dürrwald, Ralf; Dye, John M.; Easton, Andrew J.; Ebihara, Hideki; Farkas, Szilvia L.; Freitas-Astúa, Juliana; Formenty, Pierre; Fouchier, Ron A. M.; Fù, Yànpíng; Ghedin, Elodie; Goodin, Michael M.; Hewson, Roger; Horie, Masayuki; Hyndman, Timothy H.; Jiāng, Dàohóng; Kitajima, Elliot W.; Kobinger, Gary P.; Kondo, Hideki; Kurath, Gael; Lamb, Robert A.; Lenardon, Sergio; Leroy, Eric M.; Li, Ci-Xiu; Lin, Xian-Dan; Liú, Lìjiāng; Longdon, Ben; Marton, Szilvia; Maisner, Andrea; Mühlberger, Elke; Netesov, Sergey V.; Nowotny, Norbert; Patterson, Jean L.; Payne, Susan L.; Paweska, Janusz T.; Randall, Rick E.; Rima, Bertus K.; Rota, Paul; Rubbenstroth, Dennis; Schwemmle, Martin; Shi, Mang; Smither, Sophie J.; Stenglein, Mark D.; Stone, David M.; Takada, Ayato; Terregino, Calogero; Tesh, Robert B.; Tian, Jun-Hua; Tomonaga, Keizo; Tordo, Noël; Towner, Jonathan S.; Vasilakis, Nikos; Verbeek, Martin; Volchkov, Viktor E.; Wahl-Jensen, Victoria; Walsh, John A.; Walker, Peter J.; Wang, David; Wang, Lin-Fa; Wetzel, Thierry; Whitfield, Anna E.; Xiè, Jiǎtāo; Yuen, Kwok-Yung; Zhang, Yong-Zhen; Kuhn, Jens H.

2016-01-01

In 2016, the order Mononegavirales was emended through the addition of two new families (Mymonaviridae and Sunviridae), the elevation of the paramyxoviral subfamily Pneumovirinae to family status (Pneumoviridae), the addition of five free-floating genera (Anphevirus, Arlivirus, Chengtivirus, Crustavirus, and Wastrivirus), and several other changes at the genus and species levels. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV). PMID:27216929

A new taxonomy for stakeholder engagement in patient-centered outcomes research.

PubMed

Concannon, Thomas W; Meissner, Paul; Grunbaum, Jo Anne; McElwee, Newell; Guise, Jeanne-Marie; Santa, John; Conway, Patrick H; Daudelin, Denise; Morrato, Elaine H; Leslie, Laurel K

2012-08-01

Despite widespread agreement that stakeholder engagement is needed in patient-centered outcomes research (PCOR), no taxonomy exists to guide researchers and policy makers on how to address this need. We followed an iterative process, including several stages of stakeholder review, to address three questions: (1) Who are the stakeholders in PCOR? (2) What roles and responsibilities can stakeholders have in PCOR? (3) How can researchers start engaging stakeholders? We introduce a flexible taxonomy called the 7Ps of Stakeholder Engagement and Six Stages of Research for identifying stakeholders and developing engagement strategies across the full spectrum of research activities. The path toward engagement will not be uniform across every research program, but this taxonomy offers a common starting point and a flexible approach.

Taxonomies of Cyber Adversaries and Attacks: A Survey of Incidents and Approaches

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meyers, C A; Powers, S S; Faissol, D M

In this paper we construct taxonomies of cyber adversaries and methods of attack, drawing from a survey of the literature in the area of cyber crime. We begin by addressing the scope of cyber crime, noting its prevalence and effects on the US economy. We then survey the literature on cyber adversaries, presenting a taxonomy of the different types of adversaries and their corresponding methods, motivations, maliciousness, and skill levels. Subsequently we survey the literature on cyber attacks, giving a taxonomy of the different classes of attacks, subtypes, and threat descriptions. The goal of this paper is to inform futuremore » studies of cyber security on the shape and characteristics of the risk space and its associated adversaries.« less

The Bootstrap, the Jackknife, and the Randomization Test: A Sampling Taxonomy.

PubMed

Rodgers, J L

1999-10-01

A simple sampling taxonomy is defined that shows the differences between and relationships among the bootstrap, the jackknife, and the randomization test. Each method has as its goal the creation of an empirical sampling distribution that can be used to test statistical hypotheses, estimate standard errors, and/or create confidence intervals. Distinctions between the methods can be made based on the sampling approach (with replacement versus without replacement) and the sample size (replacing the whole original sample versus replacing a subset of the original sample). The taxonomy is useful for teaching the goals and purposes of resampling schemes. An extension of the taxonomy implies other possible resampling approaches that have not previously been considered. Univariate and multivariate examples are presented.

Possibilities in identification of genomic species of Burkholderia cepacia complex by PCR and RFLP.

PubMed

Navrátilová, Lucie; Chromá, Magdalena; Hanulík, Vojtech; Raclavský, Vladislav

2013-01-01

The strains belonging to Burkholderia cepacia complex are important opportunistic pathogens in immunocompromised patients and cause serious diseases. It is possible to obtain isolates from soil, water, plants and human samples. Taxonomy of this group is difficult. Burkholderia cepacia complex consists of seventeen genomic species and the genetic scheme is based on recA gene. Commonly, first five genomovars occurre in humans, mostly genomovars II and III, subdivision IIIA. Within this study we tested identification of first five genomovars by PCR with following melting analysis and RFLP. The experiments were targeted on eubacterial 16S rDNA and specific gene recA, which allowed identification of all five genomovars. RecA gene appeared as more suitable than 16S rDNA, which enabled direct identification of only genomovars II and V; genomovars I, III and IV were similar within 16S rDNA sequence.

The Integrated Taxonomy of Health Care: Classifying Both Complementary and Biomedical Practices Using a Uniform Classification Protocol

PubMed Central

Porcino, Antony; MacDougall, Colleen

2009-01-01

Background: Since the late 1980s, several taxonomies have been developed to help map and describe the interrelationships of complementary and alternative medicine (CAM) modalities. In these taxonomies, several issues are often incompletely addressed: A simple categorization process that clearly isolates a modality to a single conceptual categoryClear delineation of verticality—that is, a differentiation of scale being observed from individually applied techniques, through modalities (therapies), to whole medical systemsRecognition of CAM as part of the general field of health care Methods: Development of the Integrated Taxonomy of Health Care (ITHC) involved three stages: Development of a precise, uniform health glossaryAnalysis of the extant taxonomiesUse of an iterative process of classifying modalities and medical systems into categories until a failure to singularly classify a modality occurred, requiring a return to the glossary and adjustment of the classifying protocol Results: A full vertical taxonomy was developed that includes and clearly differentiates between techniques, modalities, domains (clusters of similar modalities), systems of health care (coordinated care system involving multiple modalities), and integrative health care. Domains are the classical primary focus of taxonomies. The ITHC has eleven domains: chemical/substance-based work, device-based work, soft tissue–focused manipulation, skeletal manipulation, fitness/movement instruction, mind–body integration/classical somatics work, mental/emotional–based work, bio-energy work based on physical manipulation, bio-energy modulation, spiritual-based work, unique assessments. Modalities are assigned to the domains based on the primary mode of interaction with the client, according the literature of the practitioners. Conclusions: The ITHC has several strengths: little interpretation is used while successfully assigning modalities to single domains; the issue of taxonomic verticality is fully resolved; and the design fully integrates the complementary health care fields of biomedicine and CAM. PMID:21589735

Frequency and Nature of Infectious Risk Moments During Acute Care Based on the INFORM Structured Classification Taxonomy.

PubMed

Clack, Lauren; Passerini, Simone; Wolfensberger, Aline; Sax, Hugo; Manser, Tanja

2018-03-01

OBJECTIVE In this study, we sought to establish a comprehensive inventory of infectious risk moments (IRMs), defined as seemingly innocuous yet frequently occurring care manipulations potentially resulting in transfer of pathogens to patients. We also aimed to develop and employ an observational taxonomy to quantify the frequency and nature of IRMs in acute-care settings. DESIGN Prospective observational study and establishment of observational taxonomy. SETTING Intensive care unit, general medical ward, and emergency ward of a university-affiliated hospital. PARTICIPANTS Healthcare workers (HCWs) METHODS Exploratory observations were conducted to identify IRMs, which were coded based on the surfaces involved in the transmission pathway to establish a structured taxonomy. Structured observations were performed using this taxonomy to quantify IRMs in all 3 settings. RESULTS Following 129.17 hours of exploratory observations, identified IRMs involved HCW hands, gloves, care devices, mobile objects, and HCW clothing and accessories. A structured taxonomy called INFORM (INFectiOus Risk Moment) was established to classify each IRM according to the source, vector, and endpoint of potential pathogen transfer. We observed 1,138 IRMs during 53.77 hours of structured observations (31.25 active care hours) for an average foundation of 42.8 IRMs per active care hour overall, and average densities of 34.9, 36.8, and 56.3 IRMs in the intensive care, medical, and emergency wards, respectively. CONCLUSIONS Hands and gloves remain among the most important contributors to the transfer of pathogens within the healthcare setting, but medical devices, mobile objects, invasive devices, and HCW clothing and accessories may also contribute to patient colonization and/or infection. The INFORM observational taxonomy and IRM inventory presented may benefit clinical risk assessment, training and education, and future research. Infect Control Hosp Epidemiol 2018;39:272-279.

Building a taxonomy of integrated palliative care initiatives: results from a focus group.

PubMed

Ewert, Benjamin; Hodiamont, Farina; van Wijngaarden, Jeroen; Payne, Sheila; Groot, Marieke; Hasselaar, Jeroen; Menten, Johann; Radbruch, Lukas

2016-03-01

Empirical evidence suggests that integrated palliative care (IPC) increases the quality of care for palliative patients and supports professional caregivers. Existing IPC initiatives in Europe vary in their design and are hardly comparable. InSuP-C, a European Union research project, aimed to build a taxonomy of IPC initiatives applicable across diseases, healthcare sectors and systems. The taxonomy of IPC initiatives was developed in cooperation with an international and multidisciplinary focus group of 18 experts. Subsequently, a consensus meeting of 10 experts revised a preliminary taxonomy and adopted the final classification system. Consisting of eight categories, with two to four items each, the taxonomy covers the process and structure of IPC initiatives. If two items in at least one category apply to an initiative, a minimum level of integration is assumed to have been reached. Categories range from the type of initiative (items: pathway, model or guideline) to patients' key contact (items: non-pc specialist, pc specialist, general practitioner). Experts recommended the inclusion of two new categories: level of care (items: primary, secondary or tertiary) indicating at which stage palliative care is integrated and primary focus of intervention describing IPC givers' different roles (items: treating function, advising/consulting or training) in the care process. Empirical studies are required to investigate how the taxonomy is used in practice and whether it covers the reality of patients in need of palliative care. The InSuP-C project will test this taxonomy empirically in selected initiatives using IPC. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Patient complaints about hospital services: applying a complaint taxonomy to analyse and respond to complaints.

PubMed

Harrison, Reema; Walton, Merrilyn; Healy, Judith; Smith-Merry, Jennifer; Hobbs, Coletta

2016-04-01

To explore the applicability of a patient complaint taxonomy to data on serious complaint cases. Qualitative descriptive study. Complaints made to the New South Wales (NSW) Health Care Complaints Commission, Australia between 2005 and 2010. All 138 cases of serious complaints by patients about public hospitals and other health facilities investigated in the 5-year period. A thematic analysis of the complaints was conducted to identify particular complaint issues and the Reader et al. (Patient complaints in healthcare systems: a systematic review and coding taxonomy. BMJ Qual Saf 2014;23:678-89.) patient complaint taxonomy was then used to classify these issues into categories and sub-categories. The 138 investigated cases revealed 223 complaint issues. Complaint issues were distributed into the three domains of the patient complaint taxonomy: clinical, management and relationships. Complaint issue most commonly related to delayed diagnosis, misdiagnosis, medication errors, inadequate examinations, inadequate/nil treatment and quality of care including nursing care. The types of complaints from patients about their healthcare investigated by the NSW Commission were similar to those received by other patient complaint entities in Australia and worldwide. The application of a standard taxonomy to large numbers of complaints cases from different sources would enable the creation of aggregated data. Such data would have better statistical capacity to identify common safety and quality healthcare problems and so point to important areas for improvement. Some conceptual challenges in devising and using a taxonomy must be addressed, such as inherent problems in ensuring coding consistency, and giving greater weight to patient concerns about their treatment. © The Author 2016. Published by Oxford University Press in association with the International Society for Quality in Health Care; all rights reserved.

Refining a taxonomy for guideline implementation: results of an exercise in abstract classification

PubMed Central

2013-01-01

Background To better understand the efficacy of various implementation strategies, improved methods for describing and classifying the nature of these strategies are urgently required. The aim of this study was to develop and pilot the feasibility of a taxonomy to classify the nature and content of implementation strategies. Methods A draft implementation taxonomy was developed based on the Cochrane Effective Practice and Organisation of Care (EPOC) data collection checklist. The draft taxonomy had four domains (professional, financial, organisational and regulatory) covering 49 distinct strategies. We piloted the draft taxonomy by using it to classify the implementation strategies described in the conference abstracts of the implementation stream of the 2010 Guideline International Network Conference. Five authors classified the strategies in each abstract individually. Final categorisation was then carried out in a face-to-face consensus meeting involving three authors. Results The implementation strategies described in 71 conference abstracts were classified. Approximately 15.5% of abstracts utilised strategies that could not be categorised using the draft taxonomy. Of those strategies that could be categorised, the majority were professionally focused (57%). A total of 41% of projects used only one implementation strategy, with 29% using two and 31% three or more. The three most commonly used strategies were changes in quality assurance, quality improvement and/or performance measurement systems, changes in information and communication technology, and distribution of guideline materials (via hard-copy, audio-visual and/or electronic means). Conclusions Further refinement of the draft taxonomy is required to provide hierarchical dimensions and granularity, particularly in the areas of patient-focused interventions, those concerned with audit and feedback and quality improvement, and electronic forms of implementation, including electronic decision support. PMID:23497520

Development and evaluation of a comprehensive clinical decision support taxonomy: comparison of front-end tools in commercial and internally developed electronic health record systems

PubMed Central

Sittig, Dean F; Ash, Joan S; Feblowitz, Joshua; Meltzer, Seth; McMullen, Carmit; Guappone, Ken; Carpenter, Jim; Richardson, Joshua; Simonaitis, Linas; Evans, R Scott; Nichol, W Paul; Middleton, Blackford

2011-01-01

Background Clinical decision support (CDS) is a valuable tool for improving healthcare quality and lowering costs. However, there is no comprehensive taxonomy of types of CDS and there has been limited research on the availability of various CDS tools across current electronic health record (EHR) systems. Objective To develop and validate a taxonomy of front-end CDS tools and to assess support for these tools in major commercial and internally developed EHRs. Study design and methods We used a modified Delphi approach with a panel of 11 decision support experts to develop a taxonomy of 53 front-end CDS tools. Based on this taxonomy, a survey on CDS tools was sent to a purposive sample of commercial EHR vendors (n=9) and leading healthcare institutions with internally developed state-of-the-art EHRs (n=4). Results Responses were received from all healthcare institutions and 7 of 9 EHR vendors (response rate: 85%). All 53 types of CDS tools identified in the taxonomy were found in at least one surveyed EHR system, but only 8 functions were present in all EHRs. Medication dosing support and order facilitators were the most commonly available classes of decision support, while expert systems (eg, diagnostic decision support, ventilator management suggestions) were the least common. Conclusion We developed and validated a comprehensive taxonomy of front-end CDS tools. A subsequent survey of commercial EHR vendors and leading healthcare institutions revealed a small core set of common CDS tools, but identified significant variability in the remainder of clinical decision support content. PMID:21415065

Structural Validation of Nursing Terminologies

PubMed Central

Hardiker, Nicholas R.; Rector, Alan L.

2001-01-01

Objective: The purpose of the study is twofold: 1) to explore the applicability of combinatorial terminologies as the basis for building enumerated classifications, and 2) to investigate the usefulness of formal terminological systems for performing such classification and for assisting in the refinement of both combinatorial terminologies and enumerated classifications. Design: A formal model of the beta version of the International Classification for Nursing Practice (ICNP) was constructed in the compositional terminological language GRAIL (GALEN Representation and Integration Language). Terms drawn from the North American Nursing Diagnosis Association Taxonomy I (NANDA taxonomy) were mapped into the model and classified automatically using GALEN technology. Measurements: The resulting generated hierarchy was compared with the NANDA taxonomy to assess coverage and accuracy of classification. Results: In terms of coverage, in this study ICNP was able to capture 77 percent of NANDA terms using concepts drawn from five of its eight axes. Three axes—Body Site, Topology, and Frequency—were not needed. In terms of accuracy, where hierarchic relationships existed in the generated hierarchy or the NANDA taxonomy, or both, 6 were identical, 19 existed in the generated hierarchy alone (2 of these were considered suitable for incorporation into the NANDA taxonomy and 17 were considered inaccurate), and 23 appeared in the NANDA taxonomy alone (8 of these were considered suitable for incorporation into ICNP, 9 were considered inaccurate, and 6 reflected different, equally valid perspectives). Sixty terms appeared at the top level, with no indenting, in both the generated hierarchy and the NANDA taxonomy. Conclusions: With appropriate refinement, combinatorial terminologies such as ICNP have the potential to provide a useful foundation for representing enumerated classifications such as NANDA. Technologies such as GALEN make possible the process of building automatically enumerated classifications while providing a useful means of validating and refining both combinatorial terminologies and enumerated classifications. PMID:11320066

Refining a taxonomy for guideline implementation: results of an exercise in abstract classification.

PubMed

Mazza, Danielle; Bairstow, Phillip; Buchan, Heather; Chakraborty, Samantha Paubrey; Van Hecke, Oliver; Grech, Cathy; Kunnamo, Ilkka

2013-03-15

To better understand the efficacy of various implementation strategies, improved methods for describing and classifying the nature of these strategies are urgently required. The aim of this study was to develop and pilot the feasibility of a taxonomy to classify the nature and content of implementation strategies. A draft implementation taxonomy was developed based on the Cochrane Effective Practice and Organisation of Care (EPOC) data collection checklist. The draft taxonomy had four domains (professional, financial, organisational and regulatory) covering 49 distinct strategies. We piloted the draft taxonomy by using it to classify the implementation strategies described in the conference abstracts of the implementation stream of the 2010 Guideline International Network Conference. Five authors classified the strategies in each abstract individually. Final categorisation was then carried out in a face-to-face consensus meeting involving three authors. The implementation strategies described in 71 conference abstracts were classified. Approximately 15.5% of abstracts utilised strategies that could not be categorised using the draft taxonomy. Of those strategies that could be categorised, the majority were professionally focused (57%). A total of 41% of projects used only one implementation strategy, with 29% using two and 31% three or more. The three most commonly used strategies were changes in quality assurance, quality improvement and/or performance measurement systems, changes in information and communication technology, and distribution of guideline materials (via hard-copy, audio-visual and/or electronic means). Further refinement of the draft taxonomy is required to provide hierarchical dimensions and granularity, particularly in the areas of patient-focused interventions, those concerned with audit and feedback and quality improvement, and electronic forms of implementation, including electronic decision support.

Concept Development for Software Health Management

NASA Technical Reports Server (NTRS)

Riecks, Jung; Storm, Walter; Hollingsworth, Mark

2011-01-01

This report documents the work performed by Lockheed Martin Aeronautics (LM Aero) under NASA contract NNL06AA08B, delivery order NNL07AB06T. The Concept Development for Software Health Management (CDSHM) program was a NASA funded effort sponsored by the Integrated Vehicle Health Management Project, one of the four pillars of the NASA Aviation Safety Program. The CD-SHM program focused on defining a structured approach to software health management (SHM) through the development of a comprehensive failure taxonomy that is used to characterize the fundamental failure modes of safety-critical software.

The Importance of Biopsy in the Era of Molecular Medicine.

PubMed

Ziv, Etay; Durack, Jeremy C; Solomon, Stephen B

Recent advances in the molecular characterization of cancers have triggered interest in developing a new taxonomy of disease in oncology with the goal of using the molecular profile of a patient's tumor to predict response to treatment. Image-guided needle biopsy is central to this "precision medicine" effort. In this review, we first discuss the current role of biopsy in relation to clinical examples of molecular medicine. We then outline important bottlenecks to the advancement of precision medicine and highlight the potential role of image-guided biopsy to address these challenges.

Developing a taxonomy for mission architecture definition

NASA Technical Reports Server (NTRS)

Neubek, Deborah J.

1990-01-01

The Lunar and Mars Exploration Program Office (LMEPO) was tasked to define candidate architectures for the Space Exploration Initiative to submit to NASA senior management and an externally constituted Outreach Synthesis Group. A systematic, structured process for developing, characterizing, and describing the alternate mission architectures, and applying this process to future studies was developed. The work was done in two phases: (1) national needs were identified and categorized into objectives achievable by the Space Exploration Initiative; and (2) a program development process was created which both hierarchically and iteratively describes the program planning process.

Instruments and Taxonomy of Workplace Bullying in Health Care Organizations.

PubMed

Park, Eun-Jun; Lee, Mikyoung; Park, Myungsook

2017-12-01

This study was aimed to evaluate the methodological issues and comprehensiveness of workplace bullying instruments and to suggest a taxonomy of psychological abuse. Nineteen instruments applied in health care organizations and 469 questionnaire items mainly regarding psychological abuse were collected through a literature review. Three researchers classified the questionnaire items according to a "taxonomy of psychological abuse in the workplace." Many instruments of workplace bullying were developed in the 2000s using a reflective measurement model, but their psychometric property was not sufficient and the measurement model is questioned. Based on the questionnaire items, the "taxonomy of psychological abuse in the workplace" was modified by adding two new subcategories (unachievable work and unfair treatment) and clarifying some operational definitions. According to the modified taxonomy of 11 (sub)categories, the reviewed instruments assessed 6.5 (sub)categories on average. No instrument measured all (sub)categories. Category 4.2 (disrespect, humiliation, and rejection of the person) was measured in all instruments, followed by Categories 5 (professional discredit and denigration) and 1.2 (social isolation) behaviors. The current instruments are not comprehensive enough. It is suggested that the modified taxonomy is verified and guide more reliable and inclusive instruments in the future. Furthermore, a formative measurement model, which defines a bullying as an inventory of different types of behaviors, should be used. Copyright © 2017. Published by Elsevier B.V.

Climbing Bloom's taxonomy pyramid: Lessons from a graduate histology course.

PubMed

Zaidi, Nikki B; Hwang, Charles; Scott, Sara; Stallard, Stefanie; Purkiss, Joel; Hortsch, Michael

2017-09-01

Bloom's taxonomy was adopted to create a subject-specific scoring tool for histology multiple-choice questions (MCQs). This Bloom's Taxonomy Histology Tool (BTHT) was used to analyze teacher- and student-generated quiz and examination questions from a graduate level histology course. Multiple-choice questions using histological images were generally assigned a higher BTHT level than simple text questions. The type of microscopy technique (light or electron microscopy) used for these image-based questions did not result in any significant differences in their Bloom's taxonomy scores. The BTHT levels for teacher-generated MCQs correlated positively with higher discrimination indices and inversely with the percent of students answering these questions correctly (difficulty index), suggesting that higher-level Bloom's taxonomy questions differentiate well between higher- and lower-performing students. When examining BTHT scores for MCQs that were written by students in a Multiple-Choice Item Development Assignment (MCIDA) there was no significant correlation between these scores and the students' ability to answer teacher-generated MCQs. This suggests that the ability to answer histology MCQs relies on a different skill set than the aptitude to construct higher-level Bloom's taxonomy questions. However, students significantly improved their average BTHT scores from the midterm to the final MCIDA task, which indicates that practice, experience and feedback increased their MCQ writing proficiency. Anat Sci Educ 10: 456-464. © 2017 American Association of Anatomists. © 2017 American Association of Anatomists.

The HCBS Taxonomy: A New Language for Classifying Home- and Community-Based Services

PubMed Central

Peebles, Victoria; Bohl, Alex

2014-01-01

Introduction As states make home- and community-based services (HCBS) more accessible, researchers have become more interested in understanding service use and spending. Because state Medicaid programs differ in the types of services they offer and in how they report these services, analyzing HCBS at the national level is challenging. Objective Describe the HCBS taxonomy and present findings on HCBS waiver expenditures and users. Data This brief analyzed fee-for-service claims from 28 approved states in 2010 Medicaid Analytic eXtract (MAX) files. We summed all expenditures and counted the unique number of users across each HCBS taxonomy service and category. Methods The taxonomy was developed jointly by Truven Health (at that time Thomson Reuters) and Mathematica Policy Research, with stakeholder input, and reviewed using procedure codes. Today, the taxonomy is organized by 18 categories and over 60 specific services. Findings For calendar year 2010, 28 states spent almost $23.6 billion on HCBS, with 80 percent of expenditures categorized as round-the-clock, home-based, and day services. Other services, such as case management, or equipment, modifications, and technology were widely used, but are not particularly costly and do not account for a large proportion of expenditures in every state. Conclusions By providing a common language, the taxonomy presents detailed information on services and makes it easier to assess and identify state-level variation for HCBS. PMID:25343057

SCIRehab Project Series: The Psychology Taxonomy

PubMed Central

Wilson, Catherine; Huston, Toby; Koval, Jill; Gordon, Samuel A; Schwebel, Andrea; Gassaway, Julie

2009-01-01

Context: The integration of psychologists as members of the rehabilitation team has occurred in conjunction with the evolution and adoption of interdisciplinary teams as the standard of care in spinal cord injury (SCI) rehabilitation. Although the value of psychological services during rehabilitation is endorsed widely, specific interventions and their association with patient outcomes have not been examined adequately. Objective: To address this shortcoming, psychologists from 6 SCI centers collaborated to develop a psychology intervention taxonomy and documentation framework. Methods: Utilizing an interactive process, the lead psychologists from 6 centers compiled an inclusive list of patient characteristics assessed and interventions delivered in routine psychological practice at the participating rehabilitation facilities. These were systematically grouped, defined, and compared. Results: The resulting taxonomy became the basis of a documentation framework utilized by psychologists for the study. The psychology taxonomy includes 4 major clinical categories (assessment, psychotherapeutic interventions, psychoeducational interventions, and consultation) with 5 to 10 specific activities in each category. Conclusions: Examination of psychological interventions and their potential association with positive outcomes for persons who sustain SCI requires the development of a taxonomy. Results of these efforts illustrate similarities and differences in psychological practice among SCI centers and offer the opportunity to blend research and clinical practice in an innovative approach to evidence-based practice improvement. The established taxonomy provides a basic framework for future studies on the effect of psychological interventions. PMID:19810633

A taxonomy of state public health preparedness units: an empirical examination of organizational structure.

PubMed

Menachemi, Nir; Yeager, Valerie A; Duncan, W Jack; Katholi, Charles R; Ginter, Peter M

2012-01-01

State public health preparedness units (SPHPUs) were developed in response to federal funding to improve response to disasters: a responsibility that had not traditionally been within the purview of public health. The SPHPUs were created within the existing public health organizational structure, and their placement may have implications for how the unit functions, how communication takes place, and ultimately how well the key responsibilities are performed. This study empirically identifies a taxonomy of similarly structured SPHPUs and examines whether this structure is associated with state geographic, demographic, and threat-vulnerability characteristics. Data representing each SPHPU were extracted from publically available sources, including organizational charts and emergency preparedness plans for 2009. A cross-sectional segmentation analysis was conducted of variables representing structural attributes. Fifty state public health departments. Variables representing "span of control" and "hierarchal levels" were extracted from organizational charts. Structural "complexity" and "centralization" were extracted from state emergency preparedness documents and other secondary sources. On average, 6.6 people report to the same manager as the SPHPU director; 2.1 levels separate the SPHPU director from the state health officer; and a mean of 13.5 agencies collaborate with SPHPU during a disaster. Despite considerable variability in how SPHPUs had been structured, results of the cluster and principal component analysis identified 7 similarly structured groups. Neither the taxonomic groups nor the individual variables representing structure were found to be associated with state characteristics, including threat vulnerabilities. Our finding supports the hypothesis that SPHPUs are seemingly inadvertently (eg, not strategically) organized. This taxonomy provides the basis for which future research can examine how SPHPU structure relates to performance measures and preparedness strategies.

How older citizens engage in their health promotion: a qualitative research-driven taxonomy of experiences and meanings

PubMed Central

Menichetti, Julia; Graffigna, Guendalina

2016-01-01

Objectives In this qualitative study, we provide an in-depth exploration of older people's experiences and subjective meanings concerning their engagement in health promotion as well as the emotional and pragmatic difficulties they face during their engagement. Methods The study was designed according to the ethnoscience method, which implies a participatory process that values patients' linguistic expressions to deeply understand the phenomena under the investigation and to give it a meaning. Using this method, thanks to repeated rounds of interviews and the Q-sorting task, participants created a dictionary, with the assistance of the researcher, to describe the phenomenon of interest. They agreed on a shared taxonomy of meanings and experiences related to the phenomenon. 25 North Italian older citizens participated in this study. Results Participants described a shared taxonomy of health engagement experiences by depicting 3 main positions (ie, locked position; awakening position; climbing position), which represented different experiential domains grouped by participants into 4 main semantic areas (eg, physical care, soul care, daily lifestyle, contact with ageing). Each position is characterised by specific emotions, personal representations of meaning and healthy behaviours that may sustain or hinder older citizens' engagement in health promotion. Conclusions The results of the present study suggest the importance of deeply understanding older peoples' experiences and their subjective meanings of health promotion. In particular, the results showed how their engagement in health promotion is framed in a complex system of psychological meanings, which may sustain or hinder their ability to adopt healthy behaviours. A deeper understanding of older citizens' lived experiences, their doubts and their difficulties in engaging in health promotion may offer some important cues for orienting interventions in this area. PMID:27417196

Developing a Gap Taxonomy to Address Crew Health Risks in NASA's Human Research Program

NASA Technical Reports Server (NTRS)

Kundrot, Craig E.; Edwards, J. Michelle

2009-01-01

The mission of NASA's Human Research Program (HRP) is to understand and reduce the risk to crew health and performance in exploration missions. The HRP addresses 27 specific risks by identifying and then filling gaps in understanding the risks and in the ability to disposition the risks. The primary bases for identifying gaps have been past experience and requirements definition. This approach has been very effective in identifying some important, relevant gaps, but may be inadequate for identifying gaps outside the past experience base. We are exploring the use of a gap taxonomy as a comprehensive, underlying conceptual framework that allows a more systematic identification of gaps. The taxonomy is based on these stages in medical care: prediction, prevention, detection/diagnosis, treatment, monitoring, rehabilitation, and lifetime surveillance. This gap taxonomy approach identifies new gaps in HRP health risks. Many of the new gaps suggest risk reduction approaches that are more cost effective than present approaches. A major benefit of the gap taxonomy approach is to identify new, economical approaches that reduce the likelihood and/or consequence of a risk.

Intuitive Cognition and Models of Human-Automation Interaction.

PubMed

Patterson, Robert Earl

2017-02-01

The aim of this study was to provide an analysis of the implications of the dominance of intuitive cognition in human reasoning and decision making for conceptualizing models and taxonomies of human-automation interaction, focusing on the Parasuraman et al. model and taxonomy. Knowledge about how humans reason and make decisions, which has been shown to be largely intuitive, has implications for the design of future human-machine systems. One hundred twenty articles and books cited in other works as well as those obtained from an Internet search were reviewed. Works were deemed eligible if they were published within the past 50 years and common to a given literature. Analysis shows that intuitive cognition dominates human reasoning and decision making in all situations examined. The implications of the dominance of intuitive cognition for the Parasuraman et al. model and taxonomy are discussed. A taxonomy of human-automation interaction that incorporates intuitive cognition is suggested. Understanding the ways in which human reasoning and decision making is intuitive can provide insight for future models and taxonomies of human-automation interaction.

Puppets, robots, critics, and actors within a taxonomy of attention for developmental disorders

PubMed Central

DENNIS, MAUREEN; SINOPOLI, KATIA J.; FLETCHER, JACK M.; SCHACHAR, RUSSELL

2008-01-01

This review proposes a new taxonomy of automatic and controlled attention. The taxonomy distinguishes among the role of the attendee (puppet and robot, critic and actor), the attention process (stimulus orienting vs. response control), and the attention operation (activation vs. inhibition vs. adjustment), and identifies cognitive phenotypes by which attention is overtly expressed. We apply the taxonomy to four childhood attention disorders: attention deficit hyperactivity disorder, spina bifida meningomyelocele, traumatic brain injury, and acute lymphoblastic leukemia. Variations in attention are related to specific brain regions that support normal attention processes when intact, and produce disordered attention when impaired. The taxonomy explains group differences in behavioral inattention, hyperactivity, and impulsiveness, as well as medication response. We also discuss issues relevant to theories of the cognitive and neural architecture of attention: functional dissociations within and between automatic and controlled attention; the relative importance of type of brain damage and developmental timing to attention profile; cognitive-energetic models of attention and white matter damage; temporal processing deficits, attention deficits and cerebellar damage; and the issue of cognitive phenotypes as candidate endophenotypes. PMID:18764966

Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy.

PubMed

Campanaro, Stefano; Treu, Laura; Kougias, Panagiotis G; De Francisci, Davide; Valle, Giorgio; Angelidaki, Irini

2016-01-01

Biogas production is an economically attractive technology that has gained momentum worldwide over the past years. Biogas is produced by a biologically mediated process, widely known as "anaerobic digestion." This process is performed by a specialized and complex microbial community, in which different members have distinct roles in the establishment of a collective organization. Deciphering the complex microbial community engaged in this process is interesting both for unraveling the network of bacterial interactions and for applicability potential to the derived knowledge. In this study, we dissect the bioma involved in anaerobic digestion by means of high throughput Illumina sequencing (~51 gigabases of sequence data), disclosing nearly one million genes and extracting 106 microbial genomes by a novel strategy combining two binning processes. Microbial phylogeny and putative taxonomy performed using >400 proteins revealed that the biogas community is a trove of new species. A new approach based on functional properties as per network representation was developed to assign roles to the microbial species. The organization of the anaerobic digestion microbiome is resembled by a funnel concept, in which the microbial consortium presents a progressive functional specialization while reaching the final step of the process (i.e., methanogenesis). Key microbial genomes encoding enzymes involved in specific metabolic pathways, such as carbohydrates utilization, fatty acids degradation, amino acids fermentation, and syntrophic acetate oxidation, were identified. Additionally, the analysis identified a new uncultured archaeon that was putatively related to Methanomassiliicoccales but surprisingly having a methylotrophic methanogenic pathway. This study is a pioneer research on the phylogenetic and functional characterization of the microbial community populating biogas reactors. By applying for the first time high-throughput sequencing and a novel binning strategy, the identified genes were anchored to single genomes providing a clear understanding of their metabolic pathways and highlighting their involvement in anaerobic digestion. The overall research established a reference catalog of biogas microbial genomes that will greatly simplify future genomic studies.

Plant Taxonomy as a Field Study

ERIC Educational Resources Information Center

Dalby, D. H.

1970-01-01

Suggests methods of teaching plant identification and taxonomic theory using keys, statistical analyses, and biometrics. Population variation, genotype- environment interaction and experimental taxonomy are used in laboratory and field. (AL)

Knowledge-guided mutation in classification rules for autism treatment efficacy.

PubMed

Engle, Kelley; Rada, Roy

2017-03-01

Data mining methods in biomedical research might benefit by combining genetic algorithms with domain-specific knowledge. The objective of this research is to show how the evolution of treatment rules for autism might be guided. The semantic distance between two concepts in the taxonomy is measured by the number of relationships separating the concepts in the taxonomy. The hypothesis is that replacing a concept in a treatment rule will change the accuracy of the rule in direct proportion to the semantic distance between the concepts. The method uses a patient database and autism taxonomies. Treatment rules are developed with an algorithm that exploits the taxonomies. The results support the hypothesis. This research should both advance the understanding of autism data mining in particular and of knowledge-guided evolutionary search in biomedicine in general.

Let's rise up to unite taxonomy and technology.

PubMed

Bik, Holly M

2017-08-01

What do you think of when you think of taxonomy? An 18th century gentlemen in breeches? Or perhaps botany drawings hung on the walls of a boutique hotel? Such old-fashioned conceptions to the contrary, taxonomy is alive today although constantly struggling for survival and recognition. The scientific community is losing valuable resources as taxonomy experts age and retire, and funding for morphological studies and species descriptions remains stagnant. At the same time, organismal knowledge (morphology, ecology, physiology) has never been more important: genomic studies are becoming more taxon focused, the scientific community is recognizing the limitations of traditional "model" organisms, and taxonomic expertise is desperately needed to fight against global biodiversity declines resulting from human impacts. There has never been a better time for a taxonomic renaissance.

Let’s rise up to unite taxonomy and technology

PubMed Central

2017-01-01

What do you think of when you think of taxonomy? An 18th century gentlemen in breeches? Or perhaps botany drawings hung on the walls of a boutique hotel? Such old-fashioned conceptions to the contrary, taxonomy is alive today although constantly struggling for survival and recognition. The scientific community is losing valuable resources as taxonomy experts age and retire, and funding for morphological studies and species descriptions remains stagnant. At the same time, organismal knowledge (morphology, ecology, physiology) has never been more important: genomic studies are becoming more taxon focused, the scientific community is recognizing the limitations of traditional “model” organisms, and taxonomic expertise is desperately needed to fight against global biodiversity declines resulting from human impacts. There has never been a better time for a taxonomic renaissance. PMID:28820884

Evaluating a medical error taxonomy.

PubMed

Brixey, Juliana; Johnson, Todd R; Zhang, Jiajie

2002-01-01

Healthcare has been slow in using human factors principles to reduce medical errors. The Center for Devices and Radiological Health (CDRH) recognizes that a lack of attention to human factors during product development may lead to errors that have the potential for patient injury, or even death. In response to the need for reducing medication errors, the National Coordinating Council for Medication Errors Reporting and Prevention (NCC MERP) released the NCC MERP taxonomy that provides a standard language for reporting medication errors. This project maps the NCC MERP taxonomy of medication error to MedWatch medical errors involving infusion pumps. Of particular interest are human factors associated with medical device errors. The NCC MERP taxonomy of medication errors is limited in mapping information from MEDWATCH because of the focus on the medical device and the format of reporting.

A preference for some types of complexity comment on "perceived beauty of random texture patterns: A preference for complexity".

PubMed

Gauvrit, Nicolas; Soler-Toscano, Fernando; Guida, Alessandro

2017-03-01

In two experiments, Friedenberg and Liby (2016) studied how a diversity of complexity estimates such as density, number of blocks, GIF compression rate and edge length impact the perception of beauty of semi-random two-dimensional patterns. They concluded that aesthetics ratings are positively linked with GIF compression metrics and edge length, but not with the number of blocks. They also found an inverse U-shaped link between aesthetic judgments and density. These mixed results originate in the variety of metrics used to estimate what is loosely called "complexity" in psychology and indeed refers to conflicting notions. Here, we reanalyze their data adding two more conventional and normative mathematical measures of complexity: entropy and algorithmic complexity. We show that their results can be interpreted as an aesthetic preference for low redundancy, balanced patterns and "crooked" figures, but not for high algorithmic complexity. We conclude that participants tend to have a preference for some types of complexity, but not for all. These findings may help understand divergent results in the study of perceived beauty and complexity, and illustrate the need to specify the notion of complexity used in psychology. The field would certainly benefit from a precise taxonomy of complexity measures. Copyright © 2017 Elsevier B.V. All rights reserved.

Medical Parasitology Taxonomy Update: January 2012 to December 2015.

PubMed

Simner, P J

2017-01-01

Parasites of medical importance have long been classified taxonomically by morphological characteristics. However, molecular-based techniques have been increasingly used and relied on to determine evolutionary distances for the basis of rational hierarchal classifications. This has resulted in several different classification schemes for parasites and changes in parasite taxonomy. The purpose of this Minireview is to provide a single reference for diagnostic laboratories that summarizes new and revised clinically relevant parasite taxonomy from January 2012 through December 2015. Copyright © 2016 American Society for Microbiology.

ICTV Virus Taxonomy Profile: Nyamiviridae.

PubMed

Dietzgen, Ralf G; Ghedin, Elodie; Jiāng, Dàohóng; Kuhn, Jens H; Song, Timothy; Vasilakis, Nikos; Wang, David; Ictv Report Consortium

2017-12-01

The Nyamiviridae is a family of viruses with unsegmented, negative-sense RNA genomes of 11.3-12.2 kb that produce enveloped, spherical virions. Viruses of the genus Nyavirus are tick-borne and some also infect birds. Other nyamiviruses infecting parasitoid wasps and plant parasitic nematodes have been classified into the genera Peropuvirus and Socyvirus, respectively. This is a summary of the current International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of Nyamiviridae, which is available at www.ictv.global/report/nyamiviridae.

An Examination of a Proposed DSM-IV Pathological Gambling Hierarchy in a Treatment Seeking Population: Similarities with Substance Dependence and Evidence for Three Classification Systems.

PubMed

Christensen, Darren R; Jackson, Alun C; Dowling, Nicki A; Volberg, Rachel A; Thomas, Shane A

2015-09-01

Toce-Gerstein et al. (Addiction 98:1661-1672, 2003) investigated the distribution of Diagnostic and Statistical Manual for Mental Disorders, 4th edition (DSM-IV) pathological gambling criteria endorsement in a U.S. community sample for those people endorsing a least one of the DSM-IV criteria (n = 399). They proposed a hierarchy of gambling disorders where endorsement of 1-2 criteria were deemed 'At-Risk', 3-4 'Problem gamblers', 5-7 'Low Pathological', and 8-10 'High Pathological' gamblers. This article examines these claims in a larger Australian treatment seeking population. Data from 4,349 clients attending specialist problem gambling services were assessed for meeting the ten DSM-IV pathological gambling criteria. Results found higher overall criteria endorsement frequencies, three components, a direct relationship between criteria endorsement and gambling severity, clustering of criteria similar to the Toce-Gerstein et al. taxonomy, high accuracy scores for numerical and criteria specific taxonomies, and also high accuracy scores for dichotomous pathological gambling diagnoses. These results suggest significant complexities in the frequencies of criteria reports and relationships between criteria.

The evolution and phylogeography of the African elephant inferred from mitochondrial DNA sequence and nuclear microsatellite markers.

PubMed

Eggert, Lori S; Rasner, Caylor A; Woodruff, David S

2002-10-07

Recent genetic results support the recognition of two African elephant species: Loxodonta africana, the savannah elephant, and Loxodonta cyclotis, the forest elephant. The study, however, did not include the populations of West Africa, where the taxonomic affinities of elephants have been much debated. We examined mitochondrial cytochrome b control region sequences and four microsatellite loci to investigate the genetic differences between the forest and savannah elephants of West and Central Africa. We then combined our data with published control region sequences from across Africa to examine patterns at the continental level. Our analysis reveals several deeply divergent lineages that do not correspond with the currently recognized taxonomy: (i) the forest elephants of Central Africa; the forest and savannah elephants of West Africa; and (iii) the savannah elephants of eastern, southern and Central Africa. We propose that the complex phylogeographic patterns we detect in African elephants result from repeated continental-scale climatic changes over their five-to-six million year evolutionary history. Until there is consensus on the taxonomy, we suggest that the genetic and ecological distinctness of these lineages should be an important factor in conservation management planning.

Bio-image warehouse system: concept and implementation of a diagnosis-based data warehouse for advanced imaging modalities in neuroradiology.

PubMed

Minati, L; Ghielmetti, F; Ciobanu, V; D'Incerti, L; Maccagnano, C; Bizzi, A; Bruzzone, M G

2007-03-01

Advanced neuroimaging techniques, such as functional magnetic resonance imaging (fMRI), chemical shift spectroscopy imaging (CSI), diffusion tensor imaging (DTI), and perfusion-weighted imaging (PWI) create novel challenges in terms of data storage and management: huge amounts of raw data are generated, the results of analysis may depend on the software and settings that have been used, and most often intermediate files are inherently not compliant with the current DICOM (digital imaging and communication in medicine) standard, as they contain multidimensional complex and tensor arrays and various other types of data structures. A software architecture, referred to as Bio-Image Warehouse System (BIWS), which can be used alongside a radiology information system/picture archiving and communication system (RIS/PACS) system to store neuroimaging data for research purposes, is presented. The system architecture is conceived with the purpose of enabling to query by diagnosis according to a predefined two-layered classification taxonomy. The operational impact of the system and the time needed to get acquainted with the web-based interface and with the taxonomy are found to be limited. The development of modules enabling automated creation of statistical templates is proposed.

The spiny dogfish ('cação-bagre'): description of an envenoming in a fisherman, with taxonomic and toxinologic comments on the Squalus gender.

PubMed

Haddad, Vidal; Gadig, Otto Bismarck Fazzano

2005-07-01

The authors report an injury caused by a spiny dogfish (Squalus sp) in a professional fisherman that was got hurt in the left hand for a spine in the dorsal fin of the fish and felt excruciating local pain for 6 h and manifested local edema and erythema. The sharks of the Squalus gender, in a similar way to the gender Heterodontus, present two spines in position previous to the dorsal fins, with channels presenting a whitish mass, composed of great and vacuolated cells that produce venom. The Squalus gender has a complex taxonomy, with five nominal species mentioned in Brazil: S. acanthias, S. blainvillei, S. cubensis, S. megalops and S. mitsukurii. The species associated to the injury belongs to the group 'megalops/cubensis'. A detailed study on the taxonomy and toxinology of the Squalus gender in Brazil would be of vital importance in the resolution of those problems and it would serve as subsidy for any other works involving their representatives, besides with aspects of envenoming that this gender can cause and that has rare citations in the literature.

A six-gene phylogeny provides new insights into choanoflagellate evolution.

PubMed

Carr, Martin; Richter, Daniel J; Fozouni, Parinaz; Smith, Timothy J; Jeuck, Alexandra; Leadbeater, Barry S C; Nitsche, Frank

2017-02-01

Recent studies have shown that molecular phylogenies of the choanoflagellates (Class Choanoflagellatea) are in disagreement with their traditional taxonomy, based on morphology, and that Choanoflagellatea requires considerable taxonomic revision. Furthermore, phylogenies suggest that the morphological and ecological evolution of the group is more complex than has previously been recognized. Here we address the taxonomy of the major choanoflagellate order Craspedida, by erecting four new genera. The new genera are shown to be morphologically, ecologically and phylogenetically distinct from other choanoflagellate taxa. Furthermore, we name five novel craspedid species, as well as formally describe ten species that have been shown to be either misidentified or require taxonomic revision. Our revised phylogeny, including 18 new species and sequence data for two additional genes, provides insights into the morphological and ecological evolution of the choanoflagellates. We examine the distribution within choanoflagellates of these two additional genes, EF-1A and EFL, closely related translation GTPases which are required for protein synthesis. Mapping the presence and absence of these genes onto the phylogeny highlights multiple events of gene loss within the choanoflagellates. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Diversity of potato genetic resources

PubMed Central

Machida-Hirano, Ryoko

2015-01-01

A considerable number of highly diverse species exist in genus Solanum. Because they can adapt to a broad range of habitats, potato wild relatives are promising sources of desirable agricultural traits. Potato taxonomy is quite complex because of introgression, interspecific hybridization, auto- and allopolyploidy, sexual compatibility among many species, a mixture of sexual and asexual reproduction, possible recent species divergence, phenotypic plasticity, and the consequent high morphological similarity among species. Recent researchers using molecular tools have contributed to the identification of genes controlling several types of resistance as well as to the revision of taxonomical relationships among potato species. Historically, primitive forms of cultivated potato and its wild relatives have been used in breeding programs and there is still an enormous and unimaginable potential for discovering desirable characteristics, particularly in wild species Different methods have been developed to incorporate useful alleles from these wild species into the improved cultivars. Potato germplasm comprising of useful alleles for different breeding objectives is preserved in various gene banks worldwide. These materials, with their invaluable information, are accessible for research and breeding purposes. Precise identification of species base on the new taxonomy is essential for effective use of the germplasm collection. PMID:25931978

A Molecular Perspective on Systematics, Taxonomy and Classification Amazonian Discus Fishes of the Genus Symphysodon

PubMed Central

Amado, Manuella Villar; Farias, Izeni P.; Hrbek, Tomas

2011-01-01

With the goal of contributing to the taxonomy and systematics of the Neotropical cichlid fishes of the genus Symphysodon, we analyzed 336 individuals from 24 localities throughout the entire distributional range of the genus. We analyzed variation at 13 nuclear microsatellite markers, and subjected the data to Bayesian analysis of genetic structure. The results indicate that Symphysodon is composed of four genetic groups: group PURPLE—phenotype Heckel and abacaxi; group GREEN—phenotype green; group RED—phenotype blue and brown; and group PINK—populations of Xingú and Cametá. Although the phenotypes blue and brown are predominantly biological group RED, they also have substantial contributions from other biological groups, and the patterns of admixture of the two phenotypes are different. The two phenotypes are further characterized by distinct and divergent mtDNA haplotype groups, and show differences in mean habitat use measured as pH and conductivity. Differences in mean habitat use is also observed between most other biological groups. We therefore conclude that Symphysodon comprises five evolutionary significant units: Symphysodon discus (Heckel and abacaxi phenotypes), S. aequifasciatus (brown phenotype), S. tarzoo (green phenotype), Symphysodon sp. 1 (blue phenotype) and Symphysodon sp. 2 (Xingú group). PMID:21811676

Juvenile Sex Offending Through a Developmental Life Course Criminology Perspective.

PubMed

Lussier, Patrick

2017-02-01

Current American policies and responses to juvenile sex offending have been criticized for being based on myths, misconceptions, and unsubstantiated claims. In spite of the criticism, no organizing framework has been proposed to guide policy development with respect to the prevention of juvenile sex offending. This article proposes a developmental life course (DLC) criminology perspective to investigate the origins, development, and termination of sex offending among youth. It also provides a review of the current state of knowledge regarding various parameters characterizing the development of sex offending (e.g., prevalence, age of onset, frequency, persistence, continuity in adulthood, and versatility). The review highlights some heterogeneity across these developmental parameters suggesting the presence of different sex offending patterns among youth. In fact, it is proposed that, based on the current knowledge, such heterogeneity can be accounted for by a dual taxonomy of adolescents involved in sexual offenses: (a) the adolescent-limited and (b) the high-rate/slow-desister. The DLC criminology approach and the dual taxonomy are proposed as organizing frameworks to conduct prospective longitudinal research to better understand the origins and development of sex offending and to guide policy development and responses to at-risk youth and those who have committed sexual offenses.

The advertisement calls of Quasipaa shini (Ahl, 1930) (Anura: Dicroglossidae).

PubMed

Kong, Shen Shen; Zheng, Rong Quan; Zhang, Qi Peng

2016-12-04

The genus Quasipaa (Family Dicroglossidae) is currently composed of 11 species distributed in China and Southeast Asia: Quasipaa acanthophora (Dubois & Ohler 2009), Q. boulengeri (Günther 1889), Q. courtoisi (Angel 1922), Q. delacouri (Angel 1928), Q. exilispinosa (Liu & Hu, 1975), Q. fasciculispina (Inger 1970), Q. jiulongensis (Huang & Liu, 1985), Q. shini (Ahl 1930), Q. spinosa (David 1875), Q. verrucospinosa (Bourret 1937), Q. yei (Chen, Qu & Jiang 2002) (Frost 2016). These species are morphologically similar, and their taxonomy is subject to controversy (Che et al. 2009). Analyses of nuclear and mitochondrial genes suggest the genus likely encompass additional cryptic species (Ye et al. 2013). Bioacoustics has contributed to studies on the taxonomy of the genus (Ye et al. 2013; Shen et al. 2015), however, to date, only the advertisement calls of Q. spinosa are known (Yu & Zheng 2009; Chen et al. 2012; Shen et al. 2015). Here, we describe the advertisement calls of Q. shini, which inhabits streams in the southern part of central China(Guizhou, Hunan, Guangxi and Jiangxi) and is characterized by the presence of keratinized skin spines on the lateral surfaces of the body.

Molecular phylogeny based on six nuclear genes suggests that Echinococcus granulosus sensu lato genotypes G6/G7 and G8/G10 can be regarded as two distinct species.

PubMed

Laurimäe, Teivi; Kinkar, Liina; Moks, Epp; Romig, Thomas; Omer, Rihab A; Casulli, Adriano; Umhang, Gérald; Bagrade, Guna; Irshadullah, Malik; Sharbatkhori, Mitra; Mirhendi, Hossein; Ponce-Gordo, Francisco; Soriano, Silvia V; Varcasia, Antonio; Rostami-Nejad, Mohammad; Andresiuk, Vanessa; Saarma, Urmas

2018-05-21

Tapeworms of the species complex of Echinococcus granulosus sensu lato (s. l.) are the cause of a severe zoonotic disease - cystic echinococcosis, which is listed among the most severe parasitic diseases in humans and is prioritized by the World Health Organization. A stable taxonomy of E. granulosus s. l. is essential to the medical and veterinary communities for accurate and effective communication of the role of different species in this complex on human and animal health. E. granulosus s. l. displays high genetic diversity and has been divided into different species and genotypes. Despite several decades of research, the taxonomy of E. granulosus s. l. has remained controversial, especially the species status of genotypes G6-G10. Here the Bayesian phylogeny based on six nuclear loci (7387 bp in total) demonstrated, with very high support, the clustering of G6/G7 and G8/G10 into two separate clades. According to the evolutionary species concept, G6/G7 and G8/G10 can be regarded as two distinct species. Species differentiation can be attributed to the association with distinct host species, largely separate geographical distribution and low level of cross-fertilization. These factors have limited the gene flow between genotypic groups G6/G7 and G8/G10, resulting in the formation of distinct species. We discuss ecological and epidemiological differences that support the validity of these species.

The mermithid species Isomermis lairdi (Nematoda, Mermithidae), previously only known in Africa, found in Europe

PubMed Central

Gradinarov, Denis

2014-01-01

Abstract The present work contributs to the knowledge on the aquatic mermithids (Nematoda, Mermithidae) occurring in black flies – an insufficiently studied group of parasitic nematodes. Isomermis lairdi Mondet, Poinar & Bernadou, 1977, described from larvae of Simulium damnosum Theobald, 1903 in Western Africa, is reported to occur in Bulgaria. The species was isolated from larvae of Simulium ornatum Meigen, 1818 in a local population of simuliids in a mountain stream near Jeleznitsa Village, Sofia district. Postparasitic juveniles of mermithids were obtained from the hosts and reared to the adult stage. The species was identified by morphological and morphometrical characters of postparasitic juveniles, and of male and female individuals. In the summer of 2012 a relatively high rate of mermithid infection in a local host population was detected (prevalence up to 44.1%). In August of the next year host abundance had considerably declined and other simuliid species, Simulium variegatum Meigen, 1818 and Simulium reptans (Linnaeus, 1758), predominated in the investigated locality. In West Africa, Isomermis lairdi is considered to be a potential biological agent for reducing the population density of the Simulium damnosum complex – the main vector of human onchocerciasis. In Europe, species of the Simulium ornatum complex are among the vectors of onchocerciasis of cattle and deer. The mermithids presumably play a certain role in the epidemiology of these diseases. A brief discussion on the taxonomy of the genus Isomermis Coman, 1953, and of the feasibility of molecular methods in mermithid taxonomy is provided. The species Isomermis lairdi is reported for the first time from Europe. PMID:25493063

EPA's Information Architecture and Web Taxonomy

EPA Pesticide Factsheets

EPA's Information Architecture creates a topical organization of our website, instead of an ownership-based organization. The EPA Web Taxonomy allows audiences easy access to relevant information from EPA programs, by using a common vocabulary.

76 FR 74050 - Measured Building Energy Performance Data Taxonomy

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-30

... data sources and taxonomies. Certain data fields have enumerated types that provide a discrete set of... Utility, Electric Rate Structure, and Electricity Summer Peak Power. The Priority 3 data fields include...

Is a rehabilitation treatment taxonomy the right answer to the rehabilitation black box?

PubMed

Cieza, Alarcos; Bickenbach, Jerome

2014-01-01

In this commentary on the development of an interventions taxonomy for medical rehabilitation, a rehabilitation treatment taxonomy (RTT), we acknowledge the authors' valuable contribution to rehabilitation science, and at the same time interrogate the assumption that a taxonomy has essential added value to address the challenge of rehabilitation's black box. The tripartite analytical structure of action of treatment, active ingredient, and mechanism of action, and not an RTT, is the key to addressing the rehabilitation black box. There is a need for clearly defined operationalized requirements of how the 3 components have to be expressed. We also recommend that this concerted effort be linked to all relevant stakeholders and all international endeavors that are pursuing a common goal of enhancing rehabilitation research. Copyright © 2014 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Forensic Taxonomy of Android Social Apps.

PubMed

Azfar, Abdullah; Choo, Kim-Kwang Raymond; Liu, Lin

2017-03-01

An Android social app taxonomy incorporating artifacts that are of forensic interest will enable users and forensic investigators to identify the personally identifiable information (PII) stored by the apps. In this study, 30 popular Android social apps were examined. Artifacts of forensic interest (e.g., contacts lists, chronology of messages, and timestamp of an added contact) were recovered. In addition, images were located, and Facebook token strings used to tie account identities and gain access to information entered into Facebook by a user were identified. Based on the findings, a two-dimensional taxonomy of the forensic artifacts of the social apps is proposed. A comparative summary of existing forensic taxonomies of different categories of Android apps, designed to facilitate timely collection and analysis of evidentiary materials from Android devices, is presented. © 2016 American Academy of Forensic Sciences.

Application of an incident taxonomy for radiation therapy: Analysis of five years of data from three integrated cancer centres.

PubMed

Greenham, Stuart; Manley, Stephen; Turnbull, Kirsty; Hoffmann, Matthew; Fonseca, Amara; Westhuyzen, Justin; Last, Andrew; Aherne, Noel J; Shakespeare, Thomas P

2018-01-01

To develop and apply a clinical incident taxonomy for radiation therapy. Capturing clinical incident information that focuses on near-miss events is critical for achieving higher levels of safety and reliability. A clinical incident taxonomy for radiation therapy was established; coding categories were prescription, consent, simulation, voluming, dosimetry, treatment, bolus, shielding, imaging, quality assurance and coordination of care. The taxonomy was applied to all clinical incidents occurring at three integrated cancer centres for the years 2011-2015. Incidents were managed locally, audited and feedback disseminated to all centres. Across the five years the total incident rate (per 100 courses) was 8.54; the radiotherapy-specific coded rate was 6.71. The rate of true adverse events (unintended treatment and potential patient harm) was 1.06. Adverse events, where no harm was identified, occurred at a rate of 2.76 per 100 courses. Despite workload increases, overall and actual rates both exhibited downward trends over the 5-year period. The taxonomy captured previously unidentified quality assurance failures; centre-specific issues that contributed to variations in incident trends were also identified. The application of a taxonomy developed for radiation therapy enhances incident investigation and facilitates strategic interventions. The practice appears to be effective in our institution and contributes to the safety culture. The ratio of near miss to actual incidents could serve as a possible measure of incident reporting culture and could be incorporated into large scale incident reporting systems.

Characterizing Aeroallergens by Infrared Spectroscopy of Fungal Spores and Pollen

PubMed Central

Zimmermann, Boris; Tkalčec, Zdenko; Mešić, Armin; Kohler, Achim

2015-01-01

Background Fungal spores and plant pollen cause respiratory diseases in susceptible individuals, such as asthma, allergic rhinitis and hypersensitivity pneumonitis. Aeroallergen monitoring networks are an important part of treatment strategies, but unfortunately traditional analysis is time consuming and expensive. We have explored the use of infrared spectroscopy of pollen and spores for an inexpensive and rapid characterization of aeroallergens. Methodology The study is based on measurement of spore and pollen samples by single reflectance attenuated total reflectance Fourier transform infrared spectroscopy (SR-ATR FTIR). The experimental set includes 71 spore (Basidiomycota) and 121 pollen (Pinales, Fagales and Poales) samples. Along with fresh basidiospores, the study has been conducted on the archived samples collected within the last 50 years. Results The spectroscopic-based methodology enables clear spectral differentiation between pollen and spores, as well as the separation of confamiliar and congeneric species. In addition, the analysis of the scattering signals inherent in the infrared spectra indicates that the FTIR methodology offers indirect estimation of morphology of pollen and spores. The analysis of fresh and archived spores shows that chemical composition of spores is well preserved even after decades of storage, including the characteristic taxonomy-related signals. Therefore, biochemical analysis of fungal spores by FTIR could provide economical, reliable and timely methodologies for improving fungal taxonomy, as well as for fungal identification and monitoring. This proof of principle study shows the potential for using FTIR as a rapid tool in aeroallergen studies. In addition, the presented method is ready to be immediately implemented in biological and ecological studies for direct measurement of pollen and spores from flowers and sporocarps. PMID:25867755

The SACADA database for human reliability and human performance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Y. James Chang; Dennis Bley; Lawrence Criscione

2014-05-01

Lack of appropriate and sufficient human performance data has been identified as a key factor affecting human reliability analysis (HRA) quality especially in the estimation of human error probability (HEP). The Scenario Authoring, Characterization, and Debriefing Application (SACADA) database was developed by the U.S. Nuclear Regulatory Commission (NRC) to address this data need. An agreement between NRC and the South Texas Project Nuclear Operating Company (STPNOC) was established to support the SACADA development with aims to make the SACADA tool suitable for implementation in the nuclear power plants' operator training program to collect operator performance information. The collected data wouldmore » support the STPNOC's operator training program and be shared with the NRC for improving HRA quality. This paper discusses the SACADA data taxonomy, the theoretical foundation, the prospective data to be generated from the SACADA raw data to inform human reliability and human performance, and the considerations on the use of simulator data for HRA. Each SACADA data point consists of two information segments: context and performance results. Context is a characterization of the performance challenges to task success. The performance results are the results of performing the task. The data taxonomy uses a macrocognitive functions model for the framework. At a high level, information is classified according to the macrocognitive functions of detecting the plant abnormality, understanding the abnormality, deciding the response plan, executing the response plan, and team related aspects (i.e., communication, teamwork, and supervision). The data are expected to be useful for analyzing the relations between context, error modes and error causes in human performance.« less

Classification and Taxonomy of Vegetable Macergens

PubMed Central

Aremu, Bukola R.; Babalola, Olubukola O.

2015-01-01

Macergens are bacteria capable of releasing pectic enzymes (pectolytic bacteria). These enzymatic actions result in the separation of plant tissues leading to total plant destruction. This can be attributed to soft rot diseases in vegetables. These macergens primarily belong to the genus Erwinia and to a range of opportunistic pathogens namely: the Xanthomonas spp., Pseudomonas spp., Clostridium spp., Cytophaga spp., and Bacillus spp. They consist of taxa that displayed considerable heterogeneity and intermingled with members of other genera belonging to the Enterobacteriaceae. They have been classified based on phenotypic, chemotaxonomic and genotypic which obviously not necessary in the taxonomy of all bacterial genera for defining bacterial species and describing new ones These taxonomic markers have been used traditionally as a simple technique for identification of bacterial isolates. The most important fields of taxonomy are supposed to be based on clear, reliable and worldwide applicable criteria. Hence, this review clarifies the taxonomy of the macergens to the species level and revealed that their taxonomy is beyond complete. For discovery of additional species, further research with the use modern molecular methods like phylogenomics need to be done. This can precisely define classification of macergens resulting in occasional, but significant changes in previous taxonomic schemes of these macergens. PMID:26640465

A Review of Current and Prospective Factors for Classification of Civil Unmanned Aircraft Systems

NASA Technical Reports Server (NTRS)

Hayhurst, Kelly J.; Maddalon, Jeffrey M.; Morris, A. Terry; Neogi, Natasha; Verstynen, Harry A.

2014-01-01

While progress is being made on integrating unmanned aircraft systems (UAS) into our national airspace on a broad scale, much work remains to establish appropriate certification standards and operational procedures, particularly with respect to routine commercial operations. This paper summarizes research to examine the extent to which today's civil aircraft taxonomy applies to UAS, and, if needed, how that taxonomy could be amended to better cover different UAS designs and operations. Factors that shape the current taxonomy, as defined in the Federal Aviation Regulations, were assessed for applicability to UAS, potential incompatibilities were identified, and additional factors were proposed that might be useful for an updated aircraft taxonomy intended to cover UAS. The results suggest the possibility of constructing new groups in the taxonomy for UAS under a restricted category that share common airworthiness standards. Establishing distinct groups for UAS and associated standards that enable low risk operations for compensation or hire could be a timely step toward full integration. Such a step would allow the civil aviation industry and regulators to gain valuable experience with UAS while carefully controlling access and potential harm to the aviation system as a whole.

Classification and Taxonomy of Vegetable Macergens.

PubMed

Aremu, Bukola R; Babalola, Olubukola O

2015-01-01

Macergens are bacteria capable of releasing pectic enzymes (pectolytic bacteria). These enzymatic actions result in the separation of plant tissues leading to total plant destruction. This can be attributed to soft rot diseases in vegetables. These macergens primarily belong to the genus Erwinia and to a range of opportunistic pathogens namely: the Xanthomonas spp., Pseudomonas spp., Clostridium spp., Cytophaga spp., and Bacillus spp. They consist of taxa that displayed considerable heterogeneity and intermingled with members of other genera belonging to the Enterobacteriaceae. They have been classified based on phenotypic, chemotaxonomic and genotypic which obviously not necessary in the taxonomy of all bacterial genera for defining bacterial species and describing new ones These taxonomic markers have been used traditionally as a simple technique for identification of bacterial isolates. The most important fields of taxonomy are supposed to be based on clear, reliable and worldwide applicable criteria. Hence, this review clarifies the taxonomy of the macergens to the species level and revealed that their taxonomy is beyond complete. For discovery of additional species, further research with the use modern molecular methods like phylogenomics need to be done. This can precisely define classification of macergens resulting in occasional, but significant changes in previous taxonomic schemes of these macergens.

An Android Communication App Forensic Taxonomy.

PubMed

Azfar, Abdullah; Choo, Kim-Kwang Raymond; Liu, Lin

2016-09-01

Due to the popularity of Android devices and applications (apps), Android forensics is one of the most studied topics within mobile forensics. Communication apps, such as instant messaging and Voice over IP (VoIP), are one popular app category used by mobile device users, including criminals. Therefore, a taxonomy outlining artifacts of forensic interest involving the use of Android communication apps will facilitate the timely collection and analysis of evidentiary materials from such apps. In this paper, 30 popular Android communication apps were examined, where a logical extraction of the Android phone images was collected using XRY, a widely used mobile forensic tool. Various information of forensic interest, such as contact lists and chronology of messages, was recovered. Based on the findings, a two-dimensional taxonomy of the forensic artifacts of the communication apps is proposed, with the app categories in one dimension and the classes of artifacts in the other dimension. Finally, the artifacts identified in the study of the 30 communication apps are summarized using the taxonomy. It is expected that the proposed taxonomy and the forensic findings in this paper will assist forensic investigations involving Android communication apps. © 2016 American Academy of Forensic Sciences.

Twitter as a Tool for Health Research: A Systematic Review.

PubMed

Sinnenberg, Lauren; Buttenheim, Alison M; Padrez, Kevin; Mancheno, Christina; Ungar, Lyle; Merchant, Raina M

2017-01-01

Researchers have used traditional databases to study public health for decades. Less is known about the use of social media data sources, such as Twitter, for this purpose. To systematically review the use of Twitter in health research, define a taxonomy to describe Twitter use, and characterize the current state of Twitter in health research. We performed a literature search in PubMed, Embase, Web of Science, Google Scholar, and CINAHL through September 2015. We searched for peer-reviewed original research studies that primarily used Twitter for health research. Two authors independently screened studies and abstracted data related to the approach to analysis of Twitter data, methodology used to study Twitter, and current state of Twitter research by evaluating time of publication, research topic, discussion of ethical concerns, and study funding source. Of 1110 unique health-related articles mentioning Twitter, 137 met eligibility criteria. The primary approaches for using Twitter in health research that constitute a new taxonomy were content analysis (56%; n = 77), surveillance (26%; n = 36), engagement (14%; n = 19), recruitment (7%; n = 9), intervention (7%; n = 9), and network analysis (4%; n = 5). These studies collectively analyzed more than 5 billion tweets primarily by using the Twitter application program interface. Of 38 potential data features describing tweets and Twitter users, 23 were reported in fewer than 4% of the articles. The Twitter-based studies in this review focused on a small subset of data elements including content analysis, geotags, and language. Most studies were published recently (33% in 2015). Public health (23%; n = 31) and infectious disease (20%; n = 28) were the research fields most commonly represented in the included studies. Approximately one third of the studies mentioned ethical board approval in their articles. Primary funding sources included federal (63%), university (13%), and foundation (6%). We identified a new taxonomy to describe Twitter use in health research with 6 categories. Many data elements discernible from a user's Twitter profile, especially demographics, have been underreported in the literature and can provide new opportunities to characterize the users whose data are analyzed in these studies. Twitter-based health research is a growing field funded by a diversity of organizations. Public health implications. Future work should develop standardized reporting guidelines for health researchers who use Twitter and policies that address privacy and ethical concerns in social media research.

Taxonomy of the order Mononegavirales: update 2017.

PubMed

Amarasinghe, Gaya K; Bào, Yīmíng; Basler, Christopher F; Bavari, Sina; Beer, Martin; Bejerman, Nicolás; Blasdell, Kim R; Bochnowski, Alisa; Briese, Thomas; Bukreyev, Alexander; Calisher, Charles H; Chandran, Kartik; Collins, Peter L; Dietzgen, Ralf G; Dolnik, Olga; Dürrwald, Ralf; Dye, John M; Easton, Andrew J; Ebihara, Hideki; Fang, Qi; Formenty, Pierre; Fouchier, Ron A M; Ghedin, Elodie; Harding, Robert M; Hewson, Roger; Higgins, Colleen M; Hong, Jian; Horie, Masayuki; James, Anthony P; Jiāng, Dàohóng; Kobinger, Gary P; Kondo, Hideki; Kurath, Gael; Lamb, Robert A; Lee, Benhur; Leroy, Eric M; Li, Ming; Maisner, Andrea; Mühlberger, Elke; Netesov, Sergey V; Nowotny, Norbert; Patterson, Jean L; Payne, Susan L; Paweska, Janusz T; Pearson, Michael N; Randall, Rick E; Revill, Peter A; Rima, Bertus K; Rota, Paul; Rubbenstroth, Dennis; Schwemmle, Martin; Smither, Sophie J; Song, Qisheng; Stone, David M; Takada, Ayato; Terregino, Calogero; Tesh, Robert B; Tomonaga, Keizo; Tordo, Noël; Towner, Jonathan S; Vasilakis, Nikos; Volchkov, Viktor E; Wahl-Jensen, Victoria; Walker, Peter J; Wang, Beibei; Wang, David; Wang, Fei; Wang, Lin-Fa; Werren, John H; Whitfield, Anna E; Yan, Zhichao; Ye, Gongyin; Kuhn, Jens H

2017-08-01

In 2017, the order Mononegavirales was expanded by the inclusion of a total of 69 novel species. Five new rhabdovirus genera and one new nyamivirus genus were established to harbor 41 of these species, whereas the remaining new species were assigned to already established genera. Furthermore, non-Latinized binomial species names replaced all paramyxovirus and pneumovirus species names, thereby accomplishing application of binomial species names throughout the entire order. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).

Type material in the NCBI Taxonomy Database

PubMed Central

Federhen, Scott

2015-01-01

Type material is the taxonomic device that ties formal names to the physical specimens that serve as exemplars for the species. For the prokaryotes these are strains submitted to the culture collections; for the eukaryotes they are specimens submitted to museums or herbaria. The NCBI Taxonomy Database (http://www.ncbi.nlm.nih.gov/taxonomy) now includes annotation of type material that we use to flag sequences from type in GenBank and in Genomes. This has important implications for many NCBI resources, some of which are outlined below. PMID:25398905

A Summary of Taxonomies of Digital System Failure Modes Provided by the DigRel Task Group

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chu T. L.; Yue M.; Postma, W.

2012-06-25

Recently, the CSNI directed WGRisk to set up a task group called DIGREL to initiate a new task on developing a taxonomy of failure modes of digital components for the purposes of PSA. It is an important step towards standardized digital I&C reliability assessment techniques for PSA. The objective of this paper is to provide a comparison of the failure mode taxonomies provided by the participants. The failure modes are classified in terms of their levels of detail. Software and hardware failure modes are discussed separately.

A Falsification of the Citation Impediment in the Taxonomic Literature

PubMed Central

Steiner, Florian M.; Pautasso, Marco; Zettel, Herbert; Moder, Karl; Arthofer, Wolfgang; Schlick-Steiner, Birgit C.

2015-01-01

Current science evaluation still relies on citation performance, despite criticisms of purely bibliometric research assessments. Biological taxonomy suffers from a drain of knowledge and manpower, with poor citation performance commonly held as one reason for this impediment. But is there really such a citation impediment in taxonomy? We compared the citation numbers of 306 taxonomic and 2291 non-taxonomic research articles (2009–2012) on mosses, orchids, ciliates, ants, and snakes, using Web of Science (WoS) and correcting for journal visibility. For three of the five taxa, significant differences were absent in citation numbers between taxonomic and non-taxonomic papers. This was also true for all taxa combined, although taxonomic papers received more citations than non-taxonomic ones. Our results show that, contrary to common belief, taxonomic contributions do not generally reduce a journal's citation performance and might even increase it. The scope of many journals rarely featuring taxonomy would allow editors to encourage a larger number of taxonomic submissions. Moreover, between 1993 and 2012, taxonomic publications accumulated faster than those from all biological fields. However, less than half of the taxonomic studies were published in journals in WoS. Thus, editors of highly visible journals inviting taxonomic contributions could benefit from taxonomy's strong momentum. The taxonomic output could increase even more than at its current growth rate if: (i) taxonomists currently publishing on other topics returned to taxonomy and (ii) non-taxonomists identifying the need for taxonomic acts started publishing these, possibly in collaboration with taxonomists. Finally, considering the high number of taxonomic papers attracted by the journal Zootaxa, we expect that the taxonomic community would indeed use increased chances of publishing in WoS indexed journals. We conclude that taxonomy's standing in the present citation-focused scientific landscape could easily improve—if the community becomes aware that there is no citation impediment in taxonomy. PMID:25944475

A Falsification of the Citation Impediment in the Taxonomic Literature.

PubMed

Steiner, Florian M; Pautasso, Marco; Zettel, Herbert; Moder, Karl; Arthofer, Wolfgang; Schlick-Steiner, Birgit C

2015-09-01

Current science evaluation still relies on citation performance, despite criticisms of purely bibliometric research assessments. Biological taxonomy suffers from a drain of knowledge and manpower, with poor citation performance commonly held as one reason for this impediment. But is there really such a citation impediment in taxonomy? We compared the citation numbers of 306 taxonomic and 2291 non-taxonomic research articles (2009-2012) on mosses, orchids, ciliates, ants, and snakes, using Web of Science (WoS) and correcting for journal visibility. For three of the five taxa, significant differences were absent in citation numbers between taxonomic and non-taxonomic papers. This was also true for all taxa combined, although taxonomic papers received more citations than non-taxonomic ones. Our results show that, contrary to common belief, taxonomic contributions do not generally reduce a journal's citation performance and might even increase it. The scope of many journals rarely featuring taxonomy would allow editors to encourage a larger number of taxonomic submissions. Moreover, between 1993 and 2012, taxonomic publications accumulated faster than those from all biological fields. However, less than half of the taxonomic studies were published in journals in WoS. Thus, editors of highly visible journals inviting taxonomic contributions could benefit from taxonomy's strong momentum. The taxonomic output could increase even more than at its current growth rate if: (i) taxonomists currently publishing on other topics returned to taxonomy and (ii) non-taxonomists identifying the need for taxonomic acts started publishing these, possibly in collaboration with taxonomists. Finally, considering the high number of taxonomic papers attracted by the journal Zootaxa, we expect that the taxonomic community would indeed use increased chances of publishing in WoS indexed journals. We conclude that taxonomy's standing in the present citation-focused scientific landscape could easily improve-if the community becomes aware that there is no citation impediment in taxonomy. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

[Which definition and taxonomy of incident to use for a French reporting system in primary care settings?].

PubMed

Keriel-Gascou, M; Brami, J; Chanelière, M; Haeringer-Cholet, A; Larrieu, C; Villebrun, F; Robert, T; Michel, P

2014-02-01

There is no widely accepted definition of incident for primary care doctors in France and no taxonomic classification system for epidemiological use. In preparation for a future epidemiological study on primary care incidents in France (the ESPRIT study), this work was designed to identify the definitions and taxonomic classifications used internationally along with the usual methods and results in terms of frequency in the literature. The goal was to determine a French definition and taxonomy. Systematic review of the literature and consensus methods. An exhaustive search of epidemiological surveys was performed. A structured grid was used. After having identified the definitions used in the literature, a definition was chosen using the focus groups method. Taxonomies identified in the literature were classified by relationship, architecture, code number, and number of studies published. Subsequently, a consensus among experts, who independently tested these taxonomies on six incidents, was reached for choosing the most appropriate for epidemiological data collection (little information on a large number of cases). Twenty-four papers reporting 17 studies were selected among 139 articles. Five definitions and eight taxonomies were found. The chosen definition of incident was based on the WHO definition "A patient safety incident is an event or circumstance that could have resulted, or did result, in harm to a patient, and whose wish it is not repeated again". The test of incidents resulted in the choice of the TAPS version of the International Taxonomy of Medical Error in Primary Care for a reproducible and internationally recognized codification and the tempos method for its current use in French general practice. The definitions, taxonomies, data collection characteristics and frequency of incidents results in the international literature on incidents in primary care are key components for the preparation of an epidemiological survey on incidents in primary care. Copyright © 2014. Published by Elsevier Masson SAS.

Backyard Taxonomy.

ERIC Educational Resources Information Center

Gotsch, Margaret; Harris, Shannon

1990-01-01

Described is a backyard activity that can be used to introduce children to the divisions of the plant and animal kingdoms in their local environment. Preparation, procedures and followup are discussed. Background information on taxonomy and two activity cards are provided. (CW)

Research into the development of a knowledge acquisition taxonomy

NASA Technical Reports Server (NTRS)

Fink, Pamela K.

1991-01-01

Monthly progress reports for September 1990 to January 1991 are given. Topics that are briefly covered include problem solving and learning taxonomies, knowledge acquisition techniques, software design, air traffic control, and space shuttle flight control.

Discourse analysis and the doctor-patient relationship.

PubMed

Stiles, W B

This article describes a system of discourse analysis, called a "taxonomy of verbal response modes," which can be applied to medical interviews. The taxonomy identifies eight basic categories: disclosure, question, edification, acknowledgement, advisement, interpretation, confirmation, and reflection, which are defined by three principles of classification. The categories are mutually exclusive and exhaustive. Each mode conveys a particular interpersonal intent and also has a characteristic grammatical form. With eight forms and eight intents, the taxonomy includes sixty-four possible verbal response modes, eight "pure modes," in which form and intent coincide, and fifty-six "mixed modes," in which form and intent differ. The taxonomy has yielded fine-grained descriptions of patient-physician interaction and has identified particular types of utterances and verbal exchanges that are associated with patients' satisfaction with their medical interviews. The system provides a detailed descriptive vocabulary that may be useful for teaching interviewing skills.

A knowledge network for a dynamic taxonomy of psychiatric disease.

PubMed

Krishnan, Ranga R

2015-03-01

Current taxonomic approaches in medicine and psychiatry are limited in validity and utility. They do serve simple communication purposes for medical coding, teaching, and reimbursement, but they are not suited for the modern era with its rapid explosion of knowledge from the "omics" revolution. The National Academy of Sciences published a report entitled Toward Precision Medicine: Building a Knowledge Network for Biomedical Research and a New Taxonomy of Disease. The authors advocate a new taxonomy that would integrate molecular data, clinical data, and health outcomes in a dynamic, iterative fashion, bringing together research, public health, and health-care delivery with the interlinked goals of advancing our understanding of disease pathogenesis and thereby improving health. As the need for an information hub and a knowledge network with a dynamic taxonomy based on integration of clinical and research data is vital, and timely, this proposal merits consideration.

Structural Interventions in HIV Prevention: A Taxonomy and Descriptive Systematic Review

PubMed Central

Sipe, Theresa Ann; Barham, Terrika L.; Johnson, Wayne; Joseph, Heather; Tungol-Ashmon, Maria Luisa; O’Leary, Ann

2018-01-01

One of the four national HIV prevention goals is to incorporate combinations of effective, evidence-based approaches to prevent HIV infection. In fields of public health, techniques that alter environment and affect choice options are effective. Structural approaches may be effective in preventing HIV infection. Existing frameworks for structural interventions were lacking in breadth and/or depth. We conducted a systematic review and searched CDC’s HIV/AIDS Prevention Research Synthesis Project’s database for relevant interventions during 1988–2013. We used an iterative process to develop the taxonomy. We identified 213 structural interventions: Access (65%), Policy/Procedure (32%), Mass Media (29%), Physical Structure (27%), Capacity Building (24%), Community Mobilization (9%), and Social Determinants of Health (8%). Forty percent targeted high-risk populations (e.g., people who inject drugs [12%]). This paper describes a comprehensive, well-defined taxonomy of structural interventions with 7 categories and 20 subcategories. The taxonomy accommodated all interventions identified. PMID:29159594

Dioxin Sensitivity-Related Two Critical Amino Acids of Arylhydrocarbon Receptor May Not Correlate with the Taxonomy or Phylogeny in Avian Species

PubMed Central

FUJISAWA, Nozomi; KAWAI, Yusuke K.; NAKAYAMA, Shouta M. M.; IKENAKA, Yoshinori; YAMAMOTO, Hideaki; ISHIZUKA, Mayumi

2013-01-01

ABSTRACT There are two arylhydrocarbon receptor (AhR) isoforms in birds, AhR1 and AhR2. The varying sensitivity of AhR is reported to be related to two critical amino acids at positions 325 and 381 in the AhR1 ligand-binding domain. In this study, seven avian species whose in vivo dioxin sensitivity was known, and 13 species with no data regarding their in vivo dioxin sensitivity were examined. The two critical amino acids in the ligand-binding domain were investigated in avian species, and the results were compared with the taxonomy or phylogenetic trees for the bird AhR proteins. We found that the two critical amino acids did not correlate with the taxonomy or phylogeny of these proteins, suggesting that dioxin sensitivity was independent of taxonomy. PMID:23912877

From cognition to the system: developing a multilevel taxonomy of patient safety in general practice.

PubMed

Kostopoulou, O

The paper describes the process of developing a taxonomy of patient safety in general practice. The methodologies employed included fieldwork, task analysis and confidential reporting of patient-safety events in five West Midlands practices. Reported events were traced back to their root causes and contributing factors. The resulting taxonomy is based on a theoretical model of human cognition, includes multiple levels of classification to reflect the chain of causation and considers affective and physiological influences on performance. Events are classified at three levels. At level one, the information-processing model of cognition is used to classify errors. At level two, immediate causes are identified, internal and external to the individual. At level three, more remote causal factors are classified as either 'work organization' or 'technical' with subcategories. The properties of the taxonomy (validity, reliability, comprehensiveness) as well as its usability and acceptability remain to be tested with potential users.

A systematic review of hybrid brain-computer interfaces: Taxonomy and usability perspectives

PubMed Central

Lee, Yushin; Yun, Myung Hwan

2017-01-01

A new Brain-Computer Interface (BCI) technique, which is called a hybrid BCI, has recently been proposed to address the limitations of conventional single BCI system. Although some hybrid BCI studies have shown promising results, the field of hybrid BCI is still in its infancy and there is much to be done. Especially, since the hybrid BCI systems are so complicated and complex, it is difficult to understand the constituent and role of a hybrid BCI system at a glance. Also, the complicated and complex systems make it difficult to evaluate the usability of the systems. We systematically reviewed and analyzed the current state-of-the-art hybrid BCI studies, and proposed a systematic taxonomy for classifying the types of hybrid BCIs with multiple taxonomic criteria. After reviewing 74 journal articles, hybrid BCIs could be categorized with respect to 1) the source of brain signals, 2) the characteristics of the brain signal, and 3) the characteristics of operation in each system. In addition, we exhaustively reviewed recent literature on usability of BCIs. To identify the key evaluation dimensions of usability, we focused on task and measurement characteristics of BCI usability. We classified and summarized 31 BCI usability journal articles according to task characteristics (type and description of task) and measurement characteristics (subjective and objective measures). Afterwards, we proposed usability dimensions for BCI and hybrid BCI systems according to three core-constructs: Satisfaction, effectiveness, and efficiency with recommendations for further research. This paper can help BCI researchers, even those who are new to the field, can easily understand the complex structure of the hybrid systems at a glance. Recommendations for future research can also be helpful in establishing research directions and gaining insight in how to solve ergonomics and HCI design issues surrounding BCI and hybrid BCI systems by usability evaluation. PMID:28453547

A systematic review of hybrid brain-computer interfaces: Taxonomy and usability perspectives.

PubMed

Choi, Inchul; Rhiu, Ilsun; Lee, Yushin; Yun, Myung Hwan; Nam, Chang S

2017-01-01

A new Brain-Computer Interface (BCI) technique, which is called a hybrid BCI, has recently been proposed to address the limitations of conventional single BCI system. Although some hybrid BCI studies have shown promising results, the field of hybrid BCI is still in its infancy and there is much to be done. Especially, since the hybrid BCI systems are so complicated and complex, it is difficult to understand the constituent and role of a hybrid BCI system at a glance. Also, the complicated and complex systems make it difficult to evaluate the usability of the systems. We systematically reviewed and analyzed the current state-of-the-art hybrid BCI studies, and proposed a systematic taxonomy for classifying the types of hybrid BCIs with multiple taxonomic criteria. After reviewing 74 journal articles, hybrid BCIs could be categorized with respect to 1) the source of brain signals, 2) the characteristics of the brain signal, and 3) the characteristics of operation in each system. In addition, we exhaustively reviewed recent literature on usability of BCIs. To identify the key evaluation dimensions of usability, we focused on task and measurement characteristics of BCI usability. We classified and summarized 31 BCI usability journal articles according to task characteristics (type and description of task) and measurement characteristics (subjective and objective measures). Afterwards, we proposed usability dimensions for BCI and hybrid BCI systems according to three core-constructs: Satisfaction, effectiveness, and efficiency with recommendations for further research. This paper can help BCI researchers, even those who are new to the field, can easily understand the complex structure of the hybrid systems at a glance. Recommendations for future research can also be helpful in establishing research directions and gaining insight in how to solve ergonomics and HCI design issues surrounding BCI and hybrid BCI systems by usability evaluation.

New insights into the intricate taxonomy and phylogeny of the Sylvia curruca complex.

PubMed

Olsson, Urban; Leader, Paul J; Carey, Geoff J; Khan, Aleem Ahmed; Svensson, Lars; Alström, Per

2013-04-01

We use the mitochondrial cytochrome b from 213 individuals and the three nuclear introns BRM 15, myoglobin 2 and ODC 6-7 from a smaller subsample to evaluate the taxonomy of the Lesser Whitethroat Sylvia curruca (Aves, Passeriformes, Sylviidae) complex, which has long been controversial. We sequenced type material of the taxa althaea, blythi, margelanica and minula, and used topotypical material of caucasica, chuancheica, curruca and telengitica. The nuclear introns fail to resolve the complex, but cytochrome b recovers six major clades, revealing genetically identifiable populations corresponding to previously named taxa, and we propose that the names althaea, blythi, curruca, halimodendri, margelanica and minula, respectively, should be used for these. The margelanica clade is suggested to have a more extensive distribution than previously known, including both the taxon telengitica and a population in eastern Mongolia. The taxon minula is found to have a more restricted range than generally believed, only breeding in China. According to the mitochondrial gene tree, there is a basal dichotomy, with the taxa althaea, blythi, halimodendri and margelanica being part of one clade, well separated from a clade containing curruca and minula. Dating analysis suggests that a basal divergence separating curruca and minula from the other four taxa occurred between 4.2 and 7.2 mya; these two then diverged between 2.3 and 4.4 mya. The splits between the althaea, blythi, halimodendri and margelanica lineages is inferred to have occurred later, approximately between 1.0 and 2.5 mya (all 95% HPD). The nucleotide data suggest significant departure from demographic equilibrium in blythi (clade 1a), halimodendri (clade 2a) and minula, whereas tendencies are weaker for other clades. We propose that the names althaea, blythi, curruca, halimodendri, margelanica and minula should be used for the major clades. However, whether these are treated as subspecies or species is largely a matter of species definition and is not resolved by our data. Copyright © 2013 Elsevier Inc. All rights reserved.

Framing of scientific knowledge as a new category of health care research.

PubMed

Salvador-Carulla, Luis; Fernandez, Ana; Madden, Rosamond; Lukersmith, Sue; Colagiuri, Ruth; Torkfar, Ghazal; Sturmberg, Joachim

2014-12-01

The new area of health system research requires a revision of the taxonomy of scientific knowledge that may facilitate a better understanding and representation of complex health phenomena in research discovery, corroboration and implementation. A position paper by an expert group following and iterative approach. 'Scientific evidence' should be differentiated from 'elicited knowledge' of experts and users, and this latter typology should be described beyond the traditional qualitative framework. Within this context 'framing of scientific knowledge' (FSK) is defined as a group of studies of prior expert knowledge specifically aimed at generating formal scientific frames. To be distinguished from other unstructured frames, FSK must be explicit, standardized, based on the available evidence, agreed by a group of experts and subdued to the principles of commensurability, transparency for corroboration and transferability that characterize scientific research. A preliminary typology of scientific framing studies is presented. This typology includes, among others, health declarations, position papers, expert-based clinical guides, conceptual maps, classifications, expert-driven health atlases and expert-driven studies of costs and burden of illness. This grouping of expert-based studies constitutes a different kind of scientific knowledge and should be clearly differentiated from 'evidence' gathered from experimental and observational studies in health system research. © 2014 John Wiley & Sons, Ltd.