Soil Taxonomy and land evaluation for forest establishment

Treesearch

Haruyoshi Ikawa

1992-01-01

Soil Taxonomy, the United States system of soil classification, can be used for land evaluation for selected purposes. One use is forest establishment in the tropics, and the soil family category is especially functional for this purpose. The soil family is a bionomial name with descriptions usually of soil texture, mineralogy, and soil temperature classes. If the...

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

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.

Classifying nursing errors in clinical management within an Australian hospital.

PubMed

Tran, D T; Johnson, M

2010-12-01

Although many classification systems relating to patient safety exist, no taxonomy was identified that classified nursing errors in clinical management. To develop a classification system for nursing errors relating to clinical management (NECM taxonomy) and to describe contributing factors and patient consequences. We analysed 241 (11%) self-reported incidents relating to clinical management in nursing in a metropolitan hospital. Descriptive analysis of numeric data and content analysis of text data were undertaken to derive the NECM taxonomy, contributing factors and consequences for patients. Clinical management incidents represented 1.63 incidents per 1000 occupied bed days. The four themes of the NECM taxonomy were nursing care process (67%), communication (22%), administrative process (5%), and knowledge and skill (6%). Half of the incidents did not cause any patient harm. Contributing factors (n=111) included the following: patient clinical, social conditions and behaviours (27%); resources (22%); environment and workload (18%); other health professionals (15%); communication (13%); and nurse's knowledge and experience (5%). The NECM taxonomy provides direction to clinicians and managers on areas in clinical management that are most vulnerable to error, and therefore, priorities for system change management. Any nurses who wish to classify nursing errors relating to clinical management could use these types of errors. This study informs further research into risk management behaviour, and self-assessment tools for clinicians. Globally, nurses need to continue to monitor and act upon patient safety issues. © 2010 The Authors. International Nursing Review © 2010 International Council of Nurses.

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/ ).

[Modern bacterial taxonomy: techniques review--application to bacteria that nodulate leguminous plants (BNL)].

PubMed

Zakhia, Frédéric; de Lajudie, Philippe

2006-03-01

Taxonomy is the science that studies the relationships between organisms. It comprises classification, nomenclature, and identification. Modern bacterial taxonomy is polyphasic. This means that it is based on several molecular techniques, each one retrieving the information at different cellular levels (proteins, fatty acids, DNA...). The obtained results are combined and analysed to reach a "consensus taxonomy" of a microorganism. Until 1970, a small number of classification techniques were available for microbiologists (mainly phenotypic characterization was performed: a legume species nodulation ability for a Rhizobium, for example). With the development of techniques based on polymerase chain reaction for characterization, the bacterial taxonomy has undergone great changes. In particular, the classification of the legume nodulating bacteria has been repeatedly modified over the last 20 years. We present here a review of the currently used molecular techniques in bacterial characterization, with examples of application of these techniques for the study of the legume nodulating bacteria.

[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.

A Taxonomy of Introductory Physics Concepts.

NASA Astrophysics Data System (ADS)

Mokaya, Fridah; Savkar, Amit; Valente, Diego

We have designed and implemented a hierarchical taxonomic classification of physics concepts for our introductory physics for engineers course sequence taught at the University of Connecticut. This classification can be used to provide a mechanism to measure student progress in learning at the level of individual concepts or clusters of concepts, and also as part of a tool to measure effectiveness of teaching pedagogy. We examine our pre- and post-test FCI results broken down by topics using Hestenes et al.'s taxonomy classification for the FCI, and compare these results with those found using our own taxonomy classification. In addition, we expand this taxonomic classification to measure performance in our other course exams, investigating possible correlations in results achieved across different assessments at the individual topic level. UCONN CLAS(College of Liberal Arts and Science).

What Works? Toward a New Classification System for Mental Health Supported Accommodation Services: The Simple Taxonomy for Supported Accommodation (STAX-SA)

PubMed Central

McPherson, Peter; Krotofil, Joanna

2018-01-01

Inconsistent terminology and variation in service models have made synthesis of the supported accommodation literature challenging. To overcome this, we developed a brief, categorical taxonomy that aimed to capture the defining features of different supported accommodation models: the simple taxonomy for supported accommodation (STAX-SA). Data from a previous review of existing classification systems were used to develop the taxonomy structure. After initial testing and amendments, the STAX-SA and an existing taxonomy were applied to 132 supported accommodation service descriptions drawn from two systematic reviews and their performance compared. To assess external validity, the STAX-SA was distributed to a sample of supported accommodation managers in England and they were asked to use it to classify their services. The final version of the STAX-SA comprised of five supported accommodation ‘types’, based on four domains; Staffing location; Level of support; Emphasis on move-on; and Physical setting. The STAX-SA accurately categorized 71.1% (n = 94) of service descriptions, outperforming the comparison tool, and was not affected by publication date or research design. The STAX-SA effectively discriminated between ‘real world’ service models in England and 53.2% (n = 17) of service managers indicated that the taxonomy was ‘Very effective’ or ‘Extremely effective’ in capturing key characteristics of their service. The STAX-SA is an effective tool for classifying supported accommodation models and represents a promising approach to synthesizing the extant effectiveness literature. The authors recommend the development of reporting guidelines for future supported accommodation publications to facilitate comparison between models. PMID:29364171

What Works? Toward a New Classification System for Mental Health Supported Accommodation Services: The Simple Taxonomy for Supported Accommodation (STAX-SA).

PubMed

McPherson, Peter; Krotofil, Joanna; Killaspy, Helen

2018-01-24

Inconsistent terminology and variation in service models have made synthesis of the supported accommodation literature challenging. To overcome this, we developed a brief, categorical taxonomy that aimed to capture the defining features of different supported accommodation models: the simple taxonomy for supported accommodation (STAX-SA). Data from a previous review of existing classification systems were used to develop the taxonomy structure. After initial testing and amendments, the STAX-SA and an existing taxonomy were applied to 132 supported accommodation service descriptions drawn from two systematic reviews and their performance compared. To assess external validity, the STAX-SA was distributed to a sample of supported accommodation managers in England and they were asked to use it to classify their services. The final version of the STAX-SA comprised of five supported accommodation 'types', based on four domains; Staffing location ; Level of support ; Emphasis on move-on ; and Physical setting . The STAX-SA accurately categorized 71.1% ( n = 94) of service descriptions, outperforming the comparison tool, and was not affected by publication date or research design. The STAX-SA effectively discriminated between 'real world' service models in England and 53.2% ( n = 17) of service managers indicated that the taxonomy was ' Very effective ' or ' Extremely effective ' in capturing key characteristics of their service. The STAX-SA is an effective tool for classifying supported accommodation models and represents a promising approach to synthesizing the extant effectiveness literature. The authors recommend the development of reporting guidelines for future supported accommodation publications to facilitate comparison between models.

Object recognition based on Google's reverse image search and image similarity

NASA Astrophysics Data System (ADS)

Horváth, András.

2015-12-01

Image classification is one of the most challenging tasks in computer vision and a general multiclass classifier could solve many different tasks in image processing. Classification is usually done by shallow learning for predefined objects, which is a difficult task and very different from human vision, which is based on continuous learning of object classes and one requires years to learn a large taxonomy of objects which are not disjunct nor independent. In this paper I present a system based on Google image similarity algorithm and Google image database, which can classify a large set of different objects in a human like manner, identifying related classes and taxonomies.

Brucella taxonomy and evolution

PubMed Central

Ficht, Thomas

2010-01-01

Taxonomy and nomenclature represent man-made systems designed to enhance understanding of the relationship between organisms by comparison of discrete sets of properties. Initial efforts at bacterial taxonomy were flawed as a result of the previous use of nonsystematic approaches including common names resulting in confusing and inaccurate nomenclature. A decision was made to start afresh with bacterial nomenclature and to avoid the hazards experienced in the taxonomic classification of higher organisms. This was achieved by developing new rules designed to simplify classification and avoid unnecessary and confusing changes. This article reviews the work of a number of scientists attempting to reconcile new molecular data describing the phylogenetic relationship between Brucella organisms and a broader family of organisms with widely variant phenotypes that include human virulence and host range against a backdrop of strict regulatory requirements that fail to recognize significant differences between organisms with similar nomenclature. PMID:20521932

Human Factors Engineering. Student Supplement,

DTIC Science & Technology

1981-08-01

a job TASK TAXONOMY A classification scheme for the different levels of activities in a system, i.e., job - task - sub-task, etc. TASK-AN~ALYSIS...with the classification of learning objectives by learning category so as to identify learningPhas III guidelines necessary for optimum learning to...correct. .4... .the sequencing of all dependent tasks. .1.. .the classification of learning objectives by learning category and the Identification of

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

DVV: a taxonomy for mixed reality visualization in image guided surgery.

PubMed

Kersten-Oertel, Marta; Jannin, Pierre; Collins, D Louis

2012-02-01

Mixed reality visualizations are increasingly studied for use in image guided surgery (IGS) systems, yet few mixed reality systems have been introduced for daily use into the operating room (OR). This may be the result of several factors: the systems are developed from a technical perspective, are rarely evaluated in the field, and/or lack consideration of the end user and the constraints of the OR. We introduce the Data, Visualization processing, View (DVV) taxonomy which defines each of the major components required to implement a mixed reality IGS system. We propose that these components be considered and used as validation criteria for introducing a mixed reality IGS system into the OR. A taxonomy of IGS visualization systems is a step toward developing a common language that will help developers and end users discuss and understand the constituents of a mixed reality visualization system, facilitating a greater presence of future systems in the OR. We evaluate the DVV taxonomy based on its goodness of fit and completeness. We demonstrate the utility of the DVV taxonomy by classifying 17 state-of-the-art research papers in the domain of mixed reality visualization IGS systems. Our classification shows that few IGS visualization systems' components have been validated and even fewer are evaluated.

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.

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

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.

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.…

Evaluating Support for the Current Classification of Eukaryotic Diversity

PubMed Central

Parfrey, Laura Wegener; Barbero, Erika; Lasser, Elyse; Dunthorn, Micah; Bhattacharya, Debashish; Patterson, David J; Katz, Laura A

2006-01-01

Perspectives on the classification of eukaryotic diversity have changed rapidly in recent years, as the four eukaryotic groups within the five-kingdom classification—plants, animals, fungi, and protists—have been transformed through numerous permutations into the current system of six “supergroups.” The intent of the supergroup classification system is to unite microbial and macroscopic eukaryotes based on phylogenetic inference. This supergroup approach is increasing in popularity in the literature and is appearing in introductory biology textbooks. We evaluate the stability and support for the current six-supergroup classification of eukaryotes based on molecular genealogies. We assess three aspects of each supergroup: (1) the stability of its taxonomy, (2) the support for monophyly (single evolutionary origin) in molecular analyses targeting a supergroup, and (3) the support for monophyly when a supergroup is included as an out-group in phylogenetic studies targeting other taxa. Our analysis demonstrates that supergroup taxonomies are unstable and that support for groups varies tremendously, indicating that the current classification scheme of eukaryotes is likely premature. We highlight several trends contributing to the instability and discuss the requirements for establishing robust clades within the eukaryotic tree of life. PMID:17194223

Polyphasic taxonomy, a consensus approach to bacterial systematics.

PubMed Central

Vandamme, P; Pot, B; Gillis, M; de Vos, P; Kersters, K; Swings, J

1996-01-01

Over the last 25 years, a much broader range of taxonomic studies of bacteria has gradually replaced the former reliance upon morphological, physiological, and biochemical characterization. This polyphasic taxonomy takes into account all available phenotypic and genotypic data and integrates them in a consensus type of classification, framed in a general phylogeny derived from 16S rRNA sequence analysis. In some cases, the consensus classification is a compromise containing a minimum of contradictions. It is thought that the more parameters that will become available in the future, the more polyphasic classification will gain stability. In this review, the practice of polyphasic taxonomy is discussed for four groups of bacteria chosen for their relevance, complexity, or both: the genera Xanthomonas and Campylobacter, the lactic acid bacteria, and the family Comamonadaceae. An evaluation of our present insights, the conclusions derived from it, and the perspectives of polyphasic taxonomy are discussed, emphasizing the keystone role of the species. Taxonomists did not succeed in standardizing species delimitation by using percent DNA hybridization values. Together with the absence of another "gold standard" for species definition, this has an enormous repercussion on bacterial taxonomy. This problem is faced in polyphasic taxonomy, which does not depend on a theory, a hypothesis, or a set of rules, presenting a pragmatic approach to a consensus type of taxonomy, integrating all available data maximally. In the future, polyphasic taxonomy will have to cope with (i) enormous amounts of data, (ii) large numbers of strains, and (iii) data fusion (data aggregation), which will demand efficient and centralized data storage. In the future, taxonomic studies will require collaborative efforts by specialized laboratories even more than now is the case. Whether these future developments will guarantee a more stable consensus classification remains an open question. PMID:8801440

Taxonomy and Classification Scheme for Artificial Space Objects

DTIC Science & Technology

2013-09-01

filter UVB and spectroscopic measurements) and albedo (including polarimetry ). Earliest classifications of asteroids [17] were based on the filter...similarities of the asteroid colors to K0 to K2V stars. The first more complete asteroid taxonomy was based on a synthesis of polarimetry , radiometry, and

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.

An alternative to soil taxonomy for describing key soil characteristics

USGS Publications Warehouse

Duniway, Michael C.; Miller, Mark E.; Brown, Joel R.; Toevs, Gordon

2013-01-01

is not a simple task. Furthermore, because the US system of soil taxonomy is not applied universally, its utility as a means for effectively describing soil characteristics to readers in other countries is limited. Finally, and most importantly, even at the finest level of soil classification there are often large within-taxa variations in critical properties that can determine ecosystem responses to drivers such as climate and land-use change.

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.

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.

Knowledge Management, User Education and Librarianship.

ERIC Educational Resources Information Center

Koenig, Michael E. D.

2003-01-01

Discusses the role of librarians in knowledge management in terms of designing information systems, creating classification systems and taxonomies, and implementing and operating the systems. Suggests the need for librarians to be involved in user education and training, including database searching, using current awareness services, and using…

Reflecting on the structure of soil classification systems: insights from a proposal for integrating subsoil data into soil information systems

NASA Astrophysics Data System (ADS)

Dondeyne, Stefaan; Juilleret, Jérôme; Vancampenhout, Karen; Deckers, Jozef; Hissler, Christophe

2017-04-01

Classification of soils in both World Reference Base for soil resources (WRB) and Soil Taxonomy hinges on the identification of diagnostic horizons and characteristics. However as these features often occur within the first 100 cm, these classification systems convey little information on subsoil characteristics. An integrated knowledge of the soil, soil-to-substratum and deeper substratum continuum is required when dealing with environmental issues such as vegetation ecology, water quality or the Critical Zone in general. Therefore, we recently proposed a classification system of the subsolum complementing current soil classification systems. By reflecting on the structure of the subsoil classification system which is inspired by WRB, we aim at fostering a discussion on some potential future developments of WRB. For classifying the subsolum we define Regolite, Saprolite, Saprock and Bedrock as four Subsolum Reference Groups each corresponding to different weathering stages of the subsoil. Principal qualifiers can be used to categorize intergrades of these Subsoil Reference Groups while morphologic and lithologic characteristics can be presented with supplementary qualifiers. We argue that adopting a low hierarchical structure - akin to WRB and in contrast to a strong hierarchical structure as in Soil Taxonomy - offers the advantage of having an open classification system avoiding the need for a priori knowledge of all possible combinations which may be encountered in the field. Just as in WRB we also propose to use principal and supplementary qualifiers as a second level of classification. However, in contrast to WRB we propose to reserve the principal qualifiers for intergrades and to regroup the supplementary qualifiers into thematic categories (morphologic or lithologic). Structuring the qualifiers in this manner should facilitate the integration and handling of both soil and subsoil classification units into soil information systems and calls for paying attention to these structural issues in future developments of WRB.

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.

Applicability of the NANDA-I and Nursing Interventions Classification taxonomies to mental health nursing practice.

PubMed

Thomé, Emi da Silva; Centena, Renata Cardoso; Behenck, Andressa da Silva; Marini, Maiko; Heldt, Elizeth

2014-10-01

To assess the applicability of the systematization of nursing care (NCS) to outpatient nursing appointments using the NANDA-I and Nursing Interventions Classification (NIC) taxonomies. Data were collected from 40 patients who had appointments with a nurse who specialized in mental health. Nursing diagnoses (NDs) and interventions were classified using the NANDA-I and NIC taxonomies, respectively. A total of 14 different NDs were detected (minimum of one and maximum of three per appointment). The most frequently made diagnoses were impaired social interaction (00052), anxiety (00146), and ineffective self-health management (00078). A total of 23 nursing interventions were prescribed (approximately two per appointment), of which the most frequent were socialization enhancement (5100), self-care assistance (1800), and exercise promotion (0200). Significant associations were found between the most frequently detected NDs and the most commonly prescribed interventions (p > .05). The NCS through the use of classification systems allows mental health nurses to better identify and assist poorly adjusted patients. The assessment of the applicability of the NCS to different areas of health care and types of medical assistance contributes significantly to the quality of nursing care. © 2014 NANDA International, Inc.

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...

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

Unbiased Taxonomic Annotation of Metagenomic Samples

PubMed Central

Fosso, Bruno; Pesole, Graziano; Rosselló, Francesc

2018-01-01

Abstract The classification of reads from a metagenomic sample using a reference taxonomy is usually based on first mapping the reads to the reference sequences and then classifying each read at a node under the lowest common ancestor of the candidate sequences in the reference taxonomy with the least classification error. However, this taxonomic annotation can be biased by an imbalanced taxonomy and also by the presence of multiple nodes in the taxonomy with the least classification error for a given read. In this article, we show that the Rand index is a better indicator of classification error than the often used area under the receiver operating characteristic (ROC) curve and F-measure for both balanced and imbalanced reference taxonomies, and we also address the second source of bias by reducing the taxonomic annotation problem for a whole metagenomic sample to a set cover problem, for which a logarithmic approximation can be obtained in linear time and an exact solution can be obtained by integer linear programming. Experimental results with a proof-of-concept implementation of the set cover approach to taxonomic annotation in a next release of the TANGO software show that the set cover approach further reduces ambiguity in the taxonomic annotation obtained with TANGO without distorting the relative abundance profile of the metagenomic sample. PMID:29028181

[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.

New Approach to Analyzing Physics Problems: A Taxonomy of Introductory Physics Problems

ERIC Educational Resources Information Center

Teodorescu, Raluca E.; Bennhold, Cornelius; Feldman, Gerald; Medsker, Larry

2013-01-01

This paper describes research on a classification of physics problems in the context of introductory physics courses. This classification, called the Taxonomy of Introductory Physics Problems (TIPP), relates physics problems to the cognitive processes required to solve them. TIPP was created in order to design educational objectives, to develop…

Taxonomies in L1 and L2 Reading Strategies: A Critical Review of Issues Surrounding Strategy-Use Definitions and Classifications in Previous Think-Aloud Research

ERIC Educational Resources Information Center

Alkhaleefah, Tarek A.

2016-01-01

Considering the various classifications of L1 and L2 reading strategies in previous think-aloud studies, the present review aims to provide a comprehensive look into those various taxonomies reported in major L1 and L2 reading studies. The rationale for this review is not only to offer a comprehensive overview of the different classifications in…

A three-parameter asteroid taxonomy

NASA Technical Reports Server (NTRS)

Tedesco, Edward F.; Williams, James G.; Matson, Dennis L.; Veeder, Glenn J.; Gradie, Jonathan C.

1989-01-01

Broadband U, V, and x photometry together with IRAS asteroid albedos have been used to construct an asteroid classification system. The system is based on three parameters (U-V and v-x color indices and visual geometric albedo), and it is able to place 96 percent of the present sample of 357 asteroids into 11 taxonomic classes. It is noted that all but one of these classes are analogous to those previously found using other classification schemes. The algorithm is shown to account for the observational uncertainties in each of the classification parameters.

Emerging Issues in Virus Taxonomy

PubMed Central

Mahy, Brian W.J.

2004-01-01

Viruses occupy a unique position in biology. Although they possess some of the properties of living systems such as having a genome, they are actually nonliving infectious entities and should not be considered microorganisms. A clear distinction should be drawn between the terms virus, virion, and virus species. Species is the most fundamental taxonomic category used in all biological classification. In 1991, the International Committee on Taxonomy of Viruses (ICTV) decided that the category of virus species should be used in virus classification together with the categories of genus and family. More than 50 ICTV study groups were given the task of demarcating the 1,550 viral species that were recognized in the 7th ICTV report, which was published in 2000. We briefly describe the changes in virus classification that were introduced in that report. We also discuss recent proposals to introduce a nonlatinized binomial nomenclature for virus species. PMID:15078590

The Variation in Recovery: Role of Gender on Outcomes of Young AMI Patients (VIRGO) Classification System: A Taxonomy for Young Women With Acute Myocardial Infarction.

PubMed

Spatz, Erica S; Curry, Leslie A; Masoudi, Frederick A; Zhou, Shengfan; Strait, Kelly M; Gross, Cary P; Curtis, Jeptha P; Lansky, Alexandra J; Soares Barreto-Filho, Jose Augusto; Lampropulos, Julianna F; Bueno, Hector; Chaudhry, Sarwat I; D'Onofrio, Gail; Safdar, Basmah; Dreyer, Rachel P; Murugiah, Karthik; Spertus, John A; Krumholz, Harlan M

2015-11-03

Current classification schemes for acute myocardial infarction (AMI) may not accommodate the breadth of clinical phenotypes in young women. We developed a novel taxonomy among young adults (≤55 years) with AMI enrolled in the Variation in Recovery: Role of Gender on Outcomes of Young AMI Patients (VIRGO) study. We first classified a subset of patients (n=600) according to the Third Universal Definition of MI using a structured abstraction tool. There was heterogeneity within type 2 AMI, and 54 patients (9%; including 51 of 412 women) were unclassified. Using an inductive approach, we iteratively grouped patients with shared clinical characteristics, with the aims of developing a more inclusive taxonomy that could distinguish unique clinical phenotypes. The final VIRGO taxonomy classified 2802 study participants as follows: class 1, plaque-mediated culprit lesion (82.5% of women; 94.9% of men); class 2, obstructive coronary artery disease with supply-demand mismatch (2a: 1.4% women; 0.9% men) and without supply-demand mismatch (2b: 2.4% women; 1.1% men); class 3, nonobstructive coronary artery disease with supply-demand mismatch (3a: 4.3% women; 0.8% men) and without supply-demand mismatch (3b: 7.0% women; 1.9% men); class 4, other identifiable mechanism (spontaneous dissection, vasospasm, embolism; 1.5% women, 0.2% men); and class 5, undetermined classification (0.8% women, 0.2% men). Approximately 1 in 8 young women with AMI is unclassified by the Universal Definition of MI. We propose a more inclusive taxonomy that could serve as a framework for understanding biological disease mechanisms, therapeutic efficacy, and prognosis in this population. © 2015 American Heart Association, Inc.

The VIRGO Classification System: A Taxonomy for Young Women with Acute Myocardial Infarction

PubMed Central

Spatz, Erica S.; Curry, Leslie A.; Masoudi, Frederick A.; Zhou, Shengfan; Strait, Kelly M.; Gross, Cary P.; Curtis, Jeptha P.; Lansky, Alexandra J.; Barreto-Filho, Jose Augusto Soares; Lampropulos, Julianna F.; Bueno, Hector; Chaudhry, Sarwat I.; D'Onofrio, Gail; Safdar, Basmah; Dreyer, Rachel P.; Murugiah, Karthik; Spertus, John A.; Krumholz, Harlan M.

2015-01-01

Background Current classification schemes for acute myocardial infarction (AMI) may not accommodate the breadth of clinical phenotypes in young women. Methods and Results We developed a novel taxonomy among young adults (<55 years) with AMI enrolled in the Variation in Recovery: Role of Gender on Outcomes of Young AMI Patients (VIRGO) study. We first classified a subset of patients (n=600) according to the Third Universal Definition of MI using a structured abstraction tool. There was heterogeneity within Type 2 AMI, and 54 patients (9%; including 51 of 412 women) were unclassified. Using an inductive approach, we iteratively grouped patients with shared clinical characteristics, with the aims of developing a more inclusive taxonomy that could distinguish unique clinical phenotypes. The final VIRGO taxonomy classified 2,802 study participants as: Class 1, plaque-mediated culprit lesion (82.5% of women; 94.9% of men); Class 2, obstructive coronary artery disease with supply-demand mismatch (2a: 1.4% women; 0.9% men;) and without supply-demand mismatch (2b: 2.4% women; 1.1% men); Class 3, non-obstructive coronary artery disease with supply-demand mismatch (3a: 4.3% women; 0.8% men) and without supply-demand mismatch (3b: 7.0% women; 1.9% men); Class 4, other identifiable mechanism: spontaneous dissection; vasospasm; embolism (1.5% women; 0.2% men); and Class 5, undetermined classification (0.8% women; 0.2% men). Conclusions Approximately 1 in 8 young women with AMI are unclassified by the Universal Definition of MI. We propose a more inclusive taxonomy that could serve as a framework for understanding biological disease mechanisms, therapeutic efficacy and prognosis in this population. PMID:26350057

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

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.

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)

Rehabilitation treatment taxonomy and the international classification of health interventions.

PubMed

Sykes, Catherine R

2014-01-01

This commentary provides some reactions to the rehabilitation treatment taxonomy project in relation to work already underway to develop an International Classification of Health Interventions. This commentary also includes some comments in response to questions posed by the authors. Copyright © 2014 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Phylogenetic Inferences Reveal a Large Extent of Novel Biodiversity in Chemically Rich Tropical Marine Cyanobacteria

PubMed Central

Gunasekera, Sarath P.; Gerwick, William H.

2013-01-01

Benthic marine cyanobacteria are known for their prolific biosynthetic capacities to produce structurally diverse secondary metabolites with biomedical application and their ability to form cyanobacterial harmful algal blooms. In an effort to provide taxonomic clarity to better guide future natural product drug discovery investigations and harmful algal bloom monitoring, this study investigated the taxonomy of tropical and subtropical natural product-producing marine cyanobacteria on the basis of their evolutionary relatedness. Our phylogenetic inferences of marine cyanobacterial strains responsible for over 100 bioactive secondary metabolites revealed an uneven taxonomic distribution, with a few groups being responsible for the vast majority of these molecules. Our data also suggest a high degree of novel biodiversity among natural product-producing strains that was previously overlooked by traditional morphology-based taxonomic approaches. This unrecognized biodiversity is primarily due to a lack of proper classification systems since the taxonomy of tropical and subtropical, benthic marine cyanobacteria has only recently been analyzed by phylogenetic methods. This evolutionary study provides a framework for a more robust classification system to better understand the taxonomy of tropical and subtropical marine cyanobacteria and the distribution of natural products in marine cyanobacteria. PMID:23315747

The Soil Series in Soil Classifications of the United States

NASA Astrophysics Data System (ADS)

Indorante, Samuel; Beaudette, Dylan; Brevik, Eric C.

2014-05-01

Organized national soil survey began in the United States in 1899, with soil types as the units being mapped. The soil series concept was introduced into the U.S. soil survey in 1903 as a way to relate soils being mapped in one area to the soils of other areas. The original concept of a soil series was all soil types formed in the same parent materials that were of the same geologic age. However, within about 15 years soil series became the primary units being mapped in U.S. soil survey. Soil types became subdivisions of soil series, with the subdivisions based on changes in texture. As the soil series became the primary mapping unit the concept of what a soil series was also changed. Instead of being based on parent materials and geologic age, the soil series of the 1920s was based on the morphology and composition of the soil profile. Another major change in the concept of soil series occurred when U.S. Soil Taxonomy was released in 1975. Under Soil Taxonomy, the soil series subdivisions were based on the uses the soils might be put to, particularly their agricultural uses (Simonson, 1997). While the concept of the soil series has changed over the years, the term soil series has been the longest-lived term in U.S. soil classification. It has appeared in every official classification system used by the U.S. soil survey (Brevik and Hartemink, 2013). The first classification system was put together by Milton Whitney in 1909 and had soil series at its second lowest level, with soil type at the lowest level. The second classification system used by the U.S. soil survey was developed by C.F. Marbut, H.H. Bennett, J.E. Lapham, and M.H. Lapham in 1913. It had soil series at the second highest level, with soil classes and soil types at more detailed levels. This was followed by another system in 1938 developed by M. Baldwin, C.E. Kellogg, and J. Thorp. In this system soil series were again at the second lowest level with soil types at the lowest level. The soil type concept was dropped and replaced by the soil phase in the 1950s in a modification of the 1938 Baldwin et al. classification (Simonson, 1997). When Soil Taxonomy was released in 1975, soil series became the most detailed (lowest) level of the classification system, and the only term maintained throughout all U.S. classifications to date. While the number of recognized soil series have increased steadily throughout the history of U.S. soil survey, there was a rapid increase in the recognition of new soil series following the introduction of Soil Taxonomy (Brevik and Hartemink, 2013). References Brevik, E.C., and A.E. Hartemink. 2013. Soil maps of the United States of America. Soil Science Society of America Journal 77:1117-1132. doi:10.2136/sssaj2012.0390. Simonson, R.W. 1997. Evolution of soil series and type concepts in the United States. Advances in Geoecology 29:79-108.

Mastering cognitive development theory in computer science education

NASA Astrophysics Data System (ADS)

Gluga, Richard; Kay, Judy; Lister, Raymond; Simon; Kleitman, Sabina

2013-03-01

To design an effective computer science curriculum, educators require a systematic method of classifying the difficulty level of learning activities and assessment tasks. This is important for curriculum design and implementation and for communication between educators. Different educators must be able to use the method consistently, so that classified activities and assessments are comparable across the subjects of a degree, and, ideally, comparable across institutions. One widespread approach to supporting this is to write learning objects in terms of Bloom's Taxonomy. This, or other such classifications, is likely to be more effective if educators can use them consistently, in the way experts would use them. To this end, we present the design and evaluation of our online interactive web-based tutorial system, which can be configured and used to offer training in different classification schemes. We report on results from three evaluations. First, 17 computer science educators complete a tutorial on using Bloom's Taxonomy to classify programming examination questions. Second, 20 computer science educators complete a Neo-Piagetian tutorial. Third evaluation was a comparison of inter-rater reliability scores of computer science educators classifying programming questions using Bloom's Taxonomy, before and after taking our tutorial. Based on the results from these evaluations, we discuss the effectiveness of our tutorial system design for teaching computer science educators how to systematically and consistently classify programming examination questions. We also discuss the suitability of Bloom's Taxonomy and Neo-Piagetian theory for achieving this goal. The Bloom's and Neo-Piagetian tutorials are made available as a community resource. The contributions of this paper are the following: the tutorial system for learning classification schemes for the purpose of coding the difficulty of computing learning materials; its evaluation; new insights into the consistency that computing educators can achieve using Bloom; and first insights into the use of Neo-Piagetian theory by a group of classifiers.

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

Classifying the Standards via Revised Bloom's Taxonomy: A Comparison of Pre-Service and In- Service Teachers

ERIC Educational Resources Information Center

Kocakaya, Serhat; Kotluk, Nihat

2016-01-01

The aim of this study is (a) to investigate the usefulness of Bloom's revised taxonomy (RBT) for classification of standards, (b) to examine the differences and similarities between pre-service teachers' and in-service teachers' classification of the same standards and (c) to determine which standards are vague and broad. The 45 standards, in the…

Should there be a "Wet" Soil Order in Soil Taxonomy?

NASA Astrophysics Data System (ADS)

Rabenhorst, Martin; Wessel, Barret; Stolt, Mark; Lindbo, David

2017-04-01

Early soil classification systems recognized wet soils at the highest categorical level. Among the Intrazonal Soils of the US classification utilized between the 1920s and 1960, were included as Great Soil Groups, the Wiesenboden, Bog, Half-Bog, Ground-Water Podzols and Ground-Water Laterites. In other systems, groups named with such terms as ground water gley and pseudogley were also used. With the advent of Soil Taxonomy and it's precursor (1960, 1975), Histosols (organic soils) were distinguished as one of the initial 10 soil orders, and while many of these organic soils are wet soils, some are not (Folists for example). Thus, for over 50 years, with the exception of Histosols, wet soils (which typically represent the wettest end of subaerial wet soils) have not been collectively recognized within taxa at the highest categorical level (order) in the US soil classification system. Rather, the wettest soils were designated at the second categorical level as wet (Aqu) suborders among the various soil orders, and more recently, subaqueous soils as "Wass" suborders of Entisols and Histosols. Soils with less-wet conditions have been recognized at the subgroup (4th) level. Further, in impoundments and regions of transgressing coastlines, submerged upland soils have been found that still classify in soil orders that do not accommodate subaqueous soils ("Wass" suborders). Notwithstanding, other contemporary soil classification systems do (have continued to) recognize wet soils at the highest level. In the World Reference Base (WRB) for example, wet soils are designated as Gleysols or Stagnosols. As efforts are underway to revisit, simplify, and revise Soil Taxonomy, questions have been raised regarding whether wet soils should again be moved back with a place among taxa at the highest category using a name such as Hydrasols, Aquasols, etc. This paper will explore and consider the questions and arguments for and against such proposals and the difficult question regarding where along the soil wetness continuum would be the best point for recognizing a wet soil order.

Discussions and decisions of the 2012–2014 International Committee on Taxonomy of Viruses (ICTV) Filoviridae Study Group, January 2012–June 2013

PubMed Central

Bukreyev, Alexander A.; Chandran, Kartik; Dolnik, Olga; Dye, John M.; Ebihara, Hideki; Leroy, Eric M.; Mühlberger, Elke; Netesov, Sergey V.; Patterson, Jean L.; Paweska, Janusz T.; Saphire, Erica Ollmann; Smither, Sophie J.; Takada, Ayato; Towner, Jonathan S.; Volchkov, Viktor E.; Warren, Travis K.; Kuhn, Jens H.

2013-01-01

The International Committee on Taxonomy of Viruses (ICTV) Filoviridae Study Group prepares proposals on the classification and nomenclature of filoviruses to reflect current knowledge or to correct disagreements with the International Code of Virus Classification and Nomenclature (ICVCN). In recent years, filovirus taxonomy has been corrected and updated, but parts of it remain controversial, and several topics remain to be debated. This article summarizes the decisions and discussion of the currently acting ICTV Filoviridae Study Group since its inauguration in January 2012. PMID:24122154

[Research on identification of cabbages and weeds combining spectral imaging technology and SAM taxonomy].

PubMed

Zu, Qin; Zhang, Shui-fa; Cao, Yang; Zhao, Hui-yi; Dang, Chang-qing

2015-02-01

Weeds automatic identification is the key technique and also the bottleneck for implementation of variable spraying and precision pesticide. Therefore, accurate, rapid and non-destructive automatic identification of weeds has become a very important research direction for precision agriculture. Hyperspectral imaging system was used to capture the hyperspectral images of cabbage seedlings and five kinds of weeds such as pigweed, barnyard grass, goosegrass, crabgrass and setaria with the wavelength ranging from 1000 to 2500 nm. In ENVI, by utilizing the MNF rotation to implement the noise reduction and de-correlation of hyperspectral data and reduce the band dimensions from 256 to 11, and extracting the region of interest to get the spectral library as standard spectra, finally, using the SAM taxonomy to identify cabbages and weeds, the classification effect was good when the spectral angle threshold was set as 0. 1 radians. In HSI Analyzer, after selecting the training pixels to obtain the standard spectrum, the SAM taxonomy was used to distinguish weeds from cabbages. Furthermore, in order to measure the recognition accuracy of weeds quantificationally, the statistical data of the weeds and non-weeds were obtained by comparing the SAM classification image with the best classification effects to the manual classification image. The experimental results demonstrated that, when the parameters were set as 5-point smoothing, 0-order derivative and 7-degree spectral angle, the best classification result was acquired and the recognition rate of weeds, non-weeds and overall samples was 80%, 97.3% and 96.8% respectively. The method that combined the spectral imaging technology and the SAM taxonomy together took full advantage of fusion information of spectrum and image. By applying the spatial classification algorithms to establishing training sets for spectral identification, checking the similarity among spectral vectors in the pixel level, integrating the advantages of spectra and images meanwhile considering their accuracy and rapidity and improving weeds detection range in the full range that could detect weeds between and within crop rows, the above method contributes relevant analysis tools and means to the application field requiring the accurate information of plants in agricultural precision management

Identifying Nursing Interventions in a Cancer Screening Program Using Nursing Interventions Classification Taxonomy.

PubMed

Benito, Llucia; Lluch, María Teresa; Falcó, Anna Marta; García, Montse; Puig, Montse

2017-04-01

This study aimed to investigate which Nursing Interventions Classification (NIC) labels correspond to specific nursing interventions provided during cancer screening to establish a nursing documentation system. This descriptive study was conducted to identify and classify the interventions that cancer screening nurses perform based on an initial list. The initial list was grouped into 15 interventions that corresponded to four domains and eight classes. The study found expert consensus regarding the duties of cancer screening nurses and identified 15 interventions that should be implemented in clinical practice for cancer screening care, according to the NIC taxonomy. This study is the first step in developing indicators to assess nursing performance in cancer screening, and it helps to establish the core competency requirements for cancer screening nurses. © 2015 NANDA International, Inc.

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.

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

A Comparison of Reimbursement Recommendations by European HTA Agencies: Is There Opportunity for Further Alignment?

PubMed Central

Allen, Nicola; Liberti, Lawrence; Walker, Stuart R.; Salek, Sam

2017-01-01

Introduction: In Europe and beyond, the rising costs of healthcare and limited healthcare resources have resulted in the implementation of health technology assessment (HTA) to inform health policy and reimbursement decision-making. European legislation has provided a harmonized route for the regulatory process with the European Medicines Agency, but reimbursement decision-making still remains the responsibility of each country. There is a recognized need to move toward a more objective and collaborative reimbursement environment for new medicines in Europe. Therefore, the aim of this study was to objectively assess and compare the national reimbursement recommendations of 9 European jurisdictions following European Medicines Agency (EMA) recommendation for centralized marketing authorization. Methods: Using publicly available data and newly developed classification tools, this study appraised 9 European reimbursement systems by assessing HTA processes and the relationship between the regulatory, HTA and decision-making organizations. Each national HTA agency was classified according to two novel taxonomies. The System taxonomy, focuses on the position of the HTA agency within the national reimbursement system according to the relationship between the regulator, the HTA-performing agency, and the reimbursement decision-making coverage body. The HTA Process taxonomy distinguishes between the individual HTA agency's approach to economic and therapeutic evaluation and the inclusion of an independent appraisal step. The taxonomic groups were subsequently compared with national HTA recommendations. Results: This study identified European national reimbursement recommendations for 102 new active substances (NASs) approved by the EMA from 2008 to 2012. These reimbursement recommendations were compared using a novel classification tool and identified alignment between the organizational structure of reimbursement systems (System taxonomy) and HTA recommendations. However, there was less alignment between the HTA processes and recommendations. Conclusions: In order to move forward to a more harmonized HTA environment within Europe, it is first necessary to understand the variation in HTA practices within Europe. This study has identified alignment between HTA recommendations and the System taxonomy and one of the major implications of this study is that such alignment could support a more collaborative HTA environment in Europe. PMID:28713265

A Comparison of Reimbursement Recommendations by European HTA Agencies: Is There Opportunity for Further Alignment?

PubMed

Allen, Nicola; Liberti, Lawrence; Walker, Stuart R; Salek, Sam

2017-01-01

Introduction: In Europe and beyond, the rising costs of healthcare and limited healthcare resources have resulted in the implementation of health technology assessment (HTA) to inform health policy and reimbursement decision-making. European legislation has provided a harmonized route for the regulatory process with the European Medicines Agency, but reimbursement decision-making still remains the responsibility of each country. There is a recognized need to move toward a more objective and collaborative reimbursement environment for new medicines in Europe. Therefore, the aim of this study was to objectively assess and compare the national reimbursement recommendations of 9 European jurisdictions following European Medicines Agency (EMA) recommendation for centralized marketing authorization. Methods: Using publicly available data and newly developed classification tools, this study appraised 9 European reimbursement systems by assessing HTA processes and the relationship between the regulatory, HTA and decision-making organizations. Each national HTA agency was classified according to two novel taxonomies. The System taxonomy, focuses on the position of the HTA agency within the national reimbursement system according to the relationship between the regulator, the HTA-performing agency, and the reimbursement decision-making coverage body. The HTA Process taxonomy distinguishes between the individual HTA agency's approach to economic and therapeutic evaluation and the inclusion of an independent appraisal step. The taxonomic groups were subsequently compared with national HTA recommendations. Results: This study identified European national reimbursement recommendations for 102 new active substances (NASs) approved by the EMA from 2008 to 2012. These reimbursement recommendations were compared using a novel classification tool and identified alignment between the organizational structure of reimbursement systems (System taxonomy) and HTA recommendations. However, there was less alignment between the HTA processes and recommendations. Conclusions: In order to move forward to a more harmonized HTA environment within Europe, it is first necessary to understand the variation in HTA practices within Europe. This study has identified alignment between HTA recommendations and the System taxonomy and one of the major implications of this study is that such alignment could support a more collaborative HTA environment in Europe.

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.

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…

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.

The RICHE taxonomy - an innovative means of classification of child health research.

PubMed

Alexander, D; Bourek, A; Kilroe, J; Rigby, M; Staines, A

2014-09-01

Research outputs increase inexorably. Health is now a required element in all policies of the European Union. There is a need for a system that helps to navigate the vast body of children's health research, identify pertinent research institutions, discover ongoing and recently funded research projects and identify gaps where there is little knowledge. The European Commission funded the Research Inventory of Child Health in Europe (RICHE) project through the Framework 7 Programme, to identify gaps in child health research in Europe. A necessary first step was to identify and index current research, for which a website repository was created. As a basis for this task, an innovative taxonomy was necessary to encompass the many arenas of children's health and development, including subjects outside the traditional areas of children's health. Drawing inspiration from existing taxonomies, library systems and other forms of classification, a multi-axial approach was selected as the best way to encompass the many influences on children's health. Six axes were identified and their contents defined. All of the axes can be viewed and searched independently, as well as in relation to each other. The axes encompass factors and service areas that impact on children, including health, education, justice, the environment and others. This has created a system that is consistent and impartial, but adaptable to an enormous variety of uses. The taxonomy has been tested and validated by a number of well-respected academics, researchers and practitioners across Europe. It forms the basis of an intuitive and accessible database. This allows research knowledge to be easily identified and for networking to take place. The RICHE taxonomy facilitates retrieval of knowledge - ongoing research as well as findings - in order to inform researchers and policy makers who wish to include children's health as an element of new policy. © 2013 John Wiley & Sons Ltd.

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.

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

A Review of Major Nursing Vocabularies and the Extent to Which They Have the Characteristics Required for Implementation in Computer-based Systems

PubMed Central

Henry, Suzanne Bakken; Warren, Judith J.; Lange, Linda; Button, Patricia

1998-01-01

Building on the work of previous authors, the Computer-based Patient Record Institute (CPRI) Work Group on Codes and Structures has described features of a classification scheme for implementation within a computer-based patient record. The authors of the current study reviewed the evaluation literature related to six major nursing vocabularies (the North American Nursing Diagnosis Association Taxonomy 1, the Nursing Interventions Classification, the Nursing Outcomes Classification, the Home Health Care Classification, the Omaha System, and the International Classification for Nursing Practice) to determine the extent to which the vocabularies include the CPRI features. None of the vocabularies met all criteria. The Omaha System, Home Health Care Classification, and International Classification for Nursing Practice each included five features. Criteria not fully met by any systems were clear and non-redundant representation of concepts, administrative cross-references, syntax and grammar, synonyms, uncertainty, context-free identifiers, and language independence. PMID:9670127

Toward genetics-based virus taxonomy: comparative analysis of a genetics-based classification and the taxonomy of picornaviruses.

PubMed

Lauber, Chris; Gorbalenya, Alexander E

2012-04-01

Virus taxonomy has received little attention from the research community despite its broad relevance. In an accompanying paper (C. Lauber and A. E. Gorbalenya, J. Virol. 86:3890-3904, 2012), we have introduced a quantitative approach to hierarchically classify viruses of a family using pairwise evolutionary distances (PEDs) as a measure of genetic divergence. When applied to the six most conserved proteins of the Picornaviridae, it clustered 1,234 genome sequences in groups at three hierarchical levels (to which we refer as the "GENETIC classification"). In this study, we compare the GENETIC classification with the expert-based picornavirus taxonomy and outline differences in the underlying frameworks regarding the relation of virus groups and genetic diversity that represent, respectively, the structure and content of a classification. To facilitate the analysis, we introduce two novel diagrams. The first connects the genetic diversity of taxa to both the PED distribution and the phylogeny of picornaviruses. The second depicts a classification and the accommodated genetic diversity in a standardized manner. Generally, we found striking agreement between the two classifications on species and genus taxa. A few disagreements concern the species Human rhinovirus A and Human rhinovirus C and the genus Aphthovirus, which were split in the GENETIC classification. Furthermore, we propose a new supergenus level and universal, level-specific PED thresholds, not reached yet by many taxa. Since the species threshold is approached mostly by taxa with large sampling sizes and those infecting multiple hosts, it may represent an upper limit on divergence, beyond which homologous recombination in the six most conserved genes between two picornaviruses might not give viable progeny.

[Classification of memory systems: a revision].

PubMed

Agrest, M

2001-12-01

The present paper exposes the arguments against considering memory as a monolytic entity and how is it to be divided into several systems in order to understand its operation. Historically this division was acknowledge by different authors but in the last few decades it received the confirmation from the scientific research. The most accepted taxonomy establishes the existence of two major memory systems: declarative and non declarative memory. The article also presents the arguments for and against this kind of division, as well as an alternative classification in five major systems: procedural, perceptual representation, semantic, primary and episodic.

Taxonomy of asteroids. [according to polarimetric, spectrophotometric, radiometric, and UBV photometric data

NASA Technical Reports Server (NTRS)

Bowell, E.; Chapman, C. R.; Gradie, J. C.; Zellner, B.; Morrison, D.

1978-01-01

A taxonomic system for asteroids is discussed which is based on seven directly observable parameters from polarimetry, spectrophotometry, radiometry, and UBV photometry. The classification scheme is entirely empirical and independent of specific mineralogical interpretations. Five broad classes (designated C, S, M, E, and R), as well as an 'unclassifiable' designation, are defined on the basis of observational data for 523 asteroids. Computer-generated type classifications and derived diameters are given for the 523 asteroids, and the application of the classification procedure is illustrated. Of the 523 asteroids classified, 190 are identified as C objects, 141 as S type, 13 as type M, three as type E, three as type R, 55 as unclassifiable, and 118 as ambiguous. The present taxonomic system is compared with several other asteroid classification systems.

A taxonomy of visualization tasks for the analysis of biological pathway data.

PubMed

Murray, Paul; McGee, Fintan; Forbes, Angus G

2017-02-15

Understanding complicated networks of interactions and chemical components is essential to solving contemporary problems in modern biology, especially in domains such as cancer and systems research. In these domains, biological pathway data is used to represent chains of interactions that occur within a given biological process. Visual representations can help researchers understand, interact with, and reason about these complex pathways in a number of ways. At the same time, these datasets offer unique challenges for visualization, due to their complexity and heterogeneity. Here, we present taxonomy of tasks that are regularly performed by researchers who work with biological pathway data. The generation of these tasks was done in conjunction with interviews with several domain experts in biology. These tasks require further classification than is provided by existing taxonomies. We also examine existing visualization techniques that support each task, and we discuss gaps in the existing visualization space revealed by our taxonomy. Our taxonomy is designed to support the development and design of future biological pathway visualization applications. We conclude by suggesting future research directions based on our taxonomy and motivated by the comments received by our domain experts.

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/.

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

Prediction and Confirmation of V-type Asteroids Beyond 2.5 AU Based on SDSS Colors

NASA Astrophysics Data System (ADS)

Binzel, Richard P.; Masi, G.; Foglia, S.

2006-09-01

We apply a taxonomic classification system developed by Masi et al. (2006, submitted to Icarus) to identify C-, S-, and V-type asteroids present within the 3rd Release of the Sloan Digital Sky Survey Moving Object Catalog (SDSS MOC3). The classifications deduced by Masi et al. for 43,000 asteroids using SDSS colors are based on the taxonomy of Bus (1999; MIT Ph.D. thesis). To link SDSS colors to the Bus taxonomy, Masi et al. (2006) use 149 objects measured in common by both SDSS and the Small Main-Belt Asteroid Spectroscopic Survey (SMASS) (Bus and Binzel 2002, Icarus 158, 106). We report results of direct testing of SDSS V-type classification predictions for six objects, where the tests were performed by visible wavelength spectroscopy (Lazzaro et al. 2004, Icarus 172, 179) and target of opportunity near-infrared spectroscopy obtained using the NASA Infrared Telescope Facility (IRTF). Vesta-like spectra and a V-type taxonomy are confirmed for five of the six predicted V-type objects sampled. Most interestingly, the SDSS taxonomy correctly predicted the V-type spectral characteristics for asteroid (21238) 1995 WV7, a 6 km asteroid located far from Vesta across the 3:1 mean motion resonance at 2.54 AU. (Proper elements a,e,i: 2.54 AU, 0.14, and 10.8 deg.) Given the 2 km/sec ejection velocity required from Vesta to reach the current orbit, and the difficulty of migrating across the 3:1 resonance (at 2.5 AU) by a process such as Yarkovsky drift or via secular resonances (Carruba et al. 2005, Astron. Astrophys. 441, 819), asteroid 21238 may be a new candidate for a basaltic asteroid having no relationship to Vesta.

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.

The PRISMS taxonomy of self-management support: derivation of a novel taxonomy and initial testing of its utility.

PubMed

Pearce, Gemma; Parke, Hannah L; Pinnock, Hilary; Epiphaniou, Eleni; Bourne, Claire L A; Sheikh, Aziz; Taylor, Stephanie J C

2016-04-01

Supporting self-management is a core response of health care systems globally to the increasing prevalence of long-term conditions. Lack of a comprehensive taxonomy (or classification) of self-management support components hinders characterization and, ultimately, understanding of these frequently complex, multi-component interventions. To develop a comprehensive, descriptive taxonomy of self-management support components. Components were derived from the 969 unique randomized controlled trials described in the 102 systematic reviews and 61 implementation trials, examining 14 diverse long-term conditions included in the Practical Reviews in Self-Management Support (PRISMS) project followed by discussion at an expert stakeholder workshop. The utility of the taxonomy was then tested using a self-management support intervention for cancer survivors. The PRISMS taxonomy comprises 14 components that might be used to support self-management (e.g. information about condition/management, provision of equipment, social support), when delivered to someone with a long-term condition or their carer. Overarching dimensions are delivery mode; personnel delivering the support; intervention targeting; and intensity, frequency and duration of the intervention. The taxonomy does not consider the effectiveness or otherwise of the different components or the overarching dimensions. The PRISMS taxonomy offers a framework to researchers describing self-management support interventions, to reviewers synthesizing evidence and to developers of health services for people with long-term conditions. © The Author(s) 2015.

Algorithm of Taxonomy: Method of Design and Implementation Mechanism

NASA Astrophysics Data System (ADS)

Shalanov, N. V.; Aletdinova, A. A.

2018-05-01

The authors propose that the method of design of the algorithm of taxonomy should be based on the calculation of integral indicators for the estimation of the level of an object according to the set of initial indicators (i. e. potential). Their values will be the values of the projected lengths of the objects on the numeric axis, which will take values [0.100]. This approach will reduce the task of multidimensional classification to the task of one-dimensional classification. The algorithm for solving the task of taxonomy contains 14 stages; the example of its implementation is illustrated by the data of 46 consumer societies of the Yakut Union of Consumer Societies of Russia.

Secondary School Course Classification System: School Codes for the Exchange of Data (SCED). NCES 2007-341

ERIC Educational Resources Information Center

Bradby, Denise; Pedroso, Rosio; Rogers, Andy

2007-01-01

This handbook presents a taxonomy and course descriptions for secondary education. The system is intended to help schools and education agencies maintain longitudinal information about students' coursework in an efficient, standardized format that facilitates the exchange of records as students transfer from one school to another, or to…

Reporting of complex interventions in clinical trials: development of a taxonomy to classify and describe fall-prevention interventions.

PubMed

Lamb, Sarah E; Becker, Clemens; Gillespie, Lesley D; Smith, Jessica L; Finnegan, Susanne; Potter, Rachel; Pfeiffer, Klaus

2011-05-17

Interventions for preventing falls in older people often involve several components, multidisciplinary teams, and implementation in a variety of settings. We have developed a classification system (taxonomy) to describe interventions used to prevent falls in older people, with the aim of improving the design and reporting of clinical trials of fall-prevention interventions, and synthesis of evidence from these trials. Thirty three international experts in falls prevention and health services research participated in a series of meetings to develop consensus. Robust techniques were used including literature reviews, expert presentations, and structured consensus workshops moderated by experienced facilitators. The taxonomy was refined using an international test panel of five health care practitioners. We assessed the chance corrected agreement of the final version by comparing taxonomy completion for 10 randomly selected published papers describing a variety of fall-prevention interventions. The taxonomy consists of four domains, summarized as the "Approach", "Base", "Components" and "Descriptors" of an intervention. Sub-domains include; where participants are identified; the theoretical approach of the intervention; clinical targeting criteria; details on assessments; descriptions of the nature and intensity of interventions. Chance corrected agreement of the final version of the taxonomy was good to excellent for all items. Further independent evaluation of the taxonomy is required. The taxonomy is a useful instrument for characterizing a broad range of interventions used in falls prevention. Investigators are encouraged to use the taxonomy to report their interventions.

Reporting of complex interventions in clinical trials: development of a taxonomy to classify and describe fall-prevention interventions

PubMed Central

2011-01-01

Background Interventions for preventing falls in older people often involve several components, multidisciplinary teams, and implementation in a variety of settings. We have developed a classification system (taxonomy) to describe interventions used to prevent falls in older people, with the aim of improving the design and reporting of clinical trials of fall-prevention interventions, and synthesis of evidence from these trials. Methods Thirty three international experts in falls prevention and health services research participated in a series of meetings to develop consensus. Robust techniques were used including literature reviews, expert presentations, and structured consensus workshops moderated by experienced facilitators. The taxonomy was refined using an international test panel of five health care practitioners. We assessed the chance corrected agreement of the final version by comparing taxonomy completion for 10 randomly selected published papers describing a variety of fall-prevention interventions. Results The taxonomy consists of four domains, summarized as the "Approach", "Base", "Components" and "Descriptors" of an intervention. Sub-domains include; where participants are identified; the theoretical approach of the intervention; clinical targeting criteria; details on assessments; descriptions of the nature and intensity of interventions. Chance corrected agreement of the final version of the taxonomy was good to excellent for all items. Further independent evaluation of the taxonomy is required. Conclusions The taxonomy is a useful instrument for characterizing a broad range of interventions used in falls prevention. Investigators are encouraged to use the taxonomy to report their interventions. PMID:21586143

Effective Team Performance in Military Environments. Final Report.

ERIC Educational Resources Information Center

Hogan, Robert; And Others

Identification of psychological factors influencing team performance in the chemical, biological, and radiological defense (CBR-D) environment were identified by a system for task classification: (1) combining Herold's task demands and Holland's taxonomy of work environments and (2) describing the development and evaluation of team tasks. This…

Mapping the Diversity among Runaways: A Descriptive Multivariate Analysis of Selected Social Psychological Background Conditions.

ERIC Educational Resources Information Center

Brennan, Tim

1980-01-01

A review of prior classification systems of runaways is followed by a descriptive taxonomy of runaways developed using cluster-analytic methods. The empirical types illustrate patterns of weakness in bonds between runaways and families, schools, or peer relationships. (Author)

Taxonomic update on proposed nomenclature and classification changes for bacteria of medical importance, 2015.

PubMed

Janda, J Michael

2016-10-01

A key aspect of medical, public health, and diagnostic microbiology laboratories is the accurate and rapid reporting and communication regarding infectious agents of clinical significance. Microbial taxonomy in the age of molecular diagnostics and phylogenetics creates changes in taxonomy at a rapid rate further complicating this process. This update focuses on the description of new species and classification changes proposed in 2015. Copyright © 2016 Elsevier Inc. All rights reserved.

Toward Genetics-Based Virus Taxonomy: Comparative Analysis of a Genetics-Based Classification and the Taxonomy of Picornaviruses

PubMed Central

Lauber, Chris

2012-01-01

Virus taxonomy has received little attention from the research community despite its broad relevance. In an accompanying paper (C. Lauber and A. E. Gorbalenya, J. Virol. 86:3890–3904, 2012), we have introduced a quantitative approach to hierarchically classify viruses of a family using pairwise evolutionary distances (PEDs) as a measure of genetic divergence. When applied to the six most conserved proteins of the Picornaviridae, it clustered 1,234 genome sequences in groups at three hierarchical levels (to which we refer as the “GENETIC classification”). In this study, we compare the GENETIC classification with the expert-based picornavirus taxonomy and outline differences in the underlying frameworks regarding the relation of virus groups and genetic diversity that represent, respectively, the structure and content of a classification. To facilitate the analysis, we introduce two novel diagrams. The first connects the genetic diversity of taxa to both the PED distribution and the phylogeny of picornaviruses. The second depicts a classification and the accommodated genetic diversity in a standardized manner. Generally, we found striking agreement between the two classifications on species and genus taxa. A few disagreements concern the species Human rhinovirus A and Human rhinovirus C and the genus Aphthovirus, which were split in the GENETIC classification. Furthermore, we propose a new supergenus level and universal, level-specific PED thresholds, not reached yet by many taxa. Since the species threshold is approached mostly by taxa with large sampling sizes and those infecting multiple hosts, it may represent an upper limit on divergence, beyond which homologous recombination in the six most conserved genes between two picornaviruses might not give viable progeny. PMID:22278238

Genetic variability of HEV isolates: inconsistencies of current classification.

PubMed

Oliveira-Filho, Edmilson F; König, Matthias; Thiel, Heinz-Jürgen

2013-07-26

Many HEV and HEV-like sequences have been reported during the last years, including isolates which may represent a number of potential new genera, new genotypes or new subtypes within the family Hepeviridae. Using the most common classification system, difficulties in the establishment of subtypes have been reported. Moreover the relevance of subtype classification for epidemiology can be questioned. In this study we have performed phylogenetic analyses based on whole capsid gene and complete HEV genomic sequences in order to evaluate the current classification of HEV at genotype and subtype levels. The results of our analyses modify the current taxonomy of genotype 3 and refine the established system for typing of HEV. In addition we suggest a classification for hepeviruses recently isolated from bats, ferrets, rats and wild boar. Copyright © 2013 Elsevier B.V. All rights reserved.

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…

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

A Call for an Empirical Taxonomy of Schools

ERIC Educational Resources Information Center

Van Ryzin, Mark J.

2008-01-01

Many educational researchers have identified issues on classifying schools and some have made use of ad-hoc classification systems in their analyses; however, these solutions are generally one-dimensional, which prohibits them from capturing the full breadth of variation among schools. To understand the amount of variation that exist in schools…

The Effects of Explicit Visual Cues in Reading Biological Diagrams

ERIC Educational Resources Information Center

Ge, Yun-Ping; Unsworth, Len; Wang, Kuo-Hua

2017-01-01

Drawing on cognitive theories, this study intends to investigate the effects of explicit visual cues which have been proposed as a critical factor in facilitating understanding of biological images. Three diagrams from Taiwanese textbooks with implicit visual cues, involving the concepts of biological classification systems, fish taxonomy, and…

Instructional Method Classifications Lack User Language and Orientation

ERIC Educational Resources Information Center

Neumann, Susanne; Koper, Rob

2010-01-01

Following publications emphasizing the need of a taxonomy for instructional methods, this article presents a literature review on classifications for learning and teaching in order to identify possible classifications for instructional methods. Data was collected for 37 classifications capturing the origins, theoretical underpinnings, purposes and…

The Affordable Care Act's implications for a public health workforce agenda: taxonomy, enumeration, and the Standard Occupational Classification system.

PubMed

Montes, J Henry; Webb, Susan C

2015-01-01

The Affordable Care Act brings a renewed emphasis on the importance of public health services and those whose occupations are defined by performing the essential public health functions. The Affordable Care Act Prevention and Public Health Fund is a signal to the field that its work is important and critical to the health of the nation. Recent reports by the Institute of Medicine describe the changing dimensions of public health work in primary care integration and the need for enhanced financing of public health as investment. Gaining knowledge about the public health workforce, that is, how many workers there are and what they are doing, is of growing interest and concern for the field. Although enumeration of the public health workforce has been attempted several times by the federal government beginning as early as 1982, it was not until the year 2000 that a major effort was undertaken to obtain more complete information. Limitations that hampered Enumeration 2000 have persisted however. With implementation of the Affordable Care Act and other new ventures, key federal agencies are developing strategies to pursue a systemic and systematic enumeration and consistent taxonomy process. Included in these efforts is use of the Bureau of Labor Statistics, Standard Occupational Classification system. A clear and accurate understanding of the public health workforce and its characteristics is a major challenge. A well-constructed, systematic enumeration process can add to our understanding of the nature and functions of that workforce. In addition, discussion of enumeration must include the need for a consensus within the field that leads to a consistent taxonomy for the public health occupations. This article will provide a stage-setting brief of historical actions regarding enumeration, and it will examine selected enumeration activities taking place currently. It will discuss positive and negative implications facing public health and the potential for enhancing the existing Standard Occupational Classification system to aid enumeration studies.

Functionality versus dimensionality in psychological taxonomies, and a puzzle of emotional valence

PubMed Central

2018-01-01

This paper applies evolutionary and functional constructivism approaches to the discussion of psychological taxonomies, as implemented in the neurochemical model Functional Ensemble of Temperament (FET). FET asserts that neurochemical systems developed in evolution to regulate functional-dynamical aspects of construction of actions: orientation, selection (integration), energetic maintenance, and management of automatic behavioural elements. As an example, the paper reviews the neurochemical mechanisms of interlocking between emotional dispositions and performance capacities. Research shows that there are no specific neurophysiological systems of positive or negative affect, and that emotional valence is rather an integrative product of many brain systems during estimations of needs and the capacities required to satisfy these needs. The interlocking between emotional valence and functional aspects of performance appears to be only partial since all monoamine and opioid receptor systems play important roles in non-emotional aspects of behaviour, in addition to emotionality. This suggests that the Positive/Negative Affect framework for DSM/ICD classifications of mental disorders oversimplifies the structure of non-emotionality symptoms of these disorders. Contingent dynamical relationships between neurochemical systems cannot be represented by linear statistical models searching for independent dimensions (such as factor analysis); nevertheless, these relationships should be reflected in psychological and psychiatric taxonomies. This article is part of the theme issue ‘Diverse perspectives on diversity: multi-disciplinary approaches to taxonomies of individual differences’. PMID:29483351

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.

The first step in the development of text mining technology for cancer risk assessment: identifying and organizing scientific evidence in risk assessment literature

PubMed Central

Korhonen, Anna; Silins, Ilona; Sun, Lin; Stenius, Ulla

2009-01-01

Background One of the most neglected areas of biomedical Text Mining (TM) is the development of systems based on carefully assessed user needs. We have recently investigated the user needs of an important task yet to be tackled by TM -- Cancer Risk Assessment (CRA). Here we take the first step towards the development of TM technology for the task: identifying and organizing the scientific evidence required for CRA in a taxonomy which is capable of supporting extensive data gathering from biomedical literature. Results The taxonomy is based on expert annotation of 1297 abstracts downloaded from relevant PubMed journals. It classifies 1742 unique keywords found in the corpus to 48 classes which specify core evidence required for CRA. We report promising results with inter-annotator agreement tests and automatic classification of PubMed abstracts to taxonomy classes. A simple user test is also reported in a near real-world CRA scenario which demonstrates along with other evaluation that the resources we have built are well-defined, accurate, and applicable in practice. Conclusion We present our annotation guidelines and a tool which we have designed for expert annotation of PubMed abstracts. A corpus annotated for keywords and document relevance is also presented, along with the taxonomy which organizes the keywords into classes defining core evidence for CRA. As demonstrated by the evaluation, the materials we have constructed provide a good basis for classification of CRA literature along multiple dimensions. They can support current manual CRA as well as facilitate the development of an approach based on TM. We discuss extending the taxonomy further via manual and machine learning approaches and the subsequent steps required to develop TM technology for the needs of CRA. PMID:19772619

Stepping stones towards a new prokaryotic taxonomy.

PubMed

Gevers, Dirk; Dawyndt, Peter; Vandamme, Peter; Willems, Anne; Vancanneyt, Marc; Swings, Jean; De Vos, Paul

2006-11-29

Technological developments provide new insights into prokaryotic evolution and diversity and provoke a continuous need to update taxonomy and revise classification schemes. Our present species concept and definition are being challenged by the growing amount of whole genomic information, which should allow improvements in the natural species definition. The continuous quest for an objective and stable method for sorting strains into coherent homogeneous groups is inherent to prokaryotic systematics and nomenclature. Morphological, biochemical, physiological, phenotypic and chemotaxonomic criteria have been complemented by molecular data and pragmatic, purpose built, species definitions are being replaced by more natural ones based on evolutionary insights. It is imperative to give due consideration to both fundamental and applied aspects of future species concepts and definitions. The present paper discusses the present practice in prokaryotic taxonomy of how this system developed and how it may evolve in the future.

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.

The chemotaxonomic classification of Rhodiola plants and its correlation with morphological characteristics and genetic taxonomy.

PubMed

Liu, Zhenli; Liu, Yuanyan; Liu, Chunsheng; Song, Zhiqian; Li, Qing; Zha, Qinglin; Lu, Cheng; Wang, Chun; Ning, Zhangchi; Zhang, Yuxin; Tian, Cheng; Lu, Aiping

2013-07-12

Rhodiola plants are used as a natural remedy in the western world and as a traditional herbal medicine in China, and are valued for their ability to enhance human resistance to stress or fatigue and to promote longevity. Due to the morphological similarities among different species, the identification of the genus remains somewhat controversial, which may affect their safety and effectiveness in clinical use. In this paper, 47 Rhodiola samples of seven species were collected from thirteen local provinces of China. They were identified by their morphological characteristics and genetic and phytochemical taxonomies. Eight bioactive chemotaxonomic markers from four chemical classes (phenylpropanoids, phenylethanol derivatives, flavonoids and phenolic acids) were determined to evaluate and distinguish the chemotaxonomy of Rhodiola samples using an HPLC-DAD/UV method. Hierarchical cluster analysis (HCA) and principal component analysis (PCA) were applied to compare the two classification methods between genetic and phytochemical taxonomy. The established chemotaxonomic classification could be effectively used for Rhodiola species identification.

The chemotaxonomic classification of Rhodiola plants and its correlation with morphological characteristics and genetic taxonomy

PubMed Central

2013-01-01

Background Rhodiola plants are used as a natural remedy in the western world and as a traditional herbal medicine in China, and are valued for their ability to enhance human resistance to stress or fatigue and to promote longevity. Due to the morphological similarities among different species, the identification of the genus remains somewhat controversial, which may affect their safety and effectiveness in clinical use. Results In this paper, 47 Rhodiola samples of seven species were collected from thirteen local provinces of China. They were identified by their morphological characteristics and genetic and phytochemical taxonomies. Eight bioactive chemotaxonomic markers from four chemical classes (phenylpropanoids, phenylethanol derivatives, flavonoids and phenolic acids) were determined to evaluate and distinguish the chemotaxonomy of Rhodiola samples using an HPLC-DAD/UV method. Hierarchical cluster analysis (HCA) and principal component analysis (PCA) were applied to compare the two classification methods between genetic and phytochemical taxonomy. Conclusions The established chemotaxonomic classification could be effectively used for Rhodiola species identification. PMID:23844866

TAXONOMY OF MEDICAL DEVICES IN THE LOGIC OF HEALTH TECHNOLOGY ASSESSMENT.

PubMed

Henschke, Cornelia; Panteli, Dimitra; Perleth, Matthias; Busse, Reinhard

2015-01-01

The suitability of general HTA methodology for medical devices is gaining interest as a topic of scientific discourse. Given the broad range of medical devices, there might be differences between groups of devices that impact both the necessity and the methods of their assessment. Our aim is to develop a taxonomy that provides researchers and policy makers with an orientation tool on how to approach the assessment of different types of medical devices. Several classifications for medical devices based on varying rationales for different regulatory and reporting purposes were analyzed in detail to develop a comprehensive taxonomic model. The taxonomy is based on relevant aspects of existing classification schemes incorporating elements of risk and functionality. Its 9 × 6 matrix distinguishes between the diagnostic or therapeutic nature of devices and considers whether the medical device is directly used by patients, constitutes part of a specific procedure, or can be used for a variety of procedures. We considered the relevance of different device categories in regard to HTA to be considerably variable, ranging from high to low. Existing medical device classifications cannot be used for HTA as they are based on different underlying logics. The developed taxonomy combines different device classification schemes used for different purposes. It aims at providing decision makers with a tool enabling them to consider device characteristics in detail across more than one dimension. The placement of device groups in the matrix can provide decision support on the necessity of conducting a full HTA.

A New Taxonomy of Cognitive Strategies for the Management of Pain.

ERIC Educational Resources Information Center

Fernandez, Ephrem P.

This paper presents cognitive strategies as one major approach to pain management. They are discussed as part of a trimodal system of pain management that also includes behavioral manipulations and physical intervention. The need for a standardized classification to deal with terminological inconsistency in the literature on cognitive management…

Classification of Innovation Objectives Set for Continuing Professional Teacher Development

ERIC Educational Resources Information Center

Tyunnikov, Yurii S.

2017-01-01

The present demand for teachers, showing advanced aptitude for innovations, is an important reason for promotion of innovative practices in the continuous teacher training. For the on-going development of a continuous training system preparing teachers for innovative activities, it is necessary to have a complete taxonomy of practical objectives.…

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.

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/

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

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

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.

Exploring human error in military aviation flight safety events using post-incident classification systems.

PubMed

Hooper, Brionny J; O'Hare, David P A

2013-08-01

Human error classification systems theoretically allow researchers to analyze postaccident data in an objective and consistent manner. The Human Factors Analysis and Classification System (HFACS) framework is one such practical analysis tool that has been widely used to classify human error in aviation. The Cognitive Error Taxonomy (CET) is another. It has been postulated that the focus on interrelationships within HFACS can facilitate the identification of the underlying causes of pilot error. The CET provides increased granularity at the level of unsafe acts. The aim was to analyze the influence of factors at higher organizational levels on the unsafe acts of front-line operators and to compare the errors of fixed-wing and rotary-wing operations. This study analyzed 288 aircraft incidents involving human error from an Australasian military organization occurring between 2001 and 2008. Action errors accounted for almost twice (44%) the proportion of rotary wing compared to fixed wing (23%) incidents. Both classificatory systems showed significant relationships between precursor factors such as the physical environment, mental and physiological states, crew resource management, training and personal readiness, and skill-based, but not decision-based, acts. The CET analysis showed different predisposing factors for different aspects of skill-based behaviors. Skill-based errors in military operations are more prevalent in rotary wing incidents and are related to higher level supervisory processes in the organization. The Cognitive Error Taxonomy provides increased granularity to HFACS analyses of unsafe acts.

A Comparison of Revised Bloom and Marzano's New Taxonomy of Learning

ERIC Educational Resources Information Center

Irvine, Jeff

2017-01-01

The seminal "Taxonomy of Educational Objectives: The Classification of Educational Goals--Handbook I, Cognitive Domain" (Bloom, Engelhart, Furst, Hill, & Krathwohl, 1956) represented years of collaboration by the Committee of College and University Examiners, and was the first of three volumes that together would become known as…

Is a Scientific Classification of Educational (Behavioral) Objectives Possible?

ERIC Educational Resources Information Center

Stigliano, Tony

Robert M. W. Travers's 1980 essay is the focal point of this paper. He argues that evaluation research requires a scientific taxonomy of human behavior and learning. Such a taxonomy must be experimentally based, mathematically expressed, theoretically sound, and predictive. He bases such criteria on the development of scientifically successful…

FBIS: A regional DNA barcode archival & analysis system for Indian fishes.

PubMed

Nagpure, Naresh Sahebrao; Rashid, Iliyas; Pathak, Ajey Kumar; Singh, Mahender; Singh, Shri Prakash; Sarkar, Uttam Kumar

2012-01-01

DNA barcode is a new tool for taxon recognition and classification of biological organisms based on sequence of a fragment of mitochondrial gene, cytochrome c oxidase I (COI). In view of the growing importance of the fish DNA barcoding for species identification, molecular taxonomy and fish diversity conservation, we developed a Fish Barcode Information System (FBIS) for Indian fishes, which will serve as a regional DNA barcode archival and analysis system. The database presently contains 2334 sequence records of COI gene for 472 aquatic species belonging to 39 orders and 136 families, collected from available published data sources. Additionally, it contains information on phenotype, distribution and IUCN Red List status of fishes. The web version of FBIS was designed using MySQL, Perl and PHP under Linux operating platform to (a) store and manage the acquisition (b) analyze and explore DNA barcode records (c) identify species and estimate genetic divergence. FBIS has also been integrated with appropriate tools for retrieving and viewing information about the database statistics and taxonomy. It is expected that FBIS would be useful as a potent information system in fish molecular taxonomy, phylogeny and genomics. The database is available for free at http://mail.nbfgr.res.in/fbis/

34 CFR 600.10 - Date, extent, duration, and consequence of eligibility.

Code of Federal Regulations, 2011 CFR

2011-07-01

... Classification of Instructional Programs (CIP) code under the taxonomy of instructional program classifications... same CIP code as another program offered by the institution but leads to a different degree or...

34 CFR 600.10 - Date, extent, duration, and consequence of eligibility.

Code of Federal Regulations, 2014 CFR

2014-07-01

... Classification of Instructional Programs (CIP) code under the taxonomy of instructional program classifications... same CIP code as another program offered by the institution but leads to a different degree or...

34 CFR 600.10 - Date, extent, duration, and consequence of eligibility.

Code of Federal Regulations, 2013 CFR

2013-07-01

... Classification of Instructional Programs (CIP) code under the taxonomy of instructional program classifications... same CIP code as another program offered by the institution but leads to a different degree or...

34 CFR 600.10 - Date, extent, duration, and consequence of eligibility.

Code of Federal Regulations, 2012 CFR

2012-07-01

... Classification of Instructional Programs (CIP) code under the taxonomy of instructional program classifications... same CIP code as another program offered by the institution but leads to a different degree or...

Mental health professionals' natural taxonomies of mental disorders: implications for the clinical utility of the ICD-11 and the DSM-5.

PubMed

Reed, Geoffrey M; Roberts, Michael C; Keeley, Jared; Hooppell, Catherine; Matsumoto, Chihiro; Sharan, Pratap; Robles, Rebeca; Carvalho, Hudson; Wu, Chunyan; Gureje, Oye; Leal-Leturia, Itzear; Flanagan, Elizabeth H; Correia, João Mendonça; Maruta, Toshimasa; Ayuso-Mateos, José Luís; de Jesus Mari, Jair; Xiao, Zeping; Evans, Spencer C; Saxena, Shekhar; Medina-Mora, María Elena

2013-12-01

To examine the conceptualizations held by psychiatrists and psychologists around the world of the relationships among mental disorders in order to inform decisions about the structure of the classification of mental and behavioral disorders in World Health Organization's International Classification of Diseases and Related Health Problems 11th Revision (ICD-11). 517 mental health professionals in 8 countries sorted 60 cards containing the names of mental disorders into groups of similar disorders, and then formed a hierarchical structure by aggregating and disaggregating these groupings. Distance matrices were created from the sorting data and used in cluster and correlation analyses. Clinicians' taxonomies were rational, interpretable, and extremely stable across countries, diagnostic system used, and profession. Clinicians' consensus classification structure was different from ICD-10 and the American Psychiatric Association's Diagnostic and Statistical Manual of Mental Disorders 4th Edition (DSM-IV), but in many respects consistent with ICD-11 proposals. The clinical utility of the ICD-11 may be improved by making its structure more compatible with the common conceptual organization of mental disorders observed across diverse global clinicians. © 2013 Wiley Periodicals, Inc.

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.

Primate immunodeficiency virus classification and nomenclature: Review

DOE PAGES

Foley, Brian T.; Leitner, Thomas; Paraskevis, Dimitrios; ...

2016-10-24

The International Committee for the Taxonomy and Nomenclature of Viruses does not rule on virus classifications below the species level. The definition of species for viruses cannot be clearly defined for all types of viruses. The complex and interesting epidemiology of Human Immunodeficiency Viruses demands a detailed and informative nomenclature system, while at the same time it presents challenges such that many of the rules need to be flexibly applied or modified over time. As a result, this review outlines the nomenclature system for primate lentiviruses and provides an update on new findings since the last review was written inmore » 2000.« less

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.

SCIRehab Project Series: The Therapeutic Recreation Taxonomy

PubMed Central

Cahow, Claire; Skolnick, Susan; Joyce, Joan; Jug, Julie; Dragon, Charlotte; Gassaway, Julie

2009-01-01

Background/Objective: Outcomes research of therapeutic recreation (TR) activities and interventions for spinal cord injury (SCI) rehabilitation is made more difficult by a lack of uniform descriptions and the absence of a formal treatments classification system (taxonomy). The objective of this study was to describe a taxonomy developed by Certified Therapeutic Recreation Specialists. Methods: TR lead clinicians and researchers from 6 SCI rehabilitation centers developed a TR documentation system to describe the details of each TR session involving patients with SCI enrolled in the SCIRehab study. The SCIRehab study uses the practice-based evidence methodology, a rigorous observational methodology that examines current practice without introducing additional treatments, to capture details of each TR session for 1,500 SCI rehabilitation patients at 6 US inpatient SCI rehabilitation facilities. This may be the first attempt to document the many details of the TR rehabilitation process for patients with SCI. Results: The TR taxonomy consists of 6 activities (eg, leisure education and counseling, outings, and leisure skill work in center) and activity-specific interventions, as well as time spent on each activity. Activity descriptions are enhanced with additional details that focus on assistance needs for each activity, patient ability to direct care, and patient/family involvement, which may help to determine TR activity selection. Conclusion: Development and application of a TR taxonomy, which is comprehensive for patients with SCI and efficient to use, are feasible despite significantly different TR programs at the 6 SCIRehab centers. PMID:19810631

A taxonomy-based approach to shed light on the babel of mathematical analogies for rice simulation

USDA-ARS?s Scientific Manuscript database

For most biophysical domains, different models are available and the extent to which their structures differ with respect to differences in outputs was never quantified. We use a taxonomy-based approach to address the question with thirteen rice models. Classification keys and binary attributes for ...

Acknowledging Different Needs: Developing a Taxonomy of Welfare Leavers.

ERIC Educational Resources Information Center

Julnes, George; Hayashi, Kentaro; Anderson, Steven

2001-01-01

Used cluster analysis of survey data for 506 respondents to create a taxonomy of welfare leavers in Illinois based on their self-reported well-being after leaving welfare. Used classification tree analysis to identify factors associated with different types of leavers. Findings highlight the existence of many marginally successful leavers who…

[book review] Systematics and Taxonomy of Australian Birds -- Les Christidis and Walter E. Boles. Collingwood, VIC, Australia: CSIRO Publishing, 2008

USGS Publications Warehouse

Chesser, R. Terry

2009-01-01

Systematists argue that the importance of our work lies not only in the elucidation of evolutionary relationships, but also in the incorporation of evolutionary information into classifications and the use of these classifications by government agencies, nongovernmental organizations, professional scientists, and others interested in biodiversity. If this is true, and I think that it is, then synthetic publications that make our findings accessible to a wide audience, such as Christidis and Boles' new Systematics and Taxonomy of Australian Birds, may be among the most significant works that we publish.

Classification of Instructional Programs: 2000 Edition.

ERIC Educational Resources Information Center

Education Statistics Quarterly, 2002

2002-01-01

Describes the methods, processes, and procedures used to develop the Classification of Instructional Programs 2000 (CIP:2000), the National Center for Education Statistics taxonomy of instructional programs, and provides information on the CIP's structure, contents, and organization. (SLD)

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.

The medication reconciliation process and classification of discrepancies: a systematic review.

PubMed

Almanasreh, Enas; Moles, Rebekah; Chen, Timothy F

2016-09-01

Medication reconciliation is a part of the medication management process and facilitates improved patient safety during care transitions. The aims of the study were to evaluate how medication reconciliation has been conducted and how medication discrepancies have been classified. We searched MEDLINE, EMBASE, CINAHL, PubMed, International Pharmaceutical Abstracts (IPA), and Web of Science (WOS), in accordance with the PRISMA statement up to April 2016. Studies were eligible for inclusion if they evaluated the types of medication discrepancy found through the medication reconciliation process and contained a classification system for discrepancies. Data were extracted by one author based on a predefined table, and 10% of included studies were verified by two authors. Ninety-five studies met the inclusion criteria. Approximately one-third of included studies (n = 35, 36.8%) utilized a 'gold' standard medication list. The majority of studies (n = 57, 60%) used an empirical classification system and the number of classification terms ranged from 2 to 50 terms. Whilst we identified three taxonomies, only eight studies utilized these tools to categorize discrepancies, and 11.6% of included studies used different patient safety related terms rather than discrepancy to describe the disagreement between the medication lists. We suggest that clear and consistent information on prevalence, types, causes and contributory factors of medication discrepancy are required to develop suitable strategies to reduce the risk of adverse consequences on patient safety. Therefore, to obtain that information, we need a well-designed taxonomy to be able to accurately measure, report and classify medication discrepancies in clinical practice. © 2016 The British Pharmacological Society.

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

How automated image analysis techniques help scientists in species identification and classification?

PubMed

Yousef Kalafi, Elham; Town, Christopher; Kaur Dhillon, Sarinder

2017-09-04

Identification of taxonomy at a specific level is time consuming and reliant upon expert ecologists. Hence the demand for automated species identification increased over the last two decades. Automation of data classification is primarily focussed on images, incorporating and analysing image data has recently become easier due to developments in computational technology. Research efforts in identification of species include specimens' image processing, extraction of identical features, followed by classifying them into correct categories. In this paper, we discuss recent automated species identification systems, categorizing and evaluating their methods. We reviewed and compared different methods in step by step scheme of automated identification and classification systems of species images. The selection of methods is influenced by many variables such as level of classification, number of training data and complexity of images. The aim of writing this paper is to provide researchers and scientists an extensive background study on work related to automated species identification, focusing on pattern recognition techniques in building such systems for biodiversity studies.

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

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).

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

FBIS: A regional DNA barcode archival & analysis system for Indian fishes

PubMed Central

Nagpure, Naresh Sahebrao; Rashid, Iliyas; Pathak, Ajey Kumar; Singh, Mahender; Singh, Shri Prakash; Sarkar, Uttam Kumar

2012-01-01

DNA barcode is a new tool for taxon recognition and classification of biological organisms based on sequence of a fragment of mitochondrial gene, cytochrome c oxidase I (COI). In view of the growing importance of the fish DNA barcoding for species identification, molecular taxonomy and fish diversity conservation, we developed a Fish Barcode Information System (FBIS) for Indian fishes, which will serve as a regional DNA barcode archival and analysis system. The database presently contains 2334 sequence records of COI gene for 472 aquatic species belonging to 39 orders and 136 families, collected from available published data sources. Additionally, it contains information on phenotype, distribution and IUCN Red List status of fishes. The web version of FBIS was designed using MySQL, Perl and PHP under Linux operating platform to (a) store and manage the acquisition (b) analyze and explore DNA barcode records (c) identify species and estimate genetic divergence. FBIS has also been integrated with appropriate tools for retrieving and viewing information about the database statistics and taxonomy. It is expected that FBIS would be useful as a potent information system in fish molecular taxonomy, phylogeny and genomics. Availability The database is available for free at http://mail.nbfgr.res.in/fbis/ PMID:22715304

A model for anomaly classification in intrusion detection systems

NASA Astrophysics Data System (ADS)

Ferreira, V. O.; Galhardi, V. V.; Gonçalves, L. B. L.; Silva, R. C.; Cansian, A. M.

2015-09-01

Intrusion Detection Systems (IDS) are traditionally divided into two types according to the detection methods they employ, namely (i) misuse detection and (ii) anomaly detection. Anomaly detection has been widely used and its main advantage is the ability to detect new attacks. However, the analysis of anomalies generated can become expensive, since they often have no clear information about the malicious events they represent. In this context, this paper presents a model for automated classification of alerts generated by an anomaly based IDS. The main goal is either the classification of the detected anomalies in well-defined taxonomies of attacks or to identify whether it is a false positive misclassified by the IDS. Some common attacks to computer networks were considered and we achieved important results that can equip security analysts with best resources for their analyses.

Molecular classification based on apomorphic amino acids (Arthropoda, Hexapoda): Integrative taxonomy in the era of phylogenomics.

PubMed

Wu, Hao-Yang; Wang, Yan-Hui; Xie, Qiang; Ke, Yun-Ling; Bu, Wen-Jun

2016-06-17

With the great development of sequencing technologies and systematic methods, our understanding of evolutionary relationships at deeper levels within the tree of life has greatly improved over the last decade. However, the current taxonomic methodology is insufficient to describe the growing levels of diversity in both a standardised and general way due to the limitations of using only morphological traits to describe clades. Herein, we propose the idea of a molecular classification based on hierarchical and discrete amino acid characters. Clades are classified based on the results of phylogenetic analyses and described using amino acids with group specificity in phylograms. Practices based on the recently published phylogenomic datasets of insects together with 15 de novo sequenced transcriptomes in this study demonstrate that such a methodology can accommodate various higher ranks of taxonomy. Such an approach has the advantage of describing organisms in a standard and discrete way within a phylogenetic framework, thereby facilitating the recognition of clades from the view of the whole lineage, as indicated by PhyloCode. By combining identification keys and phylogenies, the molecular classification based on hierarchical and discrete characters may greatly boost the progress of integrative taxonomy.

Molecular classification based on apomorphic amino acids (Arthropoda, Hexapoda): Integrative taxonomy in the era of phylogenomics

PubMed Central

Wu, Hao-Yang; Wang, Yan-Hui; Xie, Qiang; Ke, Yun-Ling; Bu, Wen-Jun

2016-01-01

With the great development of sequencing technologies and systematic methods, our understanding of evolutionary relationships at deeper levels within the tree of life has greatly improved over the last decade. However, the current taxonomic methodology is insufficient to describe the growing levels of diversity in both a standardised and general way due to the limitations of using only morphological traits to describe clades. Herein, we propose the idea of a molecular classification based on hierarchical and discrete amino acid characters. Clades are classified based on the results of phylogenetic analyses and described using amino acids with group specificity in phylograms. Practices based on the recently published phylogenomic datasets of insects together with 15 de novo sequenced transcriptomes in this study demonstrate that such a methodology can accommodate various higher ranks of taxonomy. Such an approach has the advantage of describing organisms in a standard and discrete way within a phylogenetic framework, thereby facilitating the recognition of clades from the view of the whole lineage, as indicated by PhyloCode. By combining identification keys and phylogenies, the molecular classification based on hierarchical and discrete characters may greatly boost the progress of integrative taxonomy. PMID:27312960

[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.

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

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.

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.

Impact of public health emergencies on modern disaster taxonomy, planning, and response.

PubMed

Burkle, Frederick M; Greenough, P Gregg

2008-10-01

Current disaster taxonomy describes diversity, distinguishing characteristics, and common relations in disaster event classifications. The impact of compromised public health infrastructure and systems on health consequences defines and greatly influences the manner in which disasters are observed, planned for, and managed, especially those that are geographically widespread, population dense, and prolonged. What may first result in direct injuries and death may rapidly change to excess indirect illness and subsequent death as essential public health resources are destroyed, deteriorate, or are systematically denied to vulnerable populations. Public health and public health infrastructure and systems in developed and developing countries must be seen as strategic and security issues that deserve international public health resource monitoring attention from disaster managers, urban planners, the global humanitarian community, World Health Organization authorities, and participating parties to war and conflict. We posit here that disaster frameworks be reformed to emphasize and clarify the relation of public health emergencies and modern disasters.

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.

Making US Soil Taxonomy more scientifically applicable to environmental and food security issues.

NASA Astrophysics Data System (ADS)

Monger, Curtis; Lindbo, David L.; Wysocki, Doug; Schoeneberger, Phil; Libohova, Zamir

2017-04-01

US Department of Agriculture began mapping soils in the 1890s on a county-by-county basis until most of the conterminous United States was mapped by the late 1930s. This first-generation mapping was followed by a second-generation that re-mapped the US beginning in the 1940s. Soil classification during these periods evolved into the current system of Soil Taxonomy which is based on (1) soil features as natural phenomena and on (2) soil properties important for agriculture and other land uses. While this system has enabled communication among soil surveyors, the scientific applicability of Soil Taxonomy to address environmental and food security issues has been under-utilized. In particular, little effort has been exerted to understand how soil taxa interact and function together as larger units—as soil systems. Thus, much soil-geomorphic understanding that could be applied to process-based modeling remains unexploited. The challenge for soil taxonomists in the United States and elsewhere is to expand their expertise and work with modelers to explore how soil taxa are linked to each other, how they influence water, nutrient, and pollutant flow through the landscape, how they interact with ecology, and how they change with human land use.

Consensus statement: Virus taxonomy in the age of metagenomics.

PubMed

Simmonds, Peter; Adams, Mike J; Benkő, Mária; Breitbart, Mya; Brister, J Rodney; Carstens, Eric B; Davison, Andrew J; Delwart, Eric; Gorbalenya, Alexander E; Harrach, Balázs; Hull, Roger; King, Andrew M Q; Koonin, Eugene V; Krupovic, Mart; Kuhn, Jens H; Lefkowitz, Elliot J; Nibert, Max L; Orton, Richard; Roossinck, Marilyn J; Sabanadzovic, Sead; Sullivan, Matthew B; Suttle, Curtis A; Tesh, Robert B; van der Vlugt, René A; Varsani, Arvind; Zerbini, F Murilo

2017-03-01

The number and diversity of viral sequences that are identified in metagenomic data far exceeds that of experimentally characterized virus isolates. In a recent workshop, a panel of experts discussed the proposal that, with appropriate quality control, viruses that are known only from metagenomic data can, and should be, incorporated into the official classification scheme of the International Committee on Taxonomy of Viruses (ICTV). Although a taxonomy that is based on metagenomic sequence data alone represents a substantial departure from the traditional reliance on phenotypic properties, the development of a robust framework for sequence-based virus taxonomy is indispensable for the comprehensive characterization of the global virome. In this Consensus Statement article, we consider the rationale for why metagenomic sequence data should, and how it can, be incorporated into the ICTV taxonomy, and present proposals that have been endorsed by the Executive Committee of the ICTV.

IFIP Conference on System Modeling and Optimization (10th). Held at New York City, New York on 31 August-4 September 1981.

DTIC Science & Technology

1982-01-15

Systems U. HEILEVANN, Cyclical Taxonomy and Large Econometic Models D. HINRICHSEN, U. KRAUSE , Triangulation of Convex Polyhedra with an Application to...Classification of Economic Fluctua- tions, "Explorations in Economic Research", vol.2 (1975), pp. 167-2o2. -196- D. Hinrich3en and U. Krause Department...d’opti- misation de structures, Those de doctuer ingenieur, Universit6 de Paris VI, 1976. -211- - *. ____________________ -__-____- Wolfgang Nooss

Implementation of standardized nomenclature in the electronic medical record.

PubMed

Klehr, Joan; Hafner, Jennifer; Spelz, Leah Mylrea; Steen, Sara; Weaver, Kathy

2009-01-01

To describe a customized electronic medical record documentation system which provides an electronic health record, Epic, which was implemented in December 2006 using standardized taxonomies for nursing documentation. Descriptive data is provided regarding the development, implementation, and evaluation processes for the electronic medical record system. Nurses used standardized nursing nomenclature including NANDA-I diagnoses, Nursing Interventions Classification, and Nursing Outcomes Classification in a measurable and user-friendly format using the care plan activity. Key factors in the success of the project included close collaboration among staff nurses and information technology staff, ongoing support and encouragement from the vice president/chief nursing officer, the ready availability of expert resources, and nursing ownership of the project. Use of this evidence-based documentation enhanced institutional leadership in clinical documentation.

Next-Generation Botnet Detection and Response

DTIC Science & Technology

2008-06-24

REPORT Final Report of "Next-Generation Botnet Detection and Response" 14. ABSTRACT 16. SECURITY CLASSIFICATION OF: In this project, we developed...and Wenke Lee. ?In Proceedings of The 13th Annual Network and Distributed System Security Symposium (NDSS 2006), San Diego, CA, February 2006. 2...In Proceedings of The 16th USENIX Security Symposium ( Security 󈧋), Boston, MA, August 2007. 3. A Taxonomy of Botnet Structures. ?David Dagon, Guofei

Cross-mapping the ICNP with NANDA, HHCC, Omaha System and NIC for unified nursing language system development. International Classification for Nursing Practice. International Council of Nurses. North American Nursing Diagnosis Association. Home Health Care Classification. Nursing Interventions Classification.

PubMed

Hyun, S; Park, H A

2002-06-01

Nursing language plays an important role in describing and defining nursing phenomena and nursing actions. There are numerous vocabularies describing nursing diagnoses, interventions and outcomes in nursing. However, the lack of a standardized unified nursing language is considered a problem for further development of the discipline of nursing. In an effort to unify the nursing languages, the International Council of Nurses (ICN) has proposed the International Classification for Nursing Practice (ICNP) as a unified nursing language system. The purpose of this study was to evaluate the inclusiveness and expressiveness of the ICNP terms by cross-mapping them with the existing nursing terminologies, specifically the North American Nursing Diagnosis Association (NANDA) taxonomy I, the Omaha System, the Home Health Care Classification (HHCC) and the Nursing Interventions Classification (NIC). Nine hundred and seventy-four terms from these four classifications were cross-mapped with the ICNP terms. This was performed in accordance with the Guidelines for Composing a Nursing Diagnosis and Guidelines for Composing a Nursing Intervention, which were suggested by the ICNP development team. An expert group verified the results. The ICNP Phenomena Classification described 87.5% of the NANDA diagnoses, 89.7% of the HHCC diagnoses and 72.7% of the Omaha System problem classification scheme. The ICNP Action Classification described 79.4% of the NIC interventions, 80.6% of the HHCC interventions and 71.4% of the Omaha System intervention scheme. The results of this study suggest that the ICNP has a sound starting structure for a unified nursing language system and can be used to describe most of the existing terminologies. Recommendations for the addition of terms to the ICNP are provided.

Bunyavirus Taxonomy: Limitations and Misconceptions Associated with the Current ICTV Criteria Used for Species Demarcation.

PubMed

Blitvich, Bradley J; Beaty, Barry J; Blair, Carol D; Brault, Aaron C; Dobler, Gerhard; Drebot, Michael A; Haddow, Andrew D; Kramer, Laura D; LaBeaud, Angelle Desiree; Monath, Thomas P; Mossel, Eric C; Plante, Kenneth; Powers, Ann M; Tesh, Robert B; Turell, Michael J; Vasilakis, Nikos; Weaver, Scott C

2018-04-23

The International Committee on Taxonomy of Viruses (ICTV) has implemented numerous changes to the taxonomic classification of bunyaviruses over the years. Whereas most changes have been justified and necessary because of the need to accommodate newly discovered and unclassified viruses, other changes are a cause of concern, especially the decision to demote scores of formerly recognized species to essentially strains of newly designated species. This practice was first described in the seventh taxonomy report of the ICTV and has continued in all subsequent reports. In some instances, viruses that share less than 75% nucleotide sequence identity across their genomes produce vastly different clinical presentations, possess distinct vector and host associations, have different biosafety recommendations, and occur in nonoverlapping geographic regions are classified as strains of the same species. Complicating the matter is the fact that virus strains have been completely eliminated from ICTV reports; thus, critically important information on virus identities and their associated biological and epidemiological features cannot be readily related to the ICTV classification. Here, we summarize the current status of bunyavirus taxonomy and discuss the adverse consequences associated with the reclassification and resulting omission of numerous viruses of public health importance from ICTV reports. As members of the American Committee on Arthropod-borne Viruses, we encourage the ICTV Bunyavirus Study Group to reconsider their stance on bunyavirus taxonomy, to revise the criteria currently used for species demarcation, and to list additional strains of public and veterinary importance.

Current and future perspectives on the systematics, taxonomy and nomenclature of testate amoebae.

PubMed

Kosakyan, Anush; Gomaa, Fatma; Lara, Enrique; Lahr, Daniel J G

2016-09-01

Testate amoebae are a polyphyletic assemblage of at least three major, unrelated taxonomic groups of unicellular amoeboid eukaryotes exhibiting a test. The focus on testate amoebae in scientific research has greatly increased in the past 20 years: from an average of about 5 papers a year in the mid-1990s to the current rate of more than 50 papers published yearly. The application range of these organisms is rapidly expanding as well: from the traditional fields of environmental monitoring and paleoecology, to forensic sciences and ecotoxicology studies. These developments are nevertheless strongly dependent on reliable taxonomy and nomenclature. However, scientometric data reveal that despite an ever-increasing necessity for the use of names (the product of taxonomy), the corresponding effort has not been achieved for improving testate amoebae systematics. As a consequence, inaccurate taxonomy yields to misinterpretations in the diversity of the organisms and to potentially incorrect conclusions. These and related problems are discussed in this study, highlighting the outcome of poor taxonomic expertise in accurate classification and phylogeny of testate amoebae, and the consequences derived from it. Additionally, this study is aimed to discuss the current status of testate amoebae classification, and to present all nomenclature and taxonomic changes in higher and lower taxonomic levels of testate amoebae, as a result of recent molecular reconstructions. Finally, we conclude with a list of the needs and suggestions toward a unified and modernized taxonomy of testate amoebae. Copyright © 2016 Elsevier GmbH. All rights reserved.

The application of Aronson's taxonomy to medication errors in nursing.

PubMed

Johnson, Maree; Young, Helen

2011-01-01

Medication administration is a frequent nursing activity that is prone to error. In this study of 318 self-reported medication incidents (including near misses), very few resulted in patient harm-7% required intervention or prolonged hospitalization or caused temporary harm. Aronson's classification system provided an excellent framework for analysis of the incidents with a close connection between the type of error and the change strategy to minimize medication incidents. Taking a behavioral approach to medication error classification has provided helpful strategies for nurses such as nurse-call cards on patient lockers when patients are absent and checking of medication sign-off by outgoing and incoming staff at handover.

Development of a taxonomy for pharmaceutical interventions in HIV+ patients based on the CMO model.

PubMed

Morillo Verdugo, Ramón; Villarreal Arevalo, Andrea Lisbeth; Alvarez De Sotomayor, Maria; Robustillo Cortes, Maria de Las Aguas

2016-11-01

To agree on a proposal for pharmaceutical interventions and establish their classification taxonomy according to the CMO-Pharmaceutical Care Model (Capacity-Motivation- Opportunity). A study conducted between March and May, 2016. Two phases of development were defined. A literature review was initially conducted. Then, the DELPHI-Rand-UCLA methodology was used in order to reach a consensus about those interventions selected, and to define the taxonomy. Fifteen (15) experts, specialists in Pharmaceutical Care for HIV+ patients, were selected. This selection was explicitly conducted, following a protocol in order to avoid any bias. An initial proposal was developed according to the interventions extracted from Phase 1. These were tentatively classified according to the CMO Model, in a category based on their design and utility. Three issues were raised from the initial question: Do you agree with the proposed classification? If not, there was an option to re-categorize. Additionally, they were asked about the importance, priority and impact to achieve pharmacotherapeutic objectives that they would assign to it. Interventions were classified according to the degree of agreement. Once a consensus was reached, the final taxonomy was established. Eighteen (18) articles were finally considered. The initial proposal included 20 pharmaceutical interventions with the following classification: seven in Capacity, eight in Motivation, and five in Opportunity. Those interventions considered to have greater importance and priority were: Review and Validation, Safety, and Adherence. The interventions with the greatest impact were: Review and Validation, Coordination, Adherence, and Motivation. On the other hand, the lowest scores for importance were for: Planning and Social Coordination; and in terms of impact: Social Coordination. The taxonomy reached by consensus will allow to classify pharmaceutical interventions with the new model, and therefore to conduct an improved research and patient care. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

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.

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.

Studying Upper-Limb Amputee Prosthesis Use to Inform Device Design

DTIC Science & Technology

2016-10-01

study of the resulting videos led to a new prosthetics-use taxonomy that is generalizable to various levels of amputation and terminal devices. The...taxonomy was applied to classification of the recorded videos via custom tagging software with midi controller interface. The software creates...a motion capture studio and video cameras to record accurate and detailed upper body motion during a series of standardized tasks. These tasks are

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

Thermophilic fungi in the new age of fungal taxonomy.

PubMed

de Oliveira, Tássio Brito; Gomes, Eleni; Rodrigues, Andre

2015-01-01

Thermophilic fungi are of wide interest due to their potential to produce heat-tolerant enzymes for biotechnological processes. However, the taxonomy of such organisms remains obscure, especially given new developments in the nomenclature of fungi. Here, we examine the taxonomy of the thermophilic fungi most commonly used in industry in light of the recent taxonomic changes following the adoption of the International Code of Nomenclature for Algae, Fungi and Plants and also based on the movement One Fungus = One Name. Despite the widespread use of these fungi in applied research, several thermotolerant fungi still remain classified as thermophiles. Furthermore, we found that while some thermophilic fungi have had their genomes sequenced, many taxa still do not have barcode sequences of reference strains available in public databases. This lack of basic information is a limiting factor for the species identification of thermophilic fungi and for metagenomic studies in this field. Based on next-generation sequencing, such studies generate large amounts of data, which may reveal new species of thermophilic fungi in different substrates (composting systems, geothermal areas, piles of plant material). As discussed in this study, there are intrinsic problems associated with this method, considering the actual state of the taxonomy of thermophilic fungi. To overcome such difficulties, the taxonomic classification of this group should move towards standardizing the commonly used species names in industry and to assess the possibility of including new systems for describing species based on environmental sequences.

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

Telemedicine for Developing Countries. A Survey and Some Design Issues.

PubMed

Combi, Carlo; Pozzani, Gabriele; Pozzi, Giuseppe

2016-11-02

Developing countries need telemedicine applications that help in many situations, when physicians are a small number with respect to the population, when specialized physicians are not available, when patients and physicians in rural villages need assistance in the delivery of health care. Moreover, the requirements of telemedicine applications for developing countries are somewhat more demanding than for developed countries. Indeed, further social, organizational, and technical aspects need to be considered for successful telemedicine applications in developing countries. We consider all the major projects in telemedicine, devoted to developing countries, as described by the proper scientific literature. On the basis of such literature, we want to define a specific taxonomy that allows a proper classification and a fast overview of telemedicine projects in developing countries. Moreover, by considering both the literature and some recent direct experiences, we want to complete such overview by discussing some design issues to be taken into consideration when developing telemedicine software systems. We considered and reviewed the major conferences and journals in depth, and looked for reports on the telemedicine projects. We provide the reader with a survey of the main projects and systems, from which we derived a taxonomy of features of telemedicine systems for developing countries. We also propose and discuss some classification criteria for design issues, based on the lessons learned in this research area. We highlight some challenges and recommendations to be considered when designing a telemedicine system for developing countries.

Telemedicine for Developing Countries

PubMed Central

Combi, Carlo; Pozzani, Gabriele

2016-01-01

Summary Background Developing countries need telemedicine applications that help in many situations, when physicians are a small number with respect to the population, when specialized physicians are not available, when patients and physicians in rural villages need assistance in the delivery of health care. Moreover, the requirements of telemedicine applications for developing countries are somewhat more demanding than for developed countries. Indeed, further social, organizational, and technical aspects need to be considered for successful telemedicine applications in developing countries. Objective We consider all the major projects in telemedicine, devoted to developing countries, as described by the proper scientific literature. On the basis of such literature, we want to define a specific taxonomy that allows a proper classification and a fast overview of telemedicine projects in developing countries. Moreover, by considering both the literature and some recent direct experiences, we want to complete such overview by discussing some design issues to be taken into consideration when developing telemedicine software systems. Methods We considered and reviewed the major conferences and journals in depth, and looked for reports on the telemedicine projects. Results We provide the reader with a survey of the main projects and systems, from which we derived a taxonomy of features of telemedicine systems for developing countries. We also propose and discuss some classification criteria for design issues, based on the lessons learned in this research area. Conclusions We highlight some challenges and recommendations to be considered when designing a telemedicine system for developing countries. PMID:27803948

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

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

The new higher level classification of eukaryotes with emphasis on the taxonomy of protists.

PubMed

Adl, Sina M; Simpson, Alastair G B; Farmer, Mark A; Andersen, Robert A; Anderson, O Roger; Barta, John R; Bowser, Samuel S; Brugerolle, Guy; Fensome, Robert A; Fredericq, Suzanne; James, Timothy Y; Karpov, Sergei; Kugrens, Paul; Krug, John; Lane, Christopher E; Lewis, Louise A; Lodge, Jean; Lynn, Denis H; Mann, David G; McCourt, Richard M; Mendoza, Leonel; Moestrup, Ojvind; Mozley-Standridge, Sharon E; Nerad, Thomas A; Shearer, Carol A; Smirnov, Alexey V; Spiegel, Frederick W; Taylor, Max F J R

2005-01-01

This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists. Whereas the previous revision was primarily to incorporate the results of ultrastructural studies, this revision incorporates results from both ultrastructural research since 1980 and molecular phylogenetic studies. We propose a scheme that is based on nameless ranked systematics. The vocabulary of the taxonomy is updated, particularly to clarify the naming of groups that have been repositioned. We recognize six clusters of eukaryotes that may represent the basic groupings similar to traditional "kingdoms." The multicellular lineages emerged from within monophyletic protist lineages: animals and fungi from Opisthokonta, plants from Archaeplastida, and brown algae from Stramenopiles.

"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

A new taxonomic classification for species in Gomphus sensu lato

Treesearch

Admir J. Giachini; Michael A. Castellano

2011-01-01

Taxonomy of the Gomphales has been revisited by combining morphology and molecular data (DNA sequences) to provide a natural classification for the species of Gomphus sensu lato. Results indicate Gomphus s.l. to be non-monophyletic, leading to new combinations and the placement of its species into four genera: Gomphus...

The Development of a Taxonomy of the Life Skills Required to Become a Balanced Self-Determined Person = Essaie de Classification des Competences Necessaires pour Devenir une Personne Autonome et Bien Equilibree.

ERIC Educational Resources Information Center

Smith, Paul

Intended for use by life skills coaches and students, program evaluators, and individuals developing lesson plans and other training materials, this taxonomy includes all of the terminal performance behaviors and corresponding sub-skills required to become and function as a balanced, self-determined person who manages the problems of everyday life…

Toward automated classification of consumers' cancer-related questions with a new taxonomy of expected answer types.

PubMed

McRoy, Susan; Jones, Sean; Kurmally, Adam

2016-09-01

This article examines methods for automated question classification applied to cancer-related questions that people have asked on the web. This work is part of a broader effort to provide automated question answering for health education. We created a new corpus of consumer-health questions related to cancer and a new taxonomy for those questions. We then compared the effectiveness of different statistical methods for developing classifiers, including weighted classification and resampling. Basic methods for building classifiers were limited by the high variability in the natural distribution of questions and typical refinement approaches of feature selection and merging categories achieved only small improvements to classifier accuracy. Best performance was achieved using weighted classification and resampling methods, the latter yielding an accuracy of F1 = 0.963. Thus, it would appear that statistical classifiers can be trained on natural data, but only if natural distributions of classes are smoothed. Such classifiers would be useful for automated question answering, for enriching web-based content, or assisting clinical professionals to answer questions. © The Author(s) 2015.

Taxonomy of rare genetic metabolic bone disorders.

PubMed

Masi, L; Agnusdei, D; Bilezikian, J; Chappard, D; Chapurlat, R; Cianferotti, L; Devolgelaer, J-P; El Maghraoui, A; Ferrari, S; Javaid, M K; Kaufman, J-M; Liberman, U A; Lyritis, G; Miller, P; Napoli, N; Roldan, E; Papapoulos, S; Watts, N B; Brandi, M L

2015-10-01

This article reports a taxonomic classification of rare skeletal diseases based on metabolic phenotypes. It was prepared by The Skeletal Rare Diseases Working Group of the International Osteoporosis Foundation (IOF) and includes 116 OMIM phenotypes with 86 affected genes. Rare skeletal metabolic diseases comprise a group of diseases commonly associated with severe clinical consequences. In recent years, the description of the clinical phenotypes and radiographic features of several genetic bone disorders was paralleled by the discovery of key molecular pathways involved in the regulation of bone and mineral metabolism. Including this information in the description and classification of rare skeletal diseases may improve the recognition and management of affected patients. IOF recognized this need and formed a Skeletal Rare Diseases Working Group (SRD-WG) of basic and clinical scientists who developed a taxonomy of rare skeletal diseases based on their metabolic pathogenesis. This taxonomy of rare genetic metabolic bone disorders (RGMBDs) comprises 116 OMIM phenotypes, with 86 affected genes related to bone and mineral homeostasis. The diseases were divided into four major groups, namely, disorders due to altered osteoclast, osteoblast, or osteocyte activity; disorders due to altered bone matrix proteins; disorders due to altered bone microenvironmental regulators; and disorders due to deranged calciotropic hormonal activity. This article provides the first comprehensive taxonomy of rare metabolic skeletal diseases based on deranged metabolic activity. This classification will help in the development of common and shared diagnostic and therapeutic pathways for these patients and also in the creation of international registries of rare skeletal diseases, the first step for the development of genetic tests based on next generation sequencing and for performing large intervention trials to assess efficacy of orphan drugs.

PANDORA: keyword-based analysis of protein sets by integration of annotation sources.

PubMed

Kaplan, Noam; Vaaknin, Avishay; Linial, Michal

2003-10-01

Recent advances in high-throughput methods and the application of computational tools for automatic classification of proteins have made it possible to carry out large-scale proteomic analyses. Biological analysis and interpretation of sets of proteins is a time-consuming undertaking carried out manually by experts. We have developed PANDORA (Protein ANnotation Diagram ORiented Analysis), a web-based tool that provides an automatic representation of the biological knowledge associated with any set of proteins. PANDORA uses a unique approach of keyword-based graphical analysis that focuses on detecting subsets of proteins that share unique biological properties and the intersections of such sets. PANDORA currently supports SwissProt keywords, NCBI Taxonomy, InterPro entries and the hierarchical classification terms from ENZYME, SCOP and GO databases. The integrated study of several annotation sources simultaneously allows a representation of biological relations of structure, function, cellular location, taxonomy, domains and motifs. PANDORA is also integrated into the ProtoNet system, thus allowing testing thousands of automatically generated clusters. We illustrate how PANDORA enhances the biological understanding of large, non-uniform sets of proteins originating from experimental and computational sources, without the need for prior biological knowledge on individual proteins.

The developmental processes for NANDA International Nursing Diagnoses.

PubMed

Scroggins, Leann M

2008-01-01

This study aims to provide a step-by-step procedural guideline for the development of a nursing diagnosis that meets the necessary criteria for inclusion in the NANDA International and NNN classification systems. The guideline is based on the processes developed by the Diagnosis Development Committee of NANDA International and includes the necessary processes for development of Actual, Wellness, Health Promotion, and Risk nursing diagnoses. Definitions of Actual, Wellness, Health Promotion, and Risk nursing diagnoses along with inclusion criteria and taxonomy rules have been incorporated into the guideline to streamline the development and review processes for submitted diagnoses. A step-by-step procedural guideline will assist the submitter to move efficiently and effectively through the submission process, resulting in increased submissions and enhancement of the NANDA International and NNN classification systems.

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin.

PubMed

Bokulich, Nicholas A; Kaehler, Benjamin D; Rideout, Jai Ram; Dillon, Matthew; Bolyen, Evan; Knight, Rob; Huttley, Gavin A; Gregory Caporaso, J

2018-05-17

Taxonomic classification of marker-gene sequences is an important step in microbiome analysis. We present q2-feature-classifier ( https://github.com/qiime2/q2-feature-classifier ), a QIIME 2 plugin containing several novel machine-learning and alignment-based methods for taxonomy classification. We evaluated and optimized several commonly used classification methods implemented in QIIME 1 (RDP, BLAST, UCLUST, and SortMeRNA) and several new methods implemented in QIIME 2 (a scikit-learn naive Bayes machine-learning classifier, and alignment-based taxonomy consensus methods based on VSEARCH, and BLAST+) for classification of bacterial 16S rRNA and fungal ITS marker-gene amplicon sequence data. The naive-Bayes, BLAST+-based, and VSEARCH-based classifiers implemented in QIIME 2 meet or exceed the species-level accuracy of other commonly used methods designed for classification of marker gene sequences that were evaluated in this work. These evaluations, based on 19 mock communities and error-free sequence simulations, including classification of simulated "novel" marker-gene sequences, are available in our extensible benchmarking framework, tax-credit ( https://github.com/caporaso-lab/tax-credit-data ). Our results illustrate the importance of parameter tuning for optimizing classifier performance, and we make recommendations regarding parameter choices for these classifiers under a range of standard operating conditions. q2-feature-classifier and tax-credit are both free, open-source, BSD-licensed packages available on GitHub.

Taxonomy of the extrasolar planet.

PubMed

Plávalová, Eva

2012-04-01

When a star is described as a spectral class G2V, we know that the star is similar to our Sun. We know its approximate mass, temperature, age, and size. When working with an extrasolar planet database, it is very useful to have a taxonomy scale (classification) such as, for example, the Harvard classification for stars. The taxonomy has to be easily interpreted and present the most relevant information about extrasolar planets. I propose an extrasolar planet taxonomy scale with four parameters. The first parameter concerns the mass of an extrasolar planet in the form of units of the mass of other known planets, where M represents the mass of Mercury, E that of Earth, N Neptune, and J Jupiter. The second parameter is the planet's distance from its parent star (semimajor axis) described in a logarithm with base 10. The third parameter is the mean Dyson temperature of the extrasolar planet, for which I established four main temperature classes: F represents the Freezing class, W the Water class, G the Gaseous class, and R the Roasters class. I devised one additional class, however: P, the Pulsar class, which concerns extrasolar planets orbiting pulsar stars. The fourth parameter is eccentricity. If the attributes of the surface of the extrasolar planet are known, we are able to establish this additional parameter where t represents a terrestrial planet, g a gaseous planet, and i an ice planet. According to this taxonomy scale, for example, Earth is 1E0W0t, Neptune is 1N1.5F0i, and extrasolar planet 55 Cnc e is 9E-1.8R1.

Chapter II. Taxonomy and Phylogeny

USDA-ARS?s Scientific Manuscript database

The book chapter presents a review of the taxonomic distribution of ornamental geophytic plants (bulbs, tubers, corms, rhizomes) and the modern classification of the families within which they belong....

Nursing interventions for rehabilitation in Parkinson's disease: cross mapping of terms

PubMed Central

Tosin, Michelle Hyczy de Siqueira; Campos, Débora Moraes; de Andrade, Leonardo Tadeu; de Oliveira, Beatriz Guitton Renaud Baptista; Santana, Rosimere Ferreira

2016-01-01

ABSTRACT Objective: to perform a cross-term mapping of nursing language in the patient record with the Nursing Interventions Classification system, in rehabilitation patients with Parkinson's disease. Method: a documentary research study to perform cross mapping. A probabilistic, simple random sample composed of 67 records of patients with Parkinson's disease who participated in a rehabilitation program, between March of 2009 and April of 2013. The research was conducted in three stages, in which the nursing terms were mapped to natural language and crossed with the Nursing Interventions Classification. Results: a total of 1,077 standard interventions that, after crossing with the taxonomy and refinement performed by the experts, resulted in 32 interventions equivalent to the Nursing Interventions Classification (NIC) system. The NICs, "Education: The process of the disease.", "Contract with the patient", and "Facilitation of Learning" were present in 100% of the records. For these interventions, 40 activities were described, representing 13 activities by intervention. Conclusion: the cross mapping allowed for the identification of corresponding terms with the nursing interventions used every day in rehabilitation nursing, and compared them to the Nursing Interventions Classification. PMID:27508903

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.

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 New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists

Treesearch

SINA M. ADL; ALASTAIR G. B. SIMPSON; MARK A. FARMER; ROBERT A. ANDERSEN; O. ROGER ANDERSON; JOHN R. BARTA; SAMUEL S. BOWSER; GUY BRUGEROLLE; ROBERT A. FENSOME; SUZANNE FREDERICQ; TIMOTHY Y. JAMES; SERGEI KARPOV; PAUL KUGRENS; JOHN KRUG; CHRISTOPHER E. LANE; LOUISE A. LEWIS; JEAN LODGE; DENIS H. LYNN; DAVID G. MANN; RICHARD M. MCCOURT; LEONEL MENDOZA; ØJVIND MOESTRUP; SHARON E. MOZLEY-STANDRIDGE; THOMAS A. NERAD; CAROL A. SHEARER; ALEXEY V. SMIRNOV; FREDERICK W. SPIEGEL; MAX F.J.R. TAYLOR

2005-01-01

This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists. Whereas the previous revision was primarily to incorporate the results of ultrastructural studies, this revision incorporates results from both ultrastructural research since 1980 and molecular phylogenetic...

The new higher level classification of eukaryotes with emphasis on the taxonomy of protists

Treesearch

Sina M. Adl; Alastair G.B. Simpson; Mark A. Farmer; Robert A. Andersen; O. Roger Anderson; John R. Barta; Samuel S. Bowser; Guy Brugerolle; Robert A. Fensome; Suzanne Fredericq; Timothy Y. James; Sergei Karpov; Paul Kugrens; John Krug; Christopher E. Lane; Louise A. Lewis; Jean Lodge; Denis H. Lynn; David G. Mann; Richard M. McCourt; Leonel Mendoza; Ojvind Moestrup; Sharon E. Mozley-Standridge; Thomas A. Nerad; Carol A. Shearer; Alexey V. Smirnov; Frederick W. Speigel; Max F.J.R. Taylor

2005-01-01

This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists. Whereas the previous revision was primarily to incorporate the results of ultrastructural studies, this revision incorporates results from both ultrastructural research since 1980 and molecular phylogenetic...

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.

Classifying orofacial pains: a new proposal of taxonomy based on ontology

PubMed Central

NIXDORF, D. R.; DRANGSHOLT, M. T.; ETTLIN, D. A.; GAUL, C.; DE LEEUW, R.; SVENSSON, P.; ZAKRZEWSKA, J. M.; DE LAAT, A.; CEUSTERS, W.

2012-01-01

SUMMARY Propose a new taxonomy model based on ontological principles for disorders that manifest themselves through the symptom of persistent orofacial pain and are commonly seen in clinical practice and difficult to manage. Consensus meeting of eight experts from various geographic areas representing different perspectives (orofacial pain, headache, oral medicine and ontology) as an initial step towards improving the taxonomy. Ontological principles were introduced, reviewed and applied during the consensus building process. Diagnostic criteria for persistent dento-alveolar pain disorder (PDAP) were formulated as an example to be used to model the taxonomical structure of all orofacial pain conditions. These criteria have the advantage of being (i) anatomically defined, (ii) in accordance with other classification systems for the provision of clinical care, (iii) descriptive and succinct, (iv) easy to adapt for applications in varying settings, (v) scalable and (vi) transferable for the description of pain disorders in other orofacial regions of interest. Limitations are that the criteria introduce new terminology, do not have widespread acceptance and have yet to be tested. These results were presented to the greater conference membership and were unanimously accepted. Consensus for the diagnostic criteria of PDAP was established within this working group. This is an initial first step towards developing a coherent taxonomy for orofacial pain disorders, which is needed to improve clinical research and care. PMID:21848527

Classifying orofacial pains: a new proposal of taxonomy based on ontology.

PubMed

Nixdorf, D R; Drangsholt, M T; Ettlin, D A; Gaul, C; De Leeuw, R; Svensson, P; Zakrzewska, J M; De Laat, A; Ceusters, W

2012-03-01

We propose a new taxonomy model based on ontological principles for disorders that manifest themselves through the symptom of persistent orofacial pain and are commonly seen in clinical practice and difficult to manage. Consensus meeting of eight experts from various geographic areas representing different perspectives (orofacial pain, headache, oral medicine and ontology) as an initial step towards improving the taxonomy. Ontological principles were introduced, reviewed and applied during the consensus building process. Diagnostic criteria for persistent dento-alveolar pain disorder (PDAP) were formulated as an example to be used to model the taxonomical structure of all orofacial pain conditions. These criteria have the advantage of being (i) anatomically defined, (ii) in accordance with other classification systems for the provision of clinical care, (iii) descriptive and succinct, (iv) easy to adapt for applications in varying settings, (v) scalable and (vi) transferable for the description of pain disorders in other orofacial regions of interest. Limitations are that the criteria introduce new terminology, do not have widespread acceptance and have yet to be tested. These results were presented to the greater conference membership and were unanimously accepted. Consensus for the diagnostic criteria of PDAP was established within this working group. This is an initial first step towards developing a coherent taxonomy for orofacial pain disorders, which is needed to improve clinical research and care. © 2011 Blackwell Publishing Ltd.

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.

Conscientious Classification: A Data Scientist's Guide to Discrimination-Aware Classification.

PubMed

d'Alessandro, Brian; O'Neil, Cathy; LaGatta, Tom

2017-06-01

Recent research has helped to cultivate growing awareness that machine-learning systems fueled by big data can create or exacerbate troubling disparities in society. Much of this research comes from outside of the practicing data science community, leaving its members with little concrete guidance to proactively address these concerns. This article introduces issues of discrimination to the data science community on its own terms. In it, we tour the familiar data-mining process while providing a taxonomy of common practices that have the potential to produce unintended discrimination. We also survey how discrimination is commonly measured, and suggest how familiar development processes can be augmented to mitigate systems' discriminatory potential. We advocate that data scientists should be intentional about modeling and reducing discriminatory outcomes. Without doing so, their efforts will result in perpetuating any systemic discrimination that may exist, but under a misleading veil of data-driven objectivity.

Development and validation of Aviation Causal Contributors for Error Reporting Systems (ACCERS).

PubMed

Baker, David P; Krokos, Kelley J

2007-04-01

This investigation sought to develop a reliable and valid classification system for identifying and classifying the underlying causes of pilot errors reported under the Aviation Safety Action Program (ASAP). ASAP is a voluntary safety program that air carriers may establish to study pilot and crew performance on the line. In ASAP programs, similar to the Aviation Safety Reporting System, pilots self-report incidents by filing a short text description of the event. The identification of contributors to errors is critical if organizations are to improve human performance, yet it is difficult for analysts to extract this information from text narratives. A taxonomy was needed that could be used by pilots to classify the causes of errors. After completing a thorough literature review, pilot interviews and a card-sorting task were conducted in Studies 1 and 2 to develop the initial structure of the Aviation Causal Contributors for Event Reporting Systems (ACCERS) taxonomy. The reliability and utility of ACCERS was then tested in studies 3a and 3b by having pilots independently classify the primary and secondary causes of ASAP reports. The results provided initial evidence for the internal and external validity of ACCERS. Pilots were found to demonstrate adequate levels of agreement with respect to their category classifications. ACCERS appears to be a useful system for studying human error captured under pilot ASAP reports. Future work should focus on how ACCERS is organized and whether it can be used or modified to classify human error in ASAP programs for other aviation-related job categories such as dispatchers. Potential applications of this research include systems in which individuals self-report errors and that attempt to extract and classify the causes of those events.

Soil geomorphic classification, soil taxonomy, and effects on soil richness assessments

Treesearch

Jonathan D. Phillips; Daniel A. Marion

2007-01-01

The study of pedodiversity and soil richness depends on the notion of soils as discrete entities. Soil classifications are often criticized in this regard because they depend in part on arbitrary or subjective criteria. In this study soils were categorized on the basis of the presence or absence of six lithological and morphological characteristics. Richness vs. area...

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.

Review article: A systematic review of emergency department incident classification frameworks.

PubMed

Murray, Matthew; McCarthy, Sally

2018-06-01

As in any part of the hospital system, safety incidents can occur in the ED. These incidents arguably have a distinct character, as the ED involves unscheduled flows of urgent patients who require disparate services. To aid understanding of safety issues and support risk management of the ED, a comparison of published ED specific incident classification frameworks was performed. A review of emergency medicine, health management and general medical publications, using Ovid SP to interrogate Medline (1976-2016) was undertaken to identify any type of taxonomy or classification-like framework for ED related incidents. These frameworks were then analysed and compared. The review identified 17 publications containing an incident classification framework. Comparison of factors and themes making up the classification constituent elements revealed some commonality, but no overall consistency, nor evolution towards an ideal framework. Inconsistency arises from differences in the evidential basis and design methodology of classifications, with design itself being an inherently subjective process. It was not possible to identify an 'ideal' incident classification framework for ED risk management, and there is significant variation in the selection of categories used by frameworks. The variation in classification could risk an unbalanced emphasis in findings through application of a particular framework. Design of an ED specific, ideal incident classification framework should be informed by a much wider range of theories of how organisations and systems work, in addition to clinical and human factors. © 2017 Australasian College for Emergency Medicine and Australasian Society for Emergency Medicine.

The neuron classification problem

PubMed Central

Bota, Mihail; Swanson, Larry W.

2007-01-01

A systematic account of neuron cell types is a basic prerequisite for determining the vertebrate nervous system global wiring diagram. With comprehensive lineage and phylogenetic information unavailable, a general ontology based on structure-function taxonomy is proposed and implemented in a knowledge management system, and a prototype analysis of select regions (including retina, cerebellum, and hypothalamus) presented. The supporting Brain Architecture Knowledge Management System (BAMS) Neuron ontology is online and its user interface allows queries about terms and their definitions, classification criteria based on the original literature and “Petilla Convention” guidelines, hierarchies, and relations—with annotations documenting each ontology entry. Combined with three BAMS modules for neural regions, connections between regions and neuron types, and molecules, the Neuron ontology provides a general framework for physical descriptions and computational modeling of neural systems. The knowledge management system interacts with other web resources, is accessible in both XML and RDF/OWL, is extendible to the whole body, and awaits large-scale data population requiring community participation for timely implementation. PMID:17582506

Integrative analysis of environmental sequences using MEGAN4.

PubMed

Huson, Daniel H; Mitra, Suparna; Ruscheweyh, Hans-Joachim; Weber, Nico; Schuster, Stephan C

2011-09-01

A major challenge in the analysis of environmental sequences is data integration. The question is how to analyze different types of data in a unified approach, addressing both the taxonomic and functional aspects. To facilitate such analyses, we have substantially extended MEGAN, a widely used taxonomic analysis program. The new program, MEGAN4, provides an integrated approach to the taxonomic and functional analysis of metagenomic, metatranscriptomic, metaproteomic, and rRNA data. While taxonomic analysis is performed based on the NCBI taxonomy, functional analysis is performed using the SEED classification of subsystems and functional roles or the KEGG classification of pathways and enzymes. A number of examples illustrate how such analyses can be performed, and show that one can also import and compare classification results obtained using others' tools. MEGAN4 is freely available for academic purposes, and installers for all three major operating systems can be downloaded from www-ab.informatik.uni-tuebingen.de/software/megan.

Public health workforce taxonomy.

PubMed

Boulton, Matthew L; Beck, Angela J; Coronado, Fátima; Merrill, Jacqueline A; Friedman, Charles P; Stamas, George D; Tyus, Nadra; Sellers, Katie; Moore, Jean; Tilson, Hugh H; Leep, Carolyn J

2014-11-01

Thoroughly characterizing and continuously monitoring the public health workforce is necessary for ensuring capacity to deliver public health services. A prerequisite for this is to develop a standardized methodology for classifying public health workers, permitting valid comparisons across agencies and over time, which does not exist for the public health workforce. An expert working group, all of whom are authors on this paper, was convened during 2012-2014 to develop a public health workforce taxonomy. The purpose of the taxonomy is to facilitate the systematic characterization of all public health workers while delineating a set of minimum data elements to be used in workforce surveys. The taxonomy will improve the comparability across surveys, assist with estimating duplicate counting of workers, provide a framework for describing the size and composition of the workforce, and address other challenges to workforce enumeration. The taxonomy consists of 12 axes, with each axis describing a key characteristic of public health workers. Within each axis are multiple categories, and sometimes subcategories, that further define that worker characteristic. The workforce taxonomy axes are occupation, workplace setting, employer, education, licensure, certification, job tasks, program area, public health specialization area, funding source, condition of employment, and demographics. The taxonomy is not intended to serve as a replacement for occupational classifications but rather is a tool for systematically categorizing worker characteristics. The taxonomy will continue to evolve as organizations implement it and recommend ways to improve this tool for more accurate workforce data collection. Copyright © 2014 American Journal of Preventive Medicine. Published by Elsevier Inc. All rights reserved.

Planetary Taxonomy: Label Round Bodies "Worlds"

NASA Astrophysics Data System (ADS)

Margot, Jean-Luc; Levison, H. F.

2009-05-01

The classification of planetary bodies is as important to Astronomy as taxonomy is to other sciences. The etymological, historical, and IAU definitions of planet rely on a dynamical criterion, but some authors prefer a geophysical criterion based on "roundness". Although the former criterion is superior when it comes to classifying newly discovered objects, the conflict need not exist if we agree to identify the subset of "round" planetary objects as "worlds". This addition to the taxonomy would conveniently recognize that "round" objects such as Earth, Europa, Titan, Triton, and Pluto share some common planetary-type processes regardless of their distance from the host star. Some of these worlds are planets, others are not. Defining how round is round and handling the inevitable transition objects are non-trivial tasks. Because images at sufficient resolution are not available for the overwhelming majority of newly discovered objects, the degree of roundness is not a directly observable property and is inherently problematic as a basis for classification. We can tolerate some uncertainty in establishing the "world" status of a newly discovered object, and still establish its planet or satellite status with existing dynamical criteria. Because orbital parameters are directly observable, and because mass can often be measured either from orbital perturbations or from the presence of companions, the dynamics provide a robust and practical planet classification scheme. It may also be possible to determine which bodies are dynamically dominant from observations of the population magnitude/size distribution.

Concepts of Classification and Taxonomy Phylogenetic Classification

NASA Astrophysics Data System (ADS)

Fraix-Burnet, D.

2016-05-01

Phylogenetic approaches to classification have been heavily developed in biology by bioinformaticians. But these techniques have applications in other fields, in particular in linguistics. Their main characteristics is to search for relationships between the objects or species in study, instead of grouping them by similarity. They are thus rather well suited for any kind of evolutionary objects. For nearly fifteen years, astrocladistics has explored the use of Maximum Parsimony (or cladistics) for astronomical objects like galaxies or globular clusters. In this lesson we will learn how it works.

A Group Recommender System for Tourist Activities

NASA Astrophysics Data System (ADS)

Garcia, Inma; Sebastia, Laura; Onaindia, Eva; Guzman, Cesar

This paper introduces a method for giving recommendations of tourist activities to a group of users. This method makes recommendations based on the group tastes, their demographic classification and the places visited by the users in former trips. The group recommendation is computed from individual personal recommendations through the use of techniques such as aggregation, intersection or incremental intersection. This method is implemented as an extension of the e-Tourism tool, which is a user-adapted tourism and leisure application, whose main component is the Generalist Recommender System Kernel (GRSK), a domain-independent taxonomy-driven search engine that manages the group recommendation.

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

Foley, Brian T.; Leitner, Thomas; Paraskevis, Dimitrios

The International Committee for the Taxonomy and Nomenclature of Viruses does not rule on virus classifications below the species level. The definition of species for viruses cannot be clearly defined for all types of viruses. The complex and interesting epidemiology of Human Immunodeficiency Viruses demands a detailed and informative nomenclature system, while at the same time it presents challenges such that many of the rules need to be flexibly applied or modified over time. As a result, this review outlines the nomenclature system for primate lentiviruses and provides an update on new findings since the last review was written inmore » 2000.« less

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

AAPT Diagnostic Criteria for Chronic Abdominal, Pelvic, and Urogenital Pain: Irritable Bowel Syndrome.

PubMed

Zhou, QiQi; Wesselmann, Ursula; Walker, Lynn; Lee, Linda; Zeltzer, Lonnie; Verne, G Nicholas

2018-03-01

In conjunction with the Analgesic, Anesthetic, and Addiction Clinical Trial Translations, Innovations, Opportunities, and Networks public-private partnership with the U.S. Food and Drug Administration and the American Pain Society, the Analgesic, Anesthetic, and Addiction Clinical Trial Translations, Innovations, Opportunities, and Networks-American Pain Society Pain Taxonomy (AAPT) initiative strove to develop the characteristics of a diagnostic system useful for clinical and research purposes across disciplines and types of chronic pain conditions. After the establishment of these characteristics, a working group of clinicians and clinical and basic scientists with expertise in abdominal, pelvic, and urogenital pain began generating core diagnostic criteria and defining the related extraintestinal somatic pain and other symptoms experienced by patients. Systematic diagnostic criteria for several common abdominal, pelvic, and urogenital pain conditions are in development. In this report, we present the proposed AAPT criteria for irritable bowel syndrome (IBS), the most common chronic, noncancer abdominal pain condition. A systematic review and synthesis was conducted to complement the Rome IV Diagnostic Criteria for IBS. Future efforts will subject these proposed AAPT criteria to systematic empirical evaluation of their feasibility, reliability, and validity. The AAPT IBS criteria are part of an evidence-based classification system that provides a consistent vocabulary regarding diagnostic criteria, common features, comorbidities, consequences, and putative mechanisms of the disorder. A similar approach is being applied to other chronic and often debilitating abdominal, pelvic, and urogenital pain conditions. The AAPT's goal is to develop an evidence-based taxonomy for chronic pain on the basis of a consistently applied multidimensional framework, and encourage experts to apply this taxonomy to specific chronic pain conditions. In this report, the taxonomy is applied to IBS, a chronic abdominal pain condition. Copyright © 2018. Published by Elsevier Inc.

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.

Fish Ontology framework for taxonomy-based fish recognition

PubMed Central

Ali, Najib M.; Khan, Haris A.; Then, Amy Y-Hui; Ving Ching, Chong; Gaur, Manas

2017-01-01

Life science ontologies play an important role in Semantic Web. Given the diversity in fish species and the associated wealth of information, it is imperative to develop an ontology capable of linking and integrating this information in an automated fashion. As such, we introduce the Fish Ontology (FO), an automated classification architecture of existing fish taxa which provides taxonomic information on unknown fish based on metadata restrictions. It is designed to support knowledge discovery, provide semantic annotation of fish and fisheries resources, data integration, and information retrieval. Automated classification for unknown specimens is a unique feature that currently does not appear to exist in other known ontologies. Examples of automated classification for major groups of fish are demonstrated, showing the inferred information by introducing several restrictions at the species or specimen level. The current version of FO has 1,830 classes, includes widely used fisheries terminology, and models major aspects of fish taxonomy, grouping, and character. With more than 30,000 known fish species globally, the FO will be an indispensable tool for fish scientists and other interested users. PMID:28929028

Shedding subspecies: The influence of genetics on reptile subspecies taxonomy.

PubMed

Torstrom, Shannon M; Pangle, Kevin L; Swanson, Bradley J

2014-07-01

The subspecies concept influences multiple aspects of biology and management. The 'molecular revolution' altered traditional methods (morphological traits) of subspecies classification by applying genetic analyses resulting in alternative or contradictory classifications. We evaluated recent reptile literature for bias in the recommendations regarding subspecies status when genetic data were included. Reviewing characteristics of the study, genetic variables, genetic distance values and noting the species concepts, we found that subspecies were more likely elevated to species when using genetic analysis. However, there was no predictive relationship between variables used and taxonomic recommendation. There was a significant difference between the median genetic distance values when researchers elevated or collapsed a subspecies. Our review found nine different concepts of species used when recommending taxonomic change, and studies incorporating multiple species concepts were more likely to recommend a taxonomic change. Since using genetic techniques significantly alter reptile taxonomy there is a need to establish a standard method to determine the species-subspecies boundary in order to effectively use the subspecies classification for research and conservation purposes. Copyright © 2014 Elsevier Inc. All rights reserved.

Rehabilitation treatment taxonomy: implications and continuations.

PubMed

P Dijkers, Marcel; Hart, Tessa; Whyte, John; M Zanca, Jeanne; Packel, Andrew; Tsaousides, Theodore

2014-01-01

In relation to the conceptual framework for a rehabilitation treatment taxonomy (RTT), which has been proposed in other articles in this supplement, this article discusses a number of issues relevant to its further development, including creating distinctions within the major target classes; the nature and quantity of allowable targets of treatment; and bracketing as a way of specifying (1) the skill or knowledge taught; (2) the nature of compensation afforded by changes in the environment, assistive technology, and orthotics/prosthetics; and (3) the ingredients in homework a clinician assigns. Clarification is provided regarding the role of the International Classification of Functioning, Disability and Health, focusing a taxonomy on ingredients versus other observable aspects of treatment, and regarding our lack of knowledge and its impact on taxonomy development. Finally, this article discusses the immediate implications of the work to date and presents the need for rehabilitation stakeholders of all disciplines to be involved in further RTT development. Copyright © 2014 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

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.

The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification.

PubMed

Aiewsakun, Pakorn; Simmonds, Peter

2018-02-20

The International Committee on Taxonomy of Viruses (ICTV) classifies viruses into families, genera and species and provides a regulated system for their nomenclature that is universally used in virus descriptions. Virus taxonomic assignments have traditionally been based upon virus phenotypic properties such as host range, virion morphology and replication mechanisms, particularly at family level. However, gene sequence comparisons provide a clearer guide to their evolutionary relationships and provide the only information that may guide the incorporation of viruses detected in environmental (metagenomic) studies that lack any phenotypic data. The current study sought to determine whether the existing virus taxonomy could be reproduced by examination of genetic relationships through the extraction of protein-coding gene signatures and genome organisational features. We found large-scale consistency between genetic relationships and taxonomic assignments for viruses of all genome configurations and genome sizes. The analysis pipeline that we have called 'Genome Relationships Applied to Virus Taxonomy' (GRAViTy) was highly effective at reproducing the current assignments of viruses at family level as well as inter-family groupings into orders. Its ability to correctly differentiate assigned viruses from unassigned viruses, and classify them into the correct taxonomic group, was evaluated by threefold cross-validation technique. This predicted family membership of eukaryotic viruses with close to 100% accuracy and specificity potentially enabling the algorithm to predict assignments for the vast corpus of metagenomic sequences consistently with ICTV taxonomy rules. In an evaluation run of GRAViTy, over one half (460/921) of (near)-complete genome sequences from several large published metagenomic eukaryotic virus datasets were assigned to 127 novel family-level groupings. If corroborated by other analysis methods, these would potentially more than double the number of eukaryotic virus families in the ICTV taxonomy. A rapid and objective means to explore metagenomic viral diversity and make informed recommendations for their assignments at each taxonomic layer is essential. GRAViTy provides one means to make rule-based assignments at family and order levels in a manner that preserves the integrity and underlying organisational principles of the current ICTV taxonomy framework. Such methods are increasingly required as the vast virosphere is explored.

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.

The Earth Observation Data for Habitat Monitoring (EODHaM) system

NASA Astrophysics Data System (ADS)

Lucas, Richard; Blonda, Palma; Bunting, Peter; Jones, Gwawr; Inglada, Jordi; Arias, Marcela; Kosmidou, Vasiliki; Petrou, Zisis I.; Manakos, Ioannis; Adamo, Maria; Charnock, Rebecca; Tarantino, Cristina; Mücher, Caspar A.; Jongman, Rob H. G.; Kramer, Henk; Arvor, Damien; Honrado, Joāo Pradinho; Mairota, Paola

2015-05-01

To support decisions relating to the use and conservation of protected areas and surrounds, the EU-funded BIOdiversity multi-SOurce monitoring System: from Space TO Species (BIO_SOS) project has developed the Earth Observation Data for HAbitat Monitoring (EODHaM) system for consistent mapping and monitoring of biodiversity. The EODHaM approach has adopted the Food and Agriculture Organization Land Cover Classification System (LCCS) taxonomy and translates mapped classes to General Habitat Categories (GHCs) from which Annex I habitats (EU Habitats Directive) can be defined. The EODHaM system uses a combination of pixel and object-based procedures. The 1st and 2nd stages use earth observation (EO) data alone with expert knowledge to generate classes according to the LCCS taxonomy (Levels 1 to 3 and beyond). The 3rd stage translates the final LCCS classes into GHCs from which Annex I habitat type maps are derived. An additional module quantifies changes in the LCCS classes and their components, indices derived from earth observation, object sizes and dimensions and the translated habitat maps (i.e., GHCs or Annex I). Examples are provided of the application of EODHaM system elements to protected sites and their surrounds in Italy, Wales (UK), the Netherlands, Greece, Portugal and India.

Development of a Procurement Task Classification Scheme.

DTIC Science & Technology

1987-12-01

Office of Sci- entific Research, Arlington, Virginia, January 1970. Tornow , Walter W . and Pinto, Patrick R. "The Development of a Man- agerial Job...classification. [Ref. 4:271 -. 20 6 %° w Numerical taxonomy proponents hold [Ref. 4:271, ... that the relationships of contiguity and similarity should be...solving. 22 W i * These primitive categories are based on a sorting of learning pro- cesses into classes that have obvious differences at the

Cancer classification in the genomic era: five contemporary problems.

PubMed

Song, Qingxuan; Merajver, Sofia D; Li, Jun Z

2015-10-19

Classification is an everyday instinct as well as a full-fledged scientific discipline. Throughout the history of medicine, disease classification is central to how we develop knowledge, make diagnosis, and assign treatment. Here, we discuss the classification of cancer and the process of categorizing cancer subtypes based on their observed clinical and biological features. Traditionally, cancer nomenclature is primarily based on organ location, e.g., "lung cancer" designates a tumor originating in lung structures. Within each organ-specific major type, finer subgroups can be defined based on patient age, cell type, histological grades, and sometimes molecular markers, e.g., hormonal receptor status in breast cancer or microsatellite instability in colorectal cancer. In the past 15+ years, high-throughput technologies have generated rich new data regarding somatic variations in DNA, RNA, protein, or epigenomic features for many cancers. These data, collected for increasingly large tumor cohorts, have provided not only new insights into the biological diversity of human cancers but also exciting opportunities to discover previously unrecognized cancer subtypes. Meanwhile, the unprecedented volume and complexity of these data pose significant challenges for biostatisticians, cancer biologists, and clinicians alike. Here, we review five related issues that represent contemporary problems in cancer taxonomy and interpretation. (1) How many cancer subtypes are there? (2) How can we evaluate the robustness of a new classification system? (3) How are classification systems affected by intratumor heterogeneity and tumor evolution? (4) How should we interpret cancer subtypes? (5) Can multiple classification systems co-exist? While related issues have existed for a long time, we will focus on those aspects that have been magnified by the recent influx of complex multi-omics data. Exploration of these problems is essential for data-driven refinement of cancer classification and the successful application of these concepts in precision medicine.

Mapping health behaviors: Constructing and validating a common-sense taxonomy of health behaviors.

PubMed

Nudelman, Gabriel; Shiloh, Shoshana

2015-12-01

Health behaviors (HBs) are major determinants of health, illness, and mortality. Theoretical efforts aimed at understanding their nature and the processes involved in their initiation and maintenance have largely ignored differences among them. Therefore, the objective of this research was to establish a reliable and valid common-sense taxonomy of HBs. The first study created a comprehensive list of 66 HBs based on the views of laypeople (N = 70), health professionals (N = 30), and a literature review. In the second study, a sample of laypeople (N = 268) selected the most important HBs. In the third study, a similarity card-sorting technique was administered to a representative sample (N = 450) in an effort to uncover the structure of HBs. The fourth study replicated the structure (N = 627) and assessed its stability and generalizability. A complete list of 66 HBs was developed, of which 45 were judged as most important. Classifications of HBs identified two main categories: psychosocial, including psychological, social, and work issues; and physical, composed of risk avoidance, nutritional habits, and prevention. The hierarchical classification further separated each category into distinguishable clusters and subclusters. The results were replicated, and additional analyses revealed a high level of stability of the taxonomy across different demographic sub-groups. The taxonomy can provide a framework for research and a map for program developers looking for meaningful links between specific groups of HBs and particular behavior change techniques. This should optimize the cost-effectiveness of promotion and intervention programs, and thus increase health and decrease health-care burden. Copyright © 2015 Elsevier Ltd. All rights reserved.

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).

Reliability in content analysis: The case of semantic feature norms classification.

PubMed

Bolognesi, Marianna; Pilgram, Roosmaryn; van den Heerik, Romy

2017-12-01

Semantic feature norms (e.g., STIMULUS: car → RESPONSE: ) are commonly used in cognitive psychology to look into salient aspects of given concepts. Semantic features are typically collected in experimental settings and then manually annotated by the researchers into feature types (e.g., perceptual features, taxonomic features, etc.) by means of content analyses-that is, by using taxonomies of feature types and having independent coders perform the annotation task. However, the ways in which such content analyses are typically performed and reported are not consistent across the literature. This constitutes a serious methodological problem that might undermine the theoretical claims based on such annotations. In this study, we first offer a review of some of the released datasets of annotated semantic feature norms and the related taxonomies used for content analysis. We then provide theoretical and methodological insights in relation to the content analysis methodology. Finally, we apply content analysis to a new dataset of semantic features and show how the method should be applied in order to deliver reliable annotations and replicable coding schemes. We tackle the following issues: (1) taxonomy structure, (2) the description of categories, (3) coder training, and (4) sustainability of the coding scheme-that is, comparison of the annotations provided by trained versus novice coders. The outcomes of the project are threefold: We provide methodological guidelines for semantic feature classification; we provide a revised and adapted taxonomy that can (arguably) be applied to both concrete and abstract concepts; and we provide a dataset of annotated semantic feature norms.

A data-stream classification system for investigating terrorist threats

NASA Astrophysics Data System (ADS)

Schulz, Alexia; Dettman, Joshua; Gottschalk, Jeffrey; Kotson, Michael; Vuksani, Era; Yu, Tamara

2016-05-01

The role of cyber forensics in criminal investigations has greatly increased in recent years due to the wealth of data that is collected and available to investigators. Physical forensics has also experienced a data volume and fidelity revolution due to advances in methods for DNA and trace evidence analysis. Key to extracting insight is the ability to correlate across multi-modal data, which depends critically on identifying a touch-point connecting the separate data streams. Separate data sources may be connected because they refer to the same individual, entity or event. In this paper we present a data source classification system tailored to facilitate the investigation of potential terrorist activity. This taxonomy is structured to illuminate the defining characteristics of a particular terrorist effort and designed to guide reporting to decision makers that is complete, concise, and evidence-based. The classification system has been validated and empirically utilized in the forensic analysis of a simulated terrorist activity. Next-generation analysts can use this schema to label and correlate across existing data streams, assess which critical information may be missing from the data, and identify options for collecting additional data streams to fill information gaps.

Aquatics, Flyers, Creepers and Terrestrials--Students' Conceptions of Animal Classification.

ERIC Educational Resources Information Center

Kattmann, Ulrich

2001-01-01

Students prefer to classify creatures along the criteria of habitat and locomotion (method of movement). Discusses the educational consequences for biology instruction, particularly with regard to biological taxonomy, biodiversity, and evolution. (Contains 33 references.) (Author/YDS)

Rare diseases in clinical endocrinology: a taxonomic classification system.

PubMed

Marcucci, G; Cianferotti, L; Beck-Peccoz, P; Capezzone, M; Cetani, F; Colao, A; Davì, M V; degli Uberti, E; Del Prato, S; Elisei, R; Faggiano, A; Ferone, D; Foresta, C; Fugazzola, L; Ghigo, E; Giacchetti, G; Giorgino, F; Lenzi, A; Malandrino, P; Mannelli, M; Marcocci, C; Masi, L; Pacini, F; Opocher, G; Radicioni, A; Tonacchera, M; Vigneri, R; Zatelli, M C; Brandi, M L

2015-02-01

Rare endocrine-metabolic diseases (REMD) represent an important area in the field of medicine and pharmacology. The rare diseases of interest to endocrinologists involve all fields of endocrinology, including rare diseases of the pituitary, thyroid and adrenal glands, paraganglia, ovary and testis, disorders of bone and mineral metabolism, energy and lipid metabolism, water metabolism, and syndromes with possible involvement of multiple endocrine glands, and neuroendocrine tumors. Taking advantage of the constitution of a study group on REMD within the Italian Society of Endocrinology, consisting of basic and clinical scientists, a document on the taxonomy of REMD has been produced. This document has been designed to include mainly REMD manifesting or persisting into adulthood. The taxonomy of REMD of the adult comprises a total of 166 main disorders, 338 including all variants and subtypes, described into 11 tables. This report provides a complete taxonomy to classify REMD of the adult. In the future, the creation of registries of rare endocrine diseases to collect data on cohorts of patients and the development of common and standardized diagnostic and therapeutic pathways for each rare endocrine disease is advisable. This will help planning and performing intervention studies in larger groups of patients to prove the efficacy, effectiveness, and safety of a specific treatment.

Molecular Phylogeny of the Widely Distributed Marine Protists, Phaeodaria (Rhizaria, Cercozoa).

PubMed

Nakamura, Yasuhide; Imai, Ichiro; Yamaguchi, Atsushi; Tuji, Akihiro; Not, Fabrice; Suzuki, Noritoshi

2015-07-01

Phaeodarians are a group of widely distributed marine cercozoans. These plankton organisms can exhibit a large biomass in the environment and are supposed to play an important role in marine ecosystems and in material cycles in the ocean. Accurate knowledge of phaeodarian classification is thus necessary to better understand marine biology, however, phylogenetic information on Phaeodaria is limited. The present study analyzed 18S rDNA sequences encompassing all existing phaeodarian orders, to clarify their phylogenetic relationships and improve their taxonomic classification. The monophyly of Phaeodaria was confirmed and strongly supported by phylogenetic analysis with a larger data set than in previous studies. The phaeodarian clade contained 11 subclades which generally did not correspond to the families and orders of the current classification system. Two families (Challengeriidae and Aulosphaeridae) and two orders (Phaeogromida and Phaeocalpida) are possibly polyphyletic or paraphyletic, and consequently the classification needs to be revised at both the family and order levels by integrative taxonomy approaches. Two morphological criteria, 1) the scleracoma type and 2) its surface structure, could be useful markers at the family level. Copyright © 2015 Elsevier GmbH. All rights reserved.

Strategies of psychological terrorism perpetrated by ETA's network: delimitation and classification.

PubMed

Martín-Peña, Javier; Rodríguez-Carballeira, Alvaro; Escartín Solanelles, Jordi; Porrúa García, Clara; Willem Winkel, Frans

2010-02-01

This paper defines and analyzes the harassment perpetrated by ETA's terrorist network in the Basque Country, providing a taxonomy of its strategies of psychological violence. The usefulness of this taxonomy has been tested and contrasted by means of a content analysis of 19 testimonies of persons who were the victims of violence by the terrorist network. The taxonomy of strategies of psychological violence is made up of four dimensions that emphasize the actions on the context of the persons affected, and on their emotional state, cognitions, and behaviour. Results show the predominance of emotional and cognitive strategies. Intra-observer and inter-observer reliability analysis in coding showed a Cohen's Kappa coefficient of .92 and .87, respectively. The psychological violence analyzed in this study reflects a form of psychological terrorism that harasses and persecutes a specific sector of the population.

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

Telemedicine information analysis center.

PubMed

Zajtchuk, Joan T; Zajtchuk, Russ; Petrovic, Joseph J; Gutz, Ryan P; Walrath, Benjamin D

2004-01-01

Congress mandated a pilot project to demonstrate the feasibility of establishing a Department of Defense (DoD) telemedicine information analysis center (TIAC). The project developed a medical information support system to show the core capabilities of a TIAC. The productivity and effectiveness of telemedicine researchers and clinical practitioners can be enhanced by the existence of an information analysis center (IACs) devoted to the collection, analysis, synthesis, and dissemination of worldwide scientific and technical information related to the field of telemedicine. The work conducted under the TIAC pilot project establishes the basic IAC functions and assesses the utility of the TIAC to the military medical departments. The pilot project capabilities are Web-based and include: (1) applying the science of classification (taxonomy) to telemedicine to identify key words; (2) creating a relational database of this taxonomy to a bibliographic database using these key words; (3) developing and disseminating information via a public TIAC Web site; (4) performing a specific baseline technical area task for the U.S. Army Medical Command; and (5) providing analyses by subject matter experts.

Physical observations and taxonomy of asteroids

NASA Technical Reports Server (NTRS)

Morrison, D.

1978-01-01

Physical asteroid observations are summarized and the classification scheme to describe asteroid surfaces in relation to mineralogical composition is detailed. The principle classes, distinguished on the basis of a number of parameters involving albedo and color, are called C, S, and M.

Sequence-based classification and identification of fungi

USDA-ARS?s Scientific Manuscript database

Fungal taxonomy and ecology have been revolutionized by the application of molecular methods and both have increasing connections to genomics and functional biology. However, data streams from traditional specimen- and culture-based systematics are not yet fully integrated with those from metagenomi...

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

Divorcing Strain Classification from Species Names.

PubMed

Baltrus, David A

2016-06-01

Confusion about strain classification and nomenclature permeates modern microbiology. Although taxonomists have traditionally acted as gatekeepers of order, the numbers of, and speed at which, new strains are identified has outpaced the opportunity for professional classification for many lineages. Furthermore, the growth of bioinformatics and database-fueled investigations have placed metadata curation in the hands of researchers with little taxonomic experience. Here I describe practical challenges facing modern microbial taxonomy, provide an overview of complexities of classification for environmentally ubiquitous taxa like Pseudomonas syringae, and emphasize that classification can be independent of nomenclature. A move toward implementation of relational classification schemes based on inherent properties of whole genomes could provide sorely needed continuity in how strains are referenced across manuscripts and data sets. Copyright © 2016 Elsevier Ltd. All rights reserved.

A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3

PubMed Central

Dietmann, Sabine; Park, Jong; Notredame, Cedric; Heger, Andreas; Lappe, Michael; Holm, Liisa

2001-01-01

The Dali Domain Dictionary (http://www.ebi.ac.uk/dali/domain) is a numerical taxonomy of all known structures in the Protein Data Bank (PDB). The taxonomy is derived fully automatically from measurements of structural, functional and sequence similarities. Here, we report the extension of the classification to match the traditional four hierarchical levels corresponding to: (i) supersecondary structural motifs (attractors in fold space), (ii) the topology of globular domains (fold types), (iii) remote homologues (functional families) and (iv) homologues with sequence identity above 25% (sequence families). The computational definitions of attractors and functional families are new. In September 2000, the Dali classification contained 10 531 PDB entries comprising 17 101 chains, which were partitioned into five attractor regions, 1375 fold types, 2582 functional families and 3724 domain sequence families. Sequence families were further associated with 99 582 unique homologous sequences in the HSSP database, which increases the number of effectively known structures several-fold. The resulting database contains the description of protein domain architecture, the definition of structural neighbours around each known structure, the definition of structurally conserved cores and a comprehensive library of explicit multiple alignments of distantly related protein families. PMID:11125048

What Images Reveal: a Comparative Study of Science Images between Australian and Taiwanese Junior High School Textbooks

NASA Astrophysics Data System (ADS)

Ge, Yun-Ping; Unsworth, Len; Wang, Kuo-Hua; Chang, Huey-Por

2017-07-01

From a social semiotic perspective, image designs in science textbooks are inevitably influenced by the sociocultural context in which the books are produced. The learning environments of Australia and Taiwan vary greatly. Drawing on social semiotics and cognitive science, this study compares classificational images in Australian and Taiwanese junior high school science textbooks. Classificational images are important kinds of images, which can represent taxonomic relations among objects as reported by Kress and van Leeuwen (Reading images: the grammar of visual design, 2006). An analysis of the images from sample chapters in Australian and Taiwanese high school science textbooks showed that the majority of the Taiwanese images are covert taxonomies, which represent hierarchical relations implicitly. In contrast, Australian classificational images included diversified designs, but particularly types with a tree structure which depicted overt taxonomies, explicitly representing hierarchical super-ordinate and subordinate relations. Many of the Taiwanese images are reminiscent of the specimen images in eighteenth century science texts representing "what truly is", while more Australian images emphasize structural objectivity. Moreover, Australian images support cognitive functions which facilitate reading comprehension. The relationships between image designs and learning environments are discussed and implications for textbook research and design are addressed.

From learning taxonomies to phylogenetic learning: integration of 16S rRNA gene data into FAME-based bacterial classification.

PubMed

Slabbinck, Bram; Waegeman, Willem; Dawyndt, Peter; De Vos, Paul; De Baets, Bernard

2010-01-30

Machine learning techniques have shown to improve bacterial species classification based on fatty acid methyl ester (FAME) data. Nonetheless, FAME analysis has a limited resolution for discrimination of bacteria at the species level. In this paper, we approach the species classification problem from a taxonomic point of view. Such a taxonomy or tree is typically obtained by applying clustering algorithms on FAME data or on 16S rRNA gene data. The knowledge gained from the tree can then be used to evaluate FAME-based classifiers, resulting in a novel framework for bacterial species classification. In view of learning in a taxonomic framework, we consider two types of trees. First, a FAME tree is constructed with a supervised divisive clustering algorithm. Subsequently, based on 16S rRNA gene sequence analysis, phylogenetic trees are inferred by the NJ and UPGMA methods. In this second approach, the species classification problem is based on the combination of two different types of data. Herein, 16S rRNA gene sequence data is used for phylogenetic tree inference and the corresponding binary tree splits are learned based on FAME data. We call this learning approach 'phylogenetic learning'. Supervised Random Forest models are developed to train the classification tasks in a stratified cross-validation setting. In this way, better classification results are obtained for species that are typically hard to distinguish by a single or flat multi-class classification model. FAME-based bacterial species classification is successfully evaluated in a taxonomic framework. Although the proposed approach does not improve the overall accuracy compared to flat multi-class classification, it has some distinct advantages. First, it has better capabilities for distinguishing species on which flat multi-class classification fails. Secondly, the hierarchical classification structure allows to easily evaluate and visualize the resolution of FAME data for the discrimination of bacterial species. Summarized, by phylogenetic learning we are able to situate and evaluate FAME-based bacterial species classification in a more informative context.

From learning taxonomies to phylogenetic learning: Integration of 16S rRNA gene data into FAME-based bacterial classification

PubMed Central

2010-01-01

Background Machine learning techniques have shown to improve bacterial species classification based on fatty acid methyl ester (FAME) data. Nonetheless, FAME analysis has a limited resolution for discrimination of bacteria at the species level. In this paper, we approach the species classification problem from a taxonomic point of view. Such a taxonomy or tree is typically obtained by applying clustering algorithms on FAME data or on 16S rRNA gene data. The knowledge gained from the tree can then be used to evaluate FAME-based classifiers, resulting in a novel framework for bacterial species classification. Results In view of learning in a taxonomic framework, we consider two types of trees. First, a FAME tree is constructed with a supervised divisive clustering algorithm. Subsequently, based on 16S rRNA gene sequence analysis, phylogenetic trees are inferred by the NJ and UPGMA methods. In this second approach, the species classification problem is based on the combination of two different types of data. Herein, 16S rRNA gene sequence data is used for phylogenetic tree inference and the corresponding binary tree splits are learned based on FAME data. We call this learning approach 'phylogenetic learning'. Supervised Random Forest models are developed to train the classification tasks in a stratified cross-validation setting. In this way, better classification results are obtained for species that are typically hard to distinguish by a single or flat multi-class classification model. Conclusions FAME-based bacterial species classification is successfully evaluated in a taxonomic framework. Although the proposed approach does not improve the overall accuracy compared to flat multi-class classification, it has some distinct advantages. First, it has better capabilities for distinguishing species on which flat multi-class classification fails. Secondly, the hierarchical classification structure allows to easily evaluate and visualize the resolution of FAME data for the discrimination of bacterial species. Summarized, by phylogenetic learning we are able to situate and evaluate FAME-based bacterial species classification in a more informative context. PMID:20113515

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.

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.

Nematode parasites of fishes: recent advances and problems of their research.

PubMed

Moravec, F

2007-09-01

Although nematodes (Nematoda) belong to the most frequent and the most important parasites of fishes in the freshwater, brackish-water and marine environments throughout the world, the present knowledge of these parasites remains still incomplete, especially as to their biology and ecology, but also taxonomy, phylogeny, zoogeography, and the like. However, a certain progress in the research of fish nematodes has been achieved during recent years. An overview of some of the most important discoveries and results obtained is presented. As an example, existing problems in the taxonomy of these nematodes are shown in the dracunculoid family Philometridae (presently including 109 species in 9 genera), where they are associated mainly with some biological peculiarities of these mostly important tissue parasites. Nematodes of the Dracunculoidea as a whole remain poorly known; for example, of 139 valid species parasitizing fishes, 81 (58%) are known by females only and the males have not yet been described for members of 8 (27%) of genera. A taxonomic revision of this nematode group, based on detailed morphological, life history and molecular studies of individual species, is quite necessary; for the time being, Moravec (2006) has proposed a new classification system of dracunculoids, where, based on previous molecular studies, the Anguillicolidae is no longer listed in Dracunculoidea, but in an independent superfamily Anguillicoloidea. Important results have recently been achieved also in the taxonomy of fish nematodes belonging to other superfamilies, as well as in studies of their geographical distribution and diversity in different parts of the world and those of their biology. Opportunities for more detailed studies of fish nematodes have recently greatly improved with the use of some new methods, in particular SEM and DNA studies. There is a need to create a new classification system of these parasites reflecting phylogenetic relationships; a prerequisite for this is taxonomic revisions of different groups based on detailed studies of individual species, including mainly their morphology, biology and genetics. Further progress should concern studies on various aspects of biology, ecology and host-parasite relationships, because these data may have practical implications.

Epistemological pluralism and scientific development: an argument against authoritative nosologies.

PubMed

Markon, Kristian E

2013-10-01

The author examines the influence of authoritative nosological systems--those developed by an authoritative body or organization (e.g., the DSM, ICD, RDoC)--on the development of scientific theory and research. Although there has been extensive discussion of how such systems should be organized, and of the historical role of such systems, little focus has been placed on whether these systems impede or facilitate scientific progress. The author reviews the nature and role of constructs in scientific theory and the role of authoritative taxonomy in science. He presents an argument that, although authoritative classification systems clearly have value for nonscientific purposes, or for specific scientific purposes, the systems themselves, at least as they have been constructed thus far, likely impede scientific development by constraining competitive discourse. Implications and recommendations are discussed.

Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2016).

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; Sabanadzovic, Sead; Sanfaçon, Hélène; Siddell, Stuart G; Simmonds, Peter; Varsani, Arvind; Zerbini, Francisco Murilo; Gorbalenya, Alexander E; Davison, Andrew J

2016-10-01

This article lists the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in April 2016.Changes to virus taxonomy (the Universal Scheme of Virus Classification of the International Committee on Taxonomy of Viruses [ICTV]) now take place annually and are the result of a multi-stage process. In accordance with the ICTV Statutes ( http://www.ictvonline.org/statutes.asp ), proposals submitted to the ICTV Executive Committee (EC) undergo a review process that involves input from the ICTV Study Groups (SGs) and Subcommittees (SCs), other interested virologists, and the EC. After final approval by the EC, proposals are then presented for ratification to the full ICTV membership by publication on an ICTV web site ( http://www.ictvonline.org/ ) followed by an electronic vote. The latest set of proposals approved by the EC was made available on the ICTV website by January 2016 ( https://talk.ictvonline.org/files/proposals/ ). A list of these proposals was then emailed on 28 March 2016 to the 148 members of ICTV, namely the EC Members, Life Members, ICTV Subcommittee Members (including the SG chairs) and ICTV National Representatives. Members were then requested to vote on whether to ratify the taxonomic proposals (voting closed on 29 April 2016).

Phylogeny of Comatulidae (Echinodermata: Crinoidea: Comatulida): a new classification and an assessment of morphological characters for crinoid taxonomy.

PubMed

Summers, Mindi M; Messing, Charles G; Rouse, Greg W

2014-11-01

Comatulidae Fleming, 1828 (previously, and incorrectly, Comasteridae A.H. Clark, 1908a), is a group of feather star crinoids currently divided into four accepted subfamilies, 21 genera and approximately 95 nominal species. Comatulidae is the most commonly-encountered and species-rich crinoid group on shallow tropical coral reefs, particularly in the Indo-western Pacific region (IWP). We conducted a molecular phylogenetic analysis of the group with concatenated data from up to seven genes for 43 nominal species spanning 17 genera and all subfamilies. Basal nodes returned low support, but maximum likelihood, maximum parsimony, and Bayesian analyses were largely congruent, permitting an evaluation of current taxonomy and analysis of morphological character transformations. Two of the four current subfamilies were paraphyletic, whereas 15 of the 17 included genera returned as monophyletic. We provide a new classification with two subfamilies, Comatulinae and Comatellinae n. subfamily Summers, Messing, & Rouse, the former containing five tribes. We revised membership of analyzed genera to make them all clades and erected Anneissia n. gen. Summers, Messing, & Rouse. Transformation analyses for morphological features generally used in feather star classification (e.g., ray branching patterns, articulations) and those specifically for Comatulidae (e.g., comb pinnule form, mouth placement) were labile with considerable homoplasy. These traditional characters, in combination, allow for generic diagnoses, but in most cases we did not recover apomorphies for subfamilies, tribes, and genera. New morphological characters that will be informative for crinoid taxonomy and identification are still needed. DNA sequence data currently provides the most reliable method of identification to the species-level for many taxa of Comatulidae. Copyright © 2014 Elsevier Inc. All rights reserved.

Current state of medical device nomenclature and taxonomy systems in the UK: spotlight on GMDN and SNOMED CT

PubMed Central

White, Judith; Carolan-Rees, Grace

2013-01-01

A standardised terminology for describing medical devices can enable safe and unambiguous exchange of information. Proposed changes to EU-wide medical devices regulations mandate the use of such a system. This article reviews two important classification systems for medical devices in the UK. The Global Medical Device Nomenclature (GMDN) provides a classification system specifically for medical devices and diagnostics, and facilitates data exchange between manufacturers and regulators. SNOMED CT is the terminology of choice in the NHS for communicating, sharing and storing information about patients’ healthcare episodes. Harmonisation of GMDN and SNOMED CT will encourage use of single terminology throughout the lifetime of a device; from regulatory approval through clinical use and post-marketing surveillance. Manufacturers will be required to register medical devices with a European device database (Eudamed) and to fit certain devices with a Unique Device Identifier; both are efforts to improve transparency and traceability of medical devices. Successful implementation of these elements depends on having a consistent nomenclature for medical devices. PMID:23885299

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

[To represent needs of nursing care using nursing diagnoses: potentials and restrictions of the NANDA classification and ICNP].

PubMed

Schilder, Michael

2005-03-01

Nursing diagnoses represent individual reactions to existing or potential changes in one's state of health. They are result of a diagnostic process, which is part of the dynamic nursing care process in its whole. Thus, as a basis of nursing interventions diagnoses have to be proved continuously. The classification of the North American Nursing Diagnosis Association (NANDA) as well as the International Classification for Nursing Practice (ICNP) can be account to the international well-known classifications of nursing diagnoses. Comparing their structures, some fundamental differences between both classifications become obvious. While the NANDA classification represents a systematic structured body of nursing knowledge with regard to human health reactions patterns, the ICNP reflects a more comprehensive part of the nursing reality, since it also contains nursing interventions and outcomes. Until the latest changes by establishing the taxonomy II, NANDA diagnoses have primarily focused deficits. But in contrast to the diagnoses of the ICNP they also comprise etiological factors. To prove the applicability of both classifications to nursing practice, they have been applied to a case study of a female resident living in a nursing home. The results of analysis show that because of their different structures the NANDA classification and ICNP have their own possibilities and limitations in covering the resident's individual needs of nursing care. These characteristic potentials and restrictions have to be taken into account when one of the classification systems is going to be implemented into nursing practice.

A curated database of cyanobacterial strains relevant for modern taxonomy and phylogenetic studies.

PubMed

Ramos, Vitor; Morais, João; Vasconcelos, Vitor M

2017-04-25

The dataset herein described lays the groundwork for an online database of relevant cyanobacterial strains, named CyanoType (http://lege.ciimar.up.pt/cyanotype). It is a database that includes categorized cyanobacterial strains useful for taxonomic, phylogenetic or genomic purposes, with associated information obtained by means of a literature-based curation. The dataset lists 371 strains and represents the first version of the database (CyanoType v.1). Information for each strain includes strain synonymy and/or co-identity, strain categorization, habitat, accession numbers for molecular data, taxonomy and nomenclature notes according to three different classification schemes, hierarchical automatic classification, phylogenetic placement according to a selection of relevant studies (including this), and important bibliographic references. The database will be updated periodically, namely by adding new strains meeting the criteria for inclusion and by revising and adding up-to-date metadata for strains already listed. A global 16S rDNA-based phylogeny is provided in order to assist users when choosing the appropriate strains for their studies.

A curated database of cyanobacterial strains relevant for modern taxonomy and phylogenetic studies

PubMed Central

Ramos, Vitor; Morais, João; Vasconcelos, Vitor M.

2017-01-01

The dataset herein described lays the groundwork for an online database of relevant cyanobacterial strains, named CyanoType (http://lege.ciimar.up.pt/cyanotype). It is a database that includes categorized cyanobacterial strains useful for taxonomic, phylogenetic or genomic purposes, with associated information obtained by means of a literature-based curation. The dataset lists 371 strains and represents the first version of the database (CyanoType v.1). Information for each strain includes strain synonymy and/or co-identity, strain categorization, habitat, accession numbers for molecular data, taxonomy and nomenclature notes according to three different classification schemes, hierarchical automatic classification, phylogenetic placement according to a selection of relevant studies (including this), and important bibliographic references. The database will be updated periodically, namely by adding new strains meeting the criteria for inclusion and by revising and adding up-to-date metadata for strains already listed. A global 16S rDNA-based phylogeny is provided in order to assist users when choosing the appropriate strains for their studies. PMID:28440791

Colletotrichum – current status and future directions

PubMed Central

Cannon, P.F.; Damm, U.; Johnston, P.R.; Weir, B.S.

2012-01-01

A review is provided of the current state of understanding of Colletotrichum systematics, focusing on species-level data and the major clades. The taxonomic placement of the genus is discussed, and the evolution of our approach to species concepts and anamorph-teleomorph relationships is described. The application of multilocus technologies to phylogenetic analysis of Colletotrichum is reviewed, and selection of potential genes/loci for barcoding purposes is discussed. Host specificity and its relation to speciation and taxonomy is briefly addressed. A short review is presented of the current status of classification of the species clusters that are currently without comprehensive multilocus analyses, emphasising the orbiculare and destructivum aggregates. The future for Colletotrichum biology will be reliant on consensus classification and robust identification tools. In support of these goals, a Subcommission on Colletotrichum has been formed under the auspices of the International Commission on Taxonomy of Fungi, which will administer a carefully curated barcode database for sequence-based identification of species within the BioloMICS web environment. PMID:23136460

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.

A New Tool for Classifying Small Solar System Objects

NASA Astrophysics Data System (ADS)

Desfosses, Ryan; Arel, D.; Walker, M. E.; Ziffer, J.; Harvell, T.; Campins, H.; Fernandez, Y. R.

2011-05-01

An artificial intelligence program, AutoClass, which was developed by NASA's Artificial Intelligence Branch, uses Bayesian classification theory to automatically choose the most probable classification distribution to describe a dataset. To investigate its usefulness to the Planetary Science community, we tested its ability to reproduce the taxonomic classes as defined by Tholen and Barucci (1989). Of the 406 asteroids from the Eight Color Asteroid Survey (ECAS) we chose for our test, 346 were firmly classified and all but 3 (<1%) were classified by Autoclass as they had been in the previous classification system (Walker et al., 2011). We are now applying it to larger datasets to improve the taxonomy of currently unclassified objects. Having demonstrated AutoClass's ability to recreate existing classification effectively, we extended this work to investigations of albedo-based classification systems. To determine how predictive albedo can be, we used data from the Infrared Astronomical Satellite (IRAS) database in conjunction with the large Sloan Digital Sky Survey (SDSS), which contains color and position data for over 200,000 classified and unclassified asteroids (Ivesic et al., 2001). To judge our success we compared our results with a similar approach to classifying objects using IRAS albedo and asteroid color by Tedesco et al. (1989). Understanding the distribution of the taxonomic classes is important to understanding the history and evolution of our Solar System. AutoClass's success in categorizing ECAS, IRAS and SDSS asteroidal data highlights its potential to scan large domains for natural classes in small solar system objects. Based upon our AutoClass results, we intend to make testable predictions about asteroids observed with the Wide-field Infrared Survey Explorer (WISE).

CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy.

PubMed

Zuo, Guanghong; Hao, Bailin

2015-10-01

A faithful phylogeny and an objective taxonomy for prokaryotes should agree with each other and ultimately follow the genome data. With the number of sequenced genomes reaching tens of thousands, both tree inference and detailed comparison with taxonomy are great challenges. We now provide one solution in the latest Release 3.0 of the alignment-free and whole-genome-based web server CVTree3. The server resides in a cluster of 64 cores and is equipped with an interactive, collapsible, and expandable tree display. It is capable of comparing the tree branching order with prokaryotic classification at all taxonomic ranks from domains down to species and strains. CVTree3 allows for inquiry by taxon names and trial on lineage modifications. In addition, it reports a summary of monophyletic and non-monophyletic taxa at all ranks as well as produces print-quality subtree figures. After giving an overview of retrospective verification of the CVTree approach, the power of the new server is described for the mega-classification of prokaryotes and determination of taxonomic placement of some newly-sequenced genomes. A few discrepancies between CVTree and 16S rRNA analyses are also summarized with regard to possible taxonomic revisions. CVTree3 is freely accessible to all users at http://tlife.fudan.edu.cn/cvtree3/ without login requirements. Copyright © 2015 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy

PubMed Central

Zuo, Guanghong; Hao, Bailin

2015-01-01

A faithful phylogeny and an objective taxonomy for prokaryotes should agree with each other and ultimately follow the genome data. With the number of sequenced genomes reaching tens of thousands, both tree inference and detailed comparison with taxonomy are great challenges. We now provide one solution in the latest Release 3.0 of the alignment-free and whole-genome-based web server CVTree3. The server resides in a cluster of 64 cores and is equipped with an interactive, collapsible, and expandable tree display. It is capable of comparing the tree branching order with prokaryotic classification at all taxonomic ranks from domains down to species and strains. CVTree3 allows for inquiry by taxon names and trial on lineage modifications. In addition, it reports a summary of monophyletic and non-monophyletic taxa at all ranks as well as produces print-quality subtree figures. After giving an overview of retrospective verification of the CVTree approach, the power of the new server is described for the mega-classification of prokaryotes and determination of taxonomic placement of some newly-sequenced genomes. A few discrepancies between CVTree and 16S rRNA analyses are also summarized with regard to possible taxonomic revisions. CVTree3 is freely accessible to all users at http://tlife.fudan.edu.cn/cvtree3/ without login requirements. PMID:26563468

DNA extraction on bio-chip: history and preeminence over conventional and solid-phase extraction methods.

PubMed

Ayoib, Adilah; Hashim, Uda; Gopinath, Subash C B; Md Arshad, M K

2017-11-01

This review covers a developmental progression on early to modern taxonomy at cellular level following the advent of electron microscopy and the advancement in deoxyribonucleic acid (DNA) extraction for expatiation of biological classification at DNA level. Here, we discuss the fundamental values of conventional chemical methods of DNA extraction using liquid/liquid extraction (LLE) followed by development of solid-phase extraction (SPE) methods, as well as recent advances in microfluidics device-based system for DNA extraction on-chip. We also discuss the importance of DNA extraction as well as the advantages over conventional chemical methods, and how Lab-on-a-Chip (LOC) system plays a crucial role for the future achievements.

A Standardised Vocabulary for Identifying Benthic Biota and Substrata from Underwater Imagery: The CATAMI Classification Scheme

PubMed Central

Jordan, Alan; Rees, Tony; Gowlett-Holmes, Karen

2015-01-01

Imagery collected by still and video cameras is an increasingly important tool for minimal impact, repeatable observations in the marine environment. Data generated from imagery includes identification, annotation and quantification of biological subjects and environmental features within an image. To be long-lived and useful beyond their project-specific initial purpose, and to maximize their utility across studies and disciplines, marine imagery data should use a standardised vocabulary of defined terms. This would enable the compilation of regional, national and/or global data sets from multiple sources, contributing to broad-scale management studies and development of automated annotation algorithms. The classification scheme developed under the Collaborative and Automated Tools for Analysis of Marine Imagery (CATAMI) project provides such a vocabulary. The CATAMI classification scheme introduces Australian-wide acknowledged, standardised terminology for annotating benthic substrates and biota in marine imagery. It combines coarse-level taxonomy and morphology, and is a flexible, hierarchical classification that bridges the gap between habitat/biotope characterisation and taxonomy, acknowledging limitations when describing biological taxa through imagery. It is fully described, documented, and maintained through curated online databases, and can be applied across benthic image collection methods, annotation platforms and scoring methods. Following release in 2013, the CATAMI classification scheme was taken up by a wide variety of users, including government, academia and industry. This rapid acceptance highlights the scheme’s utility and the potential to facilitate broad-scale multidisciplinary studies of marine ecosystems when applied globally. Here we present the CATAMI classification scheme, describe its conception and features, and discuss its utility and the opportunities as well as challenges arising from its use. PMID:26509918

Migration in the Anthropocene: how collective navigation, environmental system and taxonomy shape the vulnerability of migratory species.

PubMed

Hardesty-Moore, Molly; Deinet, Stefanie; Freeman, Robin; Titcomb, Georgia C; Dillon, Erin M; Stears, Keenan; Klope, Maggie; Bui, An; Orr, Devyn; Young, Hillary S; Miller-Ter Kuile, Ana; Hughey, Lacey F; McCauley, Douglas J

2018-05-19

Recent increases in human disturbance pose significant threats to migratory species using collective movement strategies. Key threats to migrants may differ depending on behavioural traits (e.g. collective navigation), taxonomy and the environmental system (i.e. freshwater, marine or terrestrial) associated with migration. We quantitatively assess how collective navigation, taxonomic membership and environmental system impact species' vulnerability by (i) evaluating population change in migratory and non-migratory bird, mammal and fish species using the Living Planet Database (LPD), (ii) analysing the role of collective navigation and environmental system on migrant extinction risk using International Union for Conservation of Nature (IUCN) classifications and (iii) compiling literature on geographical range change of migratory species. Likelihood of population decrease differed by taxonomic group: migratory birds were more likely to experience annual declines than non-migrants, while mammals displayed the opposite pattern. Within migratory species in IUCN, we observed that collective navigation and environmental system were important predictors of extinction risk for fishes and birds, but not for mammals, which had overall higher extinction risk than other taxa. We found high phylogenetic relatedness among collectively navigating species, which could have obscured its importance in determining extinction risk. Overall, outputs from these analyses can help guide strategic interventions to conserve the most vulnerable migrations.This article is part of the theme issue 'Collective movement ecology'. © 2018 The Author(s).

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.

Update on diabetes classification.

PubMed

Thomas, Celeste C; Philipson, Louis H

2015-01-01

This article highlights the difficulties in creating a definitive classification of diabetes mellitus in the absence of a complete understanding of the pathogenesis of the major forms. This brief review shows the evolving nature of the classification of diabetes mellitus. No classification scheme is ideal, and all have some overlap and inconsistencies. The only diabetes in which it is possible to accurately diagnose by DNA sequencing, monogenic diabetes, remains undiagnosed in more than 90% of the individuals who have diabetes caused by one of the known gene mutations. The point of classification, or taxonomy, of disease, should be to give insight into both pathogenesis and treatment. It remains a source of frustration that all schemes of diabetes mellitus continue to fall short of this goal. Copyright © 2015 Elsevier Inc. All rights reserved.

[Utilization of nursing diagnosis according to Nanda's classification for the systematization of nursing care in breast feeding].

PubMed

Abrão, A C; de Gutiérrez, M R; Marin, H F

1997-04-01

The present study aimed at describing the reformulated instrument used in the puerperal woman nursing consultation based on the identified diagnoses classification according to the Taxonomy-I reviewed by NANDA, and the identification of the most frequent nursing diagnoses concerning maternal breastfeeding, based on the reformulated instrument. The diagnoses found as being over 50% were: knowledge deficit (100%); sleep pattern disturbance (75%), altered sexuality patterns (75%), ineffective breastfeeding (66.6%) and impaired physical mobility (66.6%).

Populations, Natural Selection, and Applied Organizational Science.

ERIC Educational Resources Information Center

McKelvey, Bill; Aldrich, Howard

1983-01-01

Deficiencies in existing models in organizational science may be remedied by applying the population approach, with its concepts of taxonomy, classification, evolution, and population ecology; and natural selection theory, with its principles of variation, natural selection, heredity, and struggle for existence, to the idea of organizational forms…

Surface plasmon resonance spectroscopy for analysis of influenza vaccines

USDA-ARS?s Scientific Manuscript database

The hemagglutinin (HA) compounds are surface glycoproteins of a virus that can initiate an immune response from a host organism. Hemagglutinin and the related neuraminidase (NA) compounds are the basis for virus strain classification and have become part of the accepted HN taxonomy. These compounds ...

Taxonomy-aware feature engineering for microbiome classification.

PubMed

Oudah, Mai; Henschel, Andreas

2018-06-15

What is a healthy microbiome? The pursuit of this and many related questions, especially in light of the recently recognized microbial component in a wide range of diseases has sparked a surge in metagenomic studies. They are often not simply attributable to a single pathogen but rather are the result of complex ecological processes. Relatedly, the increasing DNA sequencing depth and number of samples in metagenomic case-control studies enabled the applicability of powerful statistical methods, e.g. Machine Learning approaches. For the latter, the feature space is typically shaped by the relative abundances of operational taxonomic units, as determined by cost-effective phylogenetic marker gene profiles. While a substantial body of microbiome/microbiota research involves unsupervised and supervised Machine Learning, very little attention has been put on feature selection and engineering. We here propose the first algorithm to exploit phylogenetic hierarchy (i.e. an all-encompassing taxonomy) in feature engineering for microbiota classification. The rationale is to exploit the often mono- or oligophyletic distribution of relevant (but hidden) traits by virtue of taxonomic abstraction. The algorithm is embedded in a comprehensive microbiota classification pipeline, which we applied to a diverse range of datasets, distinguishing healthy from diseased microbiota samples. We demonstrate substantial improvements over the state-of-the-art microbiota classification tools in terms of classification accuracy, regardless of the actual Machine Learning technique while using drastically reduced feature spaces. Moreover, generalized features bear great explanatory value: they provide a concise description of conditions and thus help to provide pathophysiological insights. Indeed, the automatically and reproducibly derived features are consistent with previously published domain expert analyses.

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.

Nursing diagnosis taxonomy across the Atlantic Ocean: congruence between nurses' charting and the NANDA taxonomy.

PubMed

Thoroddsen, Asta; Thorsteinsson, Hrund Sch

2002-02-01

The purpose of this study was to analyse expressions or terms used by nurses in Iceland to describe patient problems. The classification of NANDA was used as reference. The research questions were: (a) Does NANDA terminology represent patient problems documented by Icelandic nurses? (b) If so, what kind of nursing diagnoses does it represent? (c) What kind of patient problems are not represented by NANDA terminology? (d) What are the most frequent nursing diagnoses used? A retrospective chart review was conducted in a 400 bed acute care hospital in Iceland. The sample was defined as nursing diagnosis statements in charts of patients hospitalized in two 6-month periods in two separate years. The data were analysed according to a predefined grading system based on the PES format or Problem -- (A)aetiology -- Signs and symptoms. A total of 1217 charts were used for the study, which yielded 2171 nursing diagnoses statements for analysis. Charts with at least one nursing diagnosis documented were 60.1% and the number of diagnoses per patient ranged from 0 to 10, with 65% of charts with three diagnoses or less. The number of diagnoses correlated with patients' length of stay, but not with increased age of the patients. The average number of statements per patient was 3.28. Almost 60% of the diagnoses were according to NANDA terminology, another 20% were stated as procedures, medical diagnoses or risks for complications. The 20 most frequently used nursing diagnoses accounted for 80% of all diagnoses documented. Discrepancy between nurses' documentation on emotional problems and availability of diagnosis in the NANDA taxonomy was evident. It can be concluded that the NANDA taxonomy seems to be culturally relevant for nurses in different cultures.

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.

Default taxonomy: Ernst Mayr's view of the microbial world

NASA Technical Reports Server (NTRS)

Woese, C. R.

1998-01-01

This perspective is a response to a taxonomic proposal by E. Mayr ["Two empires or three?" (1998) Proc. Natl. Acad. Sci. USA 95, 9720-9723]. Mayr has suggested that the now accepted classification of life into three primary domains, Archaea, Bacteria, and Eucarya-originally proposed by myself and others--be abandoned in favor of the earlier Prokaryote-Eukaryote classification. Although the matter appears a taxonomic quibble, it is not that simple. At issue here are differing views as to the nature of biological classification, which are underlain by differing views as to what biology is and will be--matters of concern to all biologists.

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.

A Classification of Genre Families in University Student Writing

ERIC Educational Resources Information Center

Gardner, Sheena; Nesi, Hilary

2013-01-01

As demand for English-medium higher education continues to grow internationally and participation in higher education increases, the need for a better understanding of academic writing is pressing. Prior university wide taxonomies of student writing have relied on intuition, the opinions of faculty, or data from course documentation and task…

ICF-CY: A Universal Tool for Documentation of Disability

ERIC Educational Resources Information Center

Simeonsson, Rune J.

2009-01-01

The "International Classification of Functioning, Disability and Health--ICF" (ICF-CY) conceptual framework offers a new paradigm and taxonomy of human functioning disability, which can be used to guide holistic and interdisciplinary approaches to assessment and intervention. In settings serving children, youth, or adults with disabilities, the…

Using Fungi (the Almost-Forgotten Organisms) in the Classroom.

ERIC Educational Resources Information Center

Madrazo, Gerry M., Jr.; Hounshell, Paul B.

1979-01-01

Ideas are given for including fungi in classroom activities for high school biology students. A discussion on the science of taxonomy leads into a discussion on the position of fungi in the five kingdom classification scheme of organisms. Suggestions are given for observing their growth and development. (SA)

Question Classification Taxonomies as Guides to Formulating Questions for Use in Chemistry Classrooms

ERIC Educational Resources Information Center

Festo, Kayima

2016-01-01

Teacher questions play an important role in facilitating classroom discourse. Using appropriate question types and proper questioning techniques help to create reflective-active learners. Teacher questions can elicit students' explanations, elaboration of their ideas and thinking, and they can be used to disclose students' misconceptions. Despite…

Therapist-delivered and self-help interventions for gambling problems: A review of contents.

PubMed

Rodda, Simone; Merkouris, Stephanie S; Abraham, Charles; Hodgins, David C; Cowlishaw, Sean; Dowling, Nicki A

2018-06-13

Background and aims To date, no systematic approach to identifying the content and characteristics of psychological interventions used to reduce gambling or problem gambling has been developed. This study aimed to develop a reliable classification system capable of identifying intervention characteristics that could, potentially, account for greater or lesser effectiveness. Methods Intervention descriptions were content analyzed to identify common and differentiating characteristics. A coder manual was developed and applied by three independent coders to identify the presence or absence of defined characteristics in 46 psychological and self-help gambling interventions. Results The final classification taxonomy, entitled Gambling Intervention System of CharacTerization (GIST), included 35 categories of intervention characteristics. These were assigned to four groups: (a) types of change techniques (18 categories; e.g., cognitive restructuring and relapse prevention), (b) participant and study characteristics (6 categories; e.g., recruitment strategy and remuneration policy), and (c) characteristics of the delivery and conduct of interventions (11 categories; e.g., modality of delivery and therapist involvement), and (d) evaluation characteristics (e.g., type of control group). Interrater reliability of identification of defined characteristics was high (κ = 0.80-1.00). Discussion This research provides a tool that allows systematic identification of intervention characteristics, thereby enabling consideration, not only of whether interventions are effective or not, but also of which domain-relevant characteristics account for greater or lesser effectiveness. The taxonomy also facilitates standardized description of intervention content in a field in which many diverse interventions have been evaluated. Conclusion Application of this coding tool has the potential to accelerate the development of more efficient and effective therapist-delivered and self-directed interventions to reduce gambling problems.

Developing genome-wide microsatellite markers of bamboo and their applications on molecular marker assisted taxonomy for accessions in the genus Phyllostachys.

PubMed

Zhao, Hansheng; Yang, Li; Peng, Zhenhua; Sun, Huayu; Yue, Xianghua; Lou, Yongfeng; Dong, Lili; Wang, Lili; Gao, Zhimin

2015-01-26

Morphology-based taxonomy via exiguously reproductive organ has severely limitation on bamboo taxonomy, mainly owing to infrequent and unpredictable flowering events of bamboo. Here, we present the first genome-wide analysis and application of microsatellites based on the genome of moso bamboo (Phyllostachys edulis) to assist bamboo taxonomy. Of identified 127,593 microsatellite repeat-motifs, the primers of 1,451 microsatellites were designed and 1,098 markers were physically mapped on the genome of moso bamboo. A total of 917 markers were successfully validated in 9 accessions with ~39.8% polymorphic potential. Retrieved from validated microsatellite markers, 23 markers were selected for polymorphic analysis among 78 accessions and 64 alleles were detected with an average of 2.78 alleles per primers. The cluster result indicated the majority of the accessions were consistent with their current taxonomic classification, confirming the suitability and effectiveness of the developed microsatellite markers. The variations of microsatellite marker in different species were confirmed by sequencing and in silico comparative genome mapping were investigated. Lastly, a bamboo microsatellites database (http://www.bamboogdb.org/ssr) was implemented to browse and search large information of bamboo microsatellites. Consequently, our results of microsatellite marker development are valuable for assisting bamboo taxonomy and investigating genomic studies in bamboo and related grass species.

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/

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);…

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.

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

MiDAS 2.0: an ecosystem-specific taxonomy and online database for the organisms of wastewater treatment systems expanded for anaerobic digester groups

PubMed Central

McIlroy, Simon Jon; Kirkegaard, Rasmus Hansen; McIlroy, Bianca; Nierychlo, Marta; Kristensen, Jannie Munk; Karst, Søren Michael; Albertsen, Mads

2017-01-01

Abstract Wastewater is increasingly viewed as a resource, with anaerobic digester technology being routinely implemented for biogas production. Characterising the microbial communities involved in wastewater treatment facilities and their anaerobic digesters is considered key to their optimal design and operation. Amplicon sequencing of the 16S rRNA gene allows high-throughput monitoring of these systems. The MiDAS field guide is a public resource providing amplicon sequencing protocols and an ecosystem-specific taxonomic database optimized for use with wastewater treatment facility samples. The curated taxonomy endeavours to provide a genus-level-classification for abundant phylotypes and the online field guide links this identity to published information regarding their ecology, function and distribution. This article describes the expansion of the database resources to cover the organisms of the anaerobic digester systems fed primary sludge and surplus activated sludge. The updated database includes descriptions of the abundant genus-level-taxa in influent wastewater, activated sludge and anaerobic digesters. Abundance information is also included to allow assessment of the role of emigration in the ecology of each phylotype. MiDAS is intended as a collaborative resource for the progression of research into the ecology of wastewater treatment, by providing a public repository for knowledge that is accessible to all interested in these biotechnologically important systems. Database URL: http://www.midasfieldguide.org PMID:28365734

A Five-Year Evaluation of Examination Structure in a Cardiovascular Pharmacotherapy Course

PubMed Central

Kolar, Claire; Janke, Kristin K.

2015-01-01

Objective. To evaluate the composition and effectiveness as an assessment tool of a criterion-referenced examination comprised of clinical cases tied to practice decisions, to examine the effect of varying audience response system (ARS) questions on student examination preparation, and to articulate guidelines for structuring examinations to maximize evaluation of student learning. Design. Multiple-choice items developed over 5 years were evaluated using Bloom’s Taxonomy classification, point biserial correlation, item difficulty, and grade distribution. In addition, examination items were classified into categories based on similarity to items used in ARS preparation. Assessment. As the number of items directly tied to clinical practice rose, Bloom’s Taxonomy level and item difficulty also rose. In examination years where Bloom’s levels were high but preparation was minimal, average grade distribution was lower compared with years in which student preparation was higher. Conclusion. Criterion-referenced examinations can benefit from systematic evaluation of their composition and effectiveness as assessment tools. Calculated design and delivery of classroom preparation is an asset in improving examination performance on rigorous, practice-relevant examinations. PMID:27168611

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.

Synergy of airborne LiDAR and Worldview-2 satellite imagery for land cover and habitat mapping: A BIO_SOS-EODHaM case study for the Netherlands

NASA Astrophysics Data System (ADS)

Mücher, C. A.; Roupioz, L.; Kramer, H.; Bogers, M. M. B.; Jongman, R. H. G.; Lucas, R. M.; Kosmidou, V. E.; Petrou, Z.; Manakos, I.; Padoa-Schioppa, E.; Adamo, M.; Blonda, P.

2015-05-01

A major challenge is to develop a biodiversity observation system that is cost effective and applicable in any geographic region. Measuring and reliable reporting of trends and changes in biodiversity requires amongst others detailed and accurate land cover and habitat maps in a standard and comparable way. The objective of this paper is to assess the EODHaM (EO Data for Habitat Mapping) classification results for a Dutch case study. The EODHaM system was developed within the BIO_SOS (The BIOdiversity multi-SOurce monitoring System: from Space TO Species) project and contains the decision rules for each land cover and habitat class based on spectral and height information. One of the main findings is that canopy height models, as derived from LiDAR, in combination with very high resolution satellite imagery provides a powerful input for the EODHaM system for the purpose of generic land cover and habitat mapping for any location across the globe. The assessment of the EODHaM classification results based on field data showed an overall accuracy of 74% for the land cover classes as described according to the Food and Agricultural Organization (FAO) Land Cover Classification System (LCCS) taxonomy at level 3, while the overall accuracy was lower (69.0%) for the habitat map based on the General Habitat Category (GHC) system for habitat surveillance and monitoring. A GHC habitat class is determined for each mapping unit on the basis of the composition of the individual life forms and height measurements. The classification showed very good results for forest phanerophytes (FPH) when individual life forms were analyzed in terms of their percentage coverage estimates per mapping unit from the LCCS classification and validated with field surveys. Analysis for shrubby chamaephytes (SCH) showed less accurate results, but might also be due to less accurate field estimates of percentage coverage. Overall, the EODHaM classification results encouraged us to derive the heights of all vegetated objects in the Netherlands from LiDAR data, in preparation for new habitat classifications.

A Systematic Classification for HVAC Systems and Components

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

Li, Han; Chen, Yan; Zhang, Jian

Depending on the application, the complexity of an HVAC system can range from a small fan coil unit to a large centralized air conditioning system with primary and secondary distribution loops, and central plant components. Currently, the taxonomy of HVAC systems and the components has various aspects, which can get quite complex because of the various components and system configurations. For example, based on cooling and heating medium delivered to terminal units, systems can be classified as either air systems, water systems or air-water systems. In addition, some of the system names might be commonly used in a confusing manner,more » such as “unitary system” vs. “packaged system.” Without a systematic classification, these components and system terminology can be confusing to understand or differentiate from each other, and it creates ambiguity in communication, interpretation, and documentation. It is valuable to organize and classify HVAC systems and components so that they can be easily understood and used in a consistent manner. This paper aims to develop a systematic classification of HVAC systems and components. First, we summarize the HVAC component information and definitions based on published literature, such as ASHRAE handbooks, regulations, and rating standards. Then, we identify common HVAC system types and map them to the collected components in a meaningful way. Classification charts are generated and described based on the component information. Six main categories are identified for the HVAC components and equipment, i.e., heating and cooling production, heat extraction and rejection, air handling process, distribution system, terminal use, and stand-alone system. Components for each main category are further analyzed and classified in detail. More than fifty system names are identified and grouped based on their characteristics. The result from this paper will be helpful for education, communication, and systems and component documentation.« less

A replacement name for Asthenes wyatti perijanus Phelps 1977

USGS Publications Warehouse

Chesser, R. Terry

2016-01-01

A recent near-complete phylogeny of the avian family Furnariidae (Derryberry et al. 2011) found a number of discrepancies between the phylogeny and the then-current taxonomy of the group, and several changes were proposed to reconcile the taxonomy of the family with the phylogeny. Among these was the merging of the genus Schizoeaca Cabanis 1873 into Asthenes Reichenbach 1853 (Derryberry et al. 2010). This change has now been generally adopted. The Committee on Classification and Nomenclature (South America) of the American Ornithologists’ Union (Remsen et al. 2015) passed a proposal to merge the genera in 2010, and recent global reference works (e.g., Dickinson & Christidis 2014) have likewise adopted the lumping of these genera.

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

Ventilator-Related Adverse Events: A Taxonomy and Findings From 3 Incident Reporting Systems.

PubMed

Pham, Julius Cuong; Williams, Tamara L; Sparnon, Erin M; Cillie, Tam K; Scharen, Hilda F; Marella, William M

2016-05-01

In 2009, researchers from Johns Hopkins University's Armstrong Institute for Patient Safety and Quality; public agencies, including the FDA; and private partners, including the Emergency Care Research Institute and the University HealthSystem Consortium (UHC) Safety Intelligence Patient Safety Organization, sought to form a public-private partnership for the promotion of patient safety (P5S) to advance patient safety through voluntary partnerships. The study objective was to test the concept of the P5S to advance our understanding of safety issues related to ventilator events, to develop a common classification system for categorizing adverse events related to mechanical ventilators, and to perform a comparison of adverse events across different adverse event reporting systems. We performed a cross-sectional analysis of ventilator-related adverse events reported in 2012 from the following incident reporting systems: the Pennsylvania Patient Safety Authority's Patient Safety Reporting System, UHC's Safety Intelligence Patient Safety Organization database, and the FDA's Manufacturer and User Facility Device Experience database. Once each organization had its dataset of ventilator-related adverse events, reviewers read the narrative descriptions of each event and classified it according to the developed common taxonomy. A Pennsylvania Patient Safety Authority, FDA, and UHC search provided 252, 274, and 700 relevant reports, respectively. The 3 event types most commonly reported to the UHC and the Pennsylvania Patient Safety Authority's Patient Safety Reporting System databases were airway/breathing circuit issue, human factor issues, and ventilator malfunction events. The top 3 event types reported to the FDA were ventilator malfunction, power source issue, and alarm failure. Overall, we found that (1) through the development of a common taxonomy, adverse events from 3 reporting systems can be evaluated, (2) the types of events reported in each database were related to the purpose of the database and the source of the reports, resulting in significant differences in reported event categories across the 3 systems, and (3) a public-private collaboration for investigating ventilator-related adverse events under the P5S model is feasible. Copyright © 2016 by Daedalus Enterprises.

The Tree of Animal Life

ERIC Educational Resources Information Center

Braude, Stan

2007-01-01

In this article, the author describes a short activity which introduces third- to fifth-grade students to animal classification. The Tree of Animal Life activity is a simple, sorting exercise that can help them see a bigger picture. The activity sets the stage for learning about animal taxonomy and introduces the characteristics of various animal…

The Influence of Pronunciation Learning Strategies on Mastering English Vowels

ERIC Educational Resources Information Center

Rokoszewska, Katarzyna

2012-01-01

The present paper focuses on the role of strategies in learning the pronunciation of the target language. First, an outline of various general classifications of language learning strategies is provided. Next, pronunciation learning strategies are defined and their various taxonomies are presented. This is followed by the description of the study…

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

Folk taxonomy and use of mushrooms in communities around Ngorongoro and Serengeti National Park, Tanzania.

PubMed

Tibuhwa, Donatha Damian

2012-09-21

Maasai and Kurya form two main communities around the Serengeti National Park in Tanzania which are mainly pastoralists. Changing climate to excessive drought, have recently forced them to start practicing subsistence farming which is severely affected by wild animals. This study explored status of the folk taxonomy and uses of mushrooms in the two communities as a pave way for possibilities of introducing mushroom cultivation, an alternative crop which is hardly affected by wild animals. Folk taxonomy and use mushrooms by the Kurya and Maasai communities were investigated. Information was collected by face to face interviews with 150 individuals in 6 selected villages. Using descriptive statistics by Statistic Package for the Social Science (SPSS) version 17.0, the demographic characteristics of informants were evaluated and cross relationships with the recorded data were analysed. Kurya are mycophilic with 94% of the informants recognizing utilization of the wild mushroom either as foodstuff or as tonics while the Maasai are mycophobic with 99% being unaware of the edibility of mushroom although 28% recognized mushrooms as tonic. For both communities, the knowledge of mushroom utilization and folk taxonomy increased with age of the informants, while it decreases with formal education level of the informants which imply that the basis of knowledge is mainly traditional. Comparing the two communities, the Maasai use mushrooms only for medicinal purposes and never sought them for food while the Kurya were well knowledgeable on the edibility and folk classification especially the Termitomyces species. Characters used in folkal taxonomy included color and size of the basidiomata, shape and size of the pseudorrhiza, habitats and edibility information. A new use of ascospores whereby they anaesthaesia bees during honey harvesting was discovered, and mushroom cultivation was widely welcomed (94.7%) as an alternative crop which is rarely affected by wild animals. In order to salvage a noted tremendous decrease of knowledge in mushroom utilization and folk taxonomy from vanishing, there is a need to document it throughout, and incorporate it in lower levels of our education system. Mushroom cultivation may possibly be the best alternative crop for the two communities thus should be advocated for improving livelihood and reduce human wildlife conflicts. The new recorded use of ascospores to anaesthaesia the bees during honey harvesting should be exploited and scaled up for sustainable integrated bee keeping and mushroom farming.

Formalization of the classification pattern: survey of classification modeling in information systems engineering.

PubMed

Partridge, Chris; de Cesare, Sergio; Mitchell, Andrew; Odell, James

2018-01-01

Formalization is becoming more common in all stages of the development of information systems, as a better understanding of its benefits emerges. Classification systems are ubiquitous, no more so than in domain modeling. The classification pattern that underlies these systems provides a good case study of the move toward formalization in part because it illustrates some of the barriers to formalization, including the formal complexity of the pattern and the ontological issues surrounding the "one and the many." Powersets are a way of characterizing the (complex) formal structure of the classification pattern, and their formalization has been extensively studied in mathematics since Cantor's work in the late nineteenth century. One can use this formalization to develop a useful benchmark. There are various communities within information systems engineering (ISE) that are gradually working toward a formalization of the classification pattern. However, for most of these communities, this work is incomplete, in that they have not yet arrived at a solution with the expressiveness of the powerset benchmark. This contrasts with the early smooth adoption of powerset by other information systems communities to, for example, formalize relations. One way of understanding the varying rates of adoption is recognizing that the different communities have different historical baggage. Many conceptual modeling communities emerged from work done on database design, and this creates hurdles to the adoption of the high level of expressiveness of powersets. Another relevant factor is that these communities also often feel, particularly in the case of domain modeling, a responsibility to explain the semantics of whatever formal structures they adopt. This paper aims to make sense of the formalization of the classification pattern in ISE and surveys its history through the literature, starting from the relevant theoretical works of the mathematical literature and gradually shifting focus to the ISE literature. The literature survey follows the evolution of ISE's understanding of how to formalize the classification pattern. The various proposals are assessed using the classical example of classification; the Linnaean taxonomy formalized using powersets as a benchmark for formal expressiveness. The broad conclusion of the survey is that (1) the ISE community is currently in the early stages of the process of understanding how to formalize the classification pattern, particularly in the requirements for expressiveness exemplified by powersets, and (2) that there is an opportunity to intervene and speed up the process of adoption by clarifying this expressiveness. Given the central place that the classification pattern has in domain modeling, this intervention has the potential to lead to significant improvements.

Taxonomy for complexity theory in the context of maternity care.

PubMed

Nieuwenhuijze, Marianne; Downe, Soo; Gottfreðsdóttir, Helga; Rijnders, Marlies; du Preez, Antoinette; Vaz Rebelo, Piedade

2015-09-01

The linear focus of 'normal science' is unable to adequately take account of the complex interactions that direct health care systems. There is a turn towards complexity theory as a more appropriate framework for understanding system behaviour. However, a comprehensive taxonomy for complexity theory in the context of health care is lacking. This paper aims to build a taxonomy based on the key complexity theory components that have been used in publications on complexity theory and health care, and to explore their explanatory power for health care system behaviour, specifically for maternity care. A search strategy was devised in PubMed and 31 papers were identified as relevant for the taxonomy. The final taxonomy for complexity theory included and defined 11 components. The use of waterbirth and the impact of the Term Breech trial showed that each of the components of our taxonomy has utility in helping to understand how these techniques became widely adopted. It is not just the components themselves that characterise a complex system but also the dynamics between them. Copyright © 2015 Elsevier Ltd. All rights reserved.

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...

The Aeronautical Data Link: Taxonomy, Architectural Analysis, and Optimization

NASA Technical Reports Server (NTRS)

Morris, A. Terry; Goode, Plesent W.

2002-01-01

The future Communication, Navigation, and Surveillance/Air Traffic Management (CNS/ATM) System will rely on global satellite navigation, and ground-based and satellite based communications via Multi-Protocol Networks (e.g. combined Aeronautical Telecommunications Network (ATN)/Internet Protocol (IP)) to bring about needed improvements in efficiency and safety of operations to meet increasing levels of air traffic. This paper will discuss the development of an approach that completely describes optimal data link architecture configuration and behavior to meet the multiple conflicting objectives of concurrent and different operations functions. The practical application of the approach enables the design and assessment of configurations relative to airspace operations phases. The approach includes a formal taxonomic classification, an architectural analysis methodology, and optimization techniques. The formal taxonomic classification provides a multidimensional correlation of data link performance with data link service, information protocol, spectrum, and technology mode; and to flight operations phase and environment. The architectural analysis methodology assesses the impact of a specific architecture configuration and behavior on the local ATM system performance. Deterministic and stochastic optimization techniques maximize architectural design effectiveness while addressing operational, technology, and policy constraints.

On Identifying Clusters Within the C-type Asteroids of the Sloan Digital Sky Survey

NASA Astrophysics Data System (ADS)

Poole, Renae; Ziffer, J.; Harvell, T.

2012-10-01

We applied AutoClass, a data mining technique based upon Bayesian Classification, to C-group asteroid colors in the Sloan Digital Sky Survey (SDSS). Previous taxonomic studies relied mostly on Principal Component Analysis (PCA) to differentiate asteroids within the C-group (e.g. B, G, F, Ch, Cg and Cb). AutoClass's advantage is that it calculates the most probable classification for us, removing the human factor from this part of the analysis. In our results, AutoClass divided the C-groups into two large classes and six smaller classes. The two large classes (n=4974 and 2033, respectively) display distinct regions with some overlap in color-vs-color plots. Each cluster's average spectrum is compared to 'typical' spectra of the C-group subtypes as defined by Tholen (1989) and each cluster's members are evaluated for consistency with previous taxonomies. Of the 117 asteroids classified as B-type in previous taxonomies, only 12 were found with SDSS colors that matched our criteria of having less than 0.1 magnitude error in u and 0.05 magnitude error in g, r, i, and z colors. Although this is a relatively small group, 11 of the 12 B-types were placed by AutoClass in the same cluster. By determining the C-group sub-classifications in the large SDSS database, this research furthers our understanding of the stratigraphy and composition of the main-belt.

A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes

PubMed Central

2013-01-01

Background The extant squamates (>9400 known species of lizards and snakes) are one of the most diverse and conspicuous radiations of terrestrial vertebrates, but no studies have attempted to reconstruct a phylogeny for the group with large-scale taxon sampling. Such an estimate is invaluable for comparative evolutionary studies, and to address their classification. Here, we present the first large-scale phylogenetic estimate for Squamata. Results The estimated phylogeny contains 4161 species, representing all currently recognized families and subfamilies. The analysis is based on up to 12896 base pairs of sequence data per species (average = 2497 bp) from 12 genes, including seven nuclear loci (BDNF, c-mos, NT3, PDC, R35, RAG-1, and RAG-2), and five mitochondrial genes (12S, 16S, cytochrome b, ND2, and ND4). The tree provides important confirmation for recent estimates of higher-level squamate phylogeny based on molecular data (but with more limited taxon sampling), estimates that are very different from previous morphology-based hypotheses. The tree also includes many relationships that differ from previous molecular estimates and many that differ from traditional taxonomy. Conclusions We present a new large-scale phylogeny of squamate reptiles that should be a valuable resource for future comparative studies. We also present a revised classification of squamates at the family and subfamily level to bring the taxonomy more in line with the new phylogenetic hypothesis. This classification includes new, resurrected, and modified subfamilies within gymnophthalmid and scincid lizards, and boid, colubrid, and lamprophiid snakes. PMID:23627680

eVITAL: A Preliminary Taxonomy and Electronic Toolkit of Health-Related Habits and Lifestyle

PubMed Central

Salvador-Carulla, Luis; Olson Walsh, Carolyn; Alonso, Federico; Gómez, Rafael; de Teresa, Carlos; Cabo-Soler, José Ricardo; Cano, Antonio; Ruiz, Mencía

2012-01-01

Objectives. To create a preliminary taxonomy and related toolkit of health-related habits (HrH) following a person-centered approach with a focus on primary care. Methods. From 2003–2009, a working group (n = 6 physicians) defined the knowledge base, created a framing document, and selected evaluation tools using an iterative process. Multidisciplinary focus groups (n = 29 health professionals) revised the document and evaluation protocol and participated in a feasibility study and review of the model based on a demonstration study with 11 adult volunteers in Antequera, Spain. Results. The preliminary taxonomy contains 6 domains of HrH and 1 domain of additional health descriptors, 3 subdomains, 43 dimensions, and 141 subdimensions. The evaluation tool was completed by the 11 volunteers. The eVITAL toolkit contains history and examination items for 4 levels of engagement: self-assessment, basic primary care, extended primary care, and specialty care. There was positive feedback from the volunteers and experts, but concern about the length of the evaluation. Conclusions. We present the first taxonomy of HrH, which may aid the development of the new models of care such as the personal contextual factors of the International Classification of Functioning (ICF) and the positive and negative components of the multilevel person-centered integrative diagnosis model. PMID:22545016

EAU standardised medical terminology for urologic imaging: a taxonomic approach.

PubMed

Loch, Tillmann; Carey, Brendan; Walz, Jochen; Fulgham, Pat Fox

2015-05-01

The terminology and abbreviations used in urologic imaging have generally been adopted on an ad hoc basis by different speciality groups; however, there is a need for shared nomenclature to facilitate clinical communication and collaborative research. This work reviews the current nomenclature for urologic imaging used in clinical practice and proposes a taxonomy and terminology for urologic imaging studies. A list of terms used in urologic imaging were compiled from guidelines published by the European Association of Urology and the American Urological Association and from the American College of Radiology Appropriateness Criteria. Terms searched were grouped into broad categories based on technology, and imaging terms were further stratified based on the anatomic extent, contrast or phases, technique or modifiers, and combinations or fusions. Terms that had a high degree of utilisation were classified as accepted. We propose a new taxonomy to define a more useful and acceptable nomenclature model acceptable to all health professionals involved in urology. The major advantage of a taxonomic approach to the classification of urologic imaging studies is that it provides a flexible framework for classifying the modifications of current imaging modalities and allows the incorporation of new imaging modalities. The adoption of this hierarchical classification model ranging from the most general to the most detailed descriptions should facilitate hierarchical searches of the medical literature using both general and specific terms. This work is limited in its scope, as it is not currently all-inclusive. This will hopefully be addressed by future modification as others embrace the concept and work towards uniformity in nomenclature. This paper provides a noncomprehensive list of the most widely used terms across different specialties. This list can be used as the basis for further discussion, development, and enhancement. In this paper we describe a classification system for urologic imaging terms with the aim of aiding health professionals and ensuring that the terms used are more consistent. Copyright © 2014 European Association of Urology. Published by Elsevier B.V. All rights reserved.

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.

ICDTag: a prototype for a web-based system for organizing physician-written blog posts using a hybrid taxonomy-folksonomy approach.

PubMed

Batch, Yamen; Yusof, Maryati Mohd; Noah, Shahrul Azman

2013-02-27

Medical blogs have emerged as new media, extending to a wider range of medical audiences, including health professionals and patients to share health-related information. However, extraction of quality health-related information from medical blogs is challenging primarily because these blogs lack systematic methods to organize their posts. Medical blogs can be categorized according to their author into (1) physician-written blogs, (2) nurse-written blogs, and (3) patient-written blogs. This study focuses on how to organize physician-written blog posts that discuss disease-related issues and how to extract quality information from these posts. The goal of this study was to create and implement a prototype for a Web-based system, called ICDTag, based on a hybrid taxonomy-folksonomy approach that follows a combination of a taxonomy classification schemes and user-generated tags to organize physician-written blog posts and extract information from these posts. First, the design specifications for the Web-based system were identified. This system included two modules: (1) a blogging module that was implemented as one or more blogs, and (2) an aggregator module that aggregated posts from different blogs into an aggregator website. We then developed a prototype for this system in which the blogging module included two blogs, the cardiology blog and the gastroenterology blog. To analyze the usage patterns of the prototype, we conducted an experiment with data provided by cardiologists and gastroenterologists. Next, we conducted two evaluation types: (1) an evaluation of the ICDTag blog, in which the browsing functionalities of the blogging module were evaluated from the end-user's perspective using an online questionnaire, and (2) an evaluation of information quality, in which the quality of the content on the aggregator website was assessed from the perspective of medical experts using an emailed questionnaire. Participants of this experiment included 23 cardiologists and 24 gastroenterologists. Positive evaluations on the main functions and the organization of information on the ICDTag blogs were given by 18 of the participants via an online questionnaire. These results supported our hypothesis that the use of a taxonomy-folksonomy structure has significant potential to improve the organization of information in physician-written blogs. The quality of the content on the aggregator website was assessed by 3 cardiology experts and 3 gastroenterology experts via an email questionnaire. The results of this questionnaire demonstrated that the experts considered the aggregated tags and categories semantically related to the posts' content. This study demonstrated that applying the hybrid taxonomy-folksonomy approach to physician-written blogs that discuss disease-related issues has valuable potential to make these blogs a more organized and systematic medium and supports the extraction of quality information from their posts. Thus, it is worthwhile to develop more mature systems that make use of the hybrid approach to organize posts in physician-written blogs.

Characters in Arctostaphylos taxonomy

USGS Publications Warehouse

Keeley, Jon E.; Parker, V. Thomas; Vasey, Michael C.

2017-01-01

There is value in understanding the past and how it has affected the present. Science focuses on empirical findings, and we know that our prior experiences and those of our predecessors play important roles in determining how we interpret the present. We learn from accomplishments and foibles of predecessors and appreciate the real life experiences we have gone through. In our studies of the genus Arctostaphylos Adans. we have been struck by the fascinating stories surrounding taxonomists who have played roles in the development of our current understanding of the group. In addition to providing insights, they sometimes provide humor and lessons on the value of competition versus collaboration. We offer this history of the humans that forged the taxonomy behind Arctostaphylos classification in this light.

Chemical taxonomy of the hinge-ligament proteins of bivalves according to their amino acid compositions.

PubMed Central

Kikuchi, Y; Tamiya, N

1987-01-01

The proteins in the hinge ligaments of molluscan bivalves were subjected to chemotaxonomic studies according to their amino acid compositions. The hinge-ligament protein is a new class of structure proteins, and this is the first attempt to introduce chemical taxonomy into the systematics of bivalves. The hinge-ligament proteins from morphologically close species, namely mactra (superfamily Mactracea) or scallop (family Pectinidae) species, showed high intraspecific homology in their compositions. On the other hand, inconsistent results were obtained with two types of ligament proteins in pearl oyster species (genus Pinctada). The results of our chemotaxonomic analyses were sometimes in good agreement with the morphological classifications and sometimes inconsistent, implying a complicated phylogenetic relationship among the species. PMID:3593265

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 and distribution of phenazine-1-carboxylic acid-producing Pseudomonas spp. in the dryland agroecosystem of the Inland Pacific Northwest

USDA-ARS?s Scientific Manuscript database

Five distinct phenazine-producing Pseudomonas species were found, two of which were provisionally ascribed as new species. Agroclimatic zone and the soil silt content were found to affect the distribution of the different species. This study clarifies the classification of these important plant bene...

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...

The Campus Resources of Higher Education in the United States of America: A Taxonomy of Types and A Geographical Distribution.

ERIC Educational Resources Information Center

Irwin, Judith T., Comp.

This document presents a classification of the campus resources of higher education institutions in the United States. After the foreword, the institutions are divided into 5 categories: doctoral-granting universities; comprehensive colleges and universities; general baccalaureate colleges; 2-year colleges, and separate specialized professional…

MiDAS 2.0: an ecosystem-specific taxonomy and online database for the organisms of wastewater treatment systems expanded for anaerobic digester groups.

PubMed

McIlroy, Simon Jon; Kirkegaard, Rasmus Hansen; McIlroy, Bianca; Nierychlo, Marta; Kristensen, Jannie Munk; Karst, Søren Michael; Albertsen, Mads; Nielsen, Per Halkjær

2017-01-01

Wastewater is increasingly viewed as a resource, with anaerobic digester technology being routinely implemented for biogas production. Characterising the microbial communities involved in wastewater treatment facilities and their anaerobic digesters is considered key to their optimal design and operation. Amplicon sequencing of the 16S rRNA gene allows high-throughput monitoring of these systems. The MiDAS field guide is a public resource providing amplicon sequencing protocols and an ecosystem-specific taxonomic database optimized for use with wastewater treatment facility samples. The curated taxonomy endeavours to provide a genus-level-classification for abundant phylotypes and the online field guide links this identity to published information regarding their ecology, function and distribution. This article describes the expansion of the database resources to cover the organisms of the anaerobic digester systems fed primary sludge and surplus activated sludge. The updated database includes descriptions of the abundant genus-level-taxa in influent wastewater, activated sludge and anaerobic digesters. Abundance information is also included to allow assessment of the role of emigration in the ecology of each phylotype. MiDAS is intended as a collaborative resource for the progression of research into the ecology of wastewater treatment, by providing a public repository for knowledge that is accessible to all interested in these biotechnologically important systems. http://www.midasfieldguide.org. © The Author(s) 2017. Published by Oxford University Press.

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.

Costs to Automate Demand Response - Taxonomy and Results from Field Studies and Programs

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

Piette, Mary A.; Schetrit, Oren; Kiliccote, Sila

During the past decade, the technology to automate demand response (DR) in buildings and industrial facilities has advanced significantly. Automation allows rapid, repeatable, reliable operation. This study focuses on costs for DR automation in commercial buildings with some discussion on residential buildings and industrial facilities. DR automation technology relies on numerous components, including communication systems, hardware and software gateways, standards-based messaging protocols, controls and integration platforms, and measurement and telemetry systems. This report compares cost data from several DR automation programs and pilot projects, evaluates trends in the cost per unit of DR and kilowatts (kW) available from automated systems,more » and applies a standard naming convention and classification or taxonomy for system elements. Median costs for the 56 installed automated DR systems studied here are about $200/kW. The deviation around this median is large with costs in some cases being an order of magnitude great or less than the median. This wide range is a result of variations in system age, size of load reduction, sophistication, and type of equipment included in cost analysis. The costs to automate fast DR systems for ancillary services are not fully analyzed in this report because additional research is needed to determine the total cost to install, operate, and maintain these systems. However, recent research suggests that they could be developed at costs similar to those of existing hot-summer DR automation systems. This report considers installation and configuration costs and does include the costs of owning and operating DR automation systems. Future analysis of the latter costs should include the costs to the building or facility manager costs as well as utility or third party program manager cost.« less

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.

[Opinions and nurse' satisfaction with INICIARE 2.0 scale: A qualitative study in a hospital setting].

PubMed

Porcel-Gálvez, Ana María; Hörner Schlindwein-Meirelles, Betina; Gil-García, Eugenia; Morales-Asencio, José Miguel; Guerra-Martín, María Dolores

To know the opinions and satisfaction of nurses with the use of INICIARE, an instrument developed for assessment of nursing care needs in hospitalized patients. INICIARE is based on Virginia Henderson's conceptual model, and built up with indicators of Nursing Outcomes Classification (NOC) taxonomy. Exploratory qualitative study, using focus group technique for data collection. The sessions were recorded until saturation of information. A content analysis of syntactic, semantic and pragmatic levels of transcripts was performed. Participants' informed consent was obtained. Three focus groups were developed; 24 nurses from two Public Hospitals in Andalusia (Southern Spain) participated; and four thematic categories were created to measure satisfaction with the instrument. INICIARE helped the nursing process. Its closed format, and items in NOC taxonomy streamline evaluation, facilitates its inclusion in Electronic Information Systems, and strengthens effective communication at all levels. Nurses are satisfied with the use of INICIARE scale as a tool to enhance quality of care. It also has potential to be used as a tool for decision making in management of nursing care. Copyright © 2016 Elsevier España, S.L.U. All rights reserved.

A new classification scheme of European cold-water coral habitats: Implications for ecosystem-based management of the deep sea

NASA Astrophysics Data System (ADS)

Davies, J. S.; Guillaumont, B.; Tempera, F.; Vertino, A.; Beuck, L.; Ólafsdóttir, S. H.; Smith, C. J.; Fosså, J. H.; van den Beld, I. M. J.; Savini, A.; Rengstorf, A.; Bayle, C.; Bourillet, J.-F.; Arnaud-Haond, S.; Grehan, A.

2017-11-01

Cold-water corals (CWC) can form complex structures which provide refuge, nursery grounds and physical support for a diversity of other living organisms. However, irrespectively from such ecological significance, CWCs are still vulnerable to human pressures such as fishing, pollution, ocean acidification and global warming Providing coherent and representative conservation of vulnerable marine ecosystems including CWCs is one of the aims of the Marine Protected Areas networks being implemented across European seas and oceans under the EC Habitats Directive, the Marine Strategy Framework Directive and the OSPAR Convention. In order to adequately represent ecosystem diversity, these initiatives require a standardised habitat classification that organises the variety of biological assemblages and provides consistent and functional criteria to map them across European Seas. One such classification system, EUNIS, enables a broad level classification of the deep sea based on abiotic and geomorphological features. More detailed lower biotope-related levels are currently under-developed, particularly with regards to deep-water habitats (>200 m depth). This paper proposes a hierarchical CWC biotope classification scheme that could be incorporated by existing classification schemes such as EUNIS. The scheme was developed within the EU FP7 project CoralFISH to capture the variability of CWC habitats identified using a wealth of seafloor imagery datasets from across the Northeast Atlantic and Mediterranean. Depending on the resolution of the imagery being interpreted, this hierarchical scheme allows data to be recorded from broad CWC biotope categories down to detailed taxonomy-based levels, thereby providing a flexible yet valuable information level for management. The CWC biotope classification scheme identifies 81 biotopes and highlights the limitations of the classification framework and guidance provided by EUNIS, the EC Habitats Directive, OSPAR and FAO; which largely underrepresent CWC habitats.

Functional Constructivism: In Search of Formal Descriptors.

PubMed

Trofimova, Irina

2017-10-01

The Functional Constructivism (FC) paradigm is an alternative to behaviorism and considers behavior as being generated every time anew, based on an individual's capacities, environmental resources and demands. Walter Freeman's work provided us with evidence supporting the FC principles. In this paper we make parallels between gradual construction processes leading to the formation of individual behavior and habits, and evolutionary processes leading to the establishment of biological systems. Referencing evolutionary theory, several formal descriptors of such processes are proposed. These FC descriptors refer to the most universal aspects for constructing consistent structures: expansion of degrees of freedom, integration processes based on internal and external compatibility between systems and maintenance processes, all given in four different classes of systems: (a) Zone of Proximate Development (poorly defined) systems; (b) peer systems with emerging reproduction of multiple siblings; (c) systems with internalized integration of behavioral elements ('cruise controls'); and (d) systems capable of handling low-probability, not yet present events. The recursive dynamics within this set of descriptors acting on (traditional) downward, upward and horizontal directions of evolution, is conceptualized as diagonal evolution, or di-evolution. Two examples applying these FC descriptors to taxonomy are given: classification of the functionality of neuro-transmitters and temperament traits; classification of mental disorders. The paper is an early step towards finding a formal language describing universal tendencies in highly diverse, complex and multi-level transient systems known in ecology and biology as 'contingency cycles.'

A Place for Sexual Dysfunctions in an Empirical Taxonomy of Psychopathology

PubMed Central

Forbes, Miriam K.; Baillie, Andrew J.; Eaton, Nicholas R.; Krueger, Robert F.

2017-01-01

Sexual dysfunctions commonly co-occur with various depressive and anxiety disorders. An emerging framework for understanding the classification of mental disorders suggests that such comorbidity is a manifestation of underlying dimensions of psychopathology (or “spectra”). In this review, we synthesize the evidence that sexual dysfunctions should be included in the empirical taxonomy of psychopathology as part of the internalizing spectrum, which accounts for comorbidity among the depressive and anxiety disorders. The review has four parts. Part 1 summarizes the empirical basis and utility of the empirical taxonomy of psychopathology. Part 2 reviews the prima facie evidence for the hypothesis that sexual dysfunctions are part of the internalizing spectrum (i.e., high rates of comorbidity; shared cognitive, affective, and temperament characteristics; common neural substrates and biomarkers; shared course and treatment response; and the lack of causal relationships between them). Part 3 critically analyzes and integrates the results of the eight studies that have addressed this hypothesis. Finally, Part 4 examines the implications of reconceptualizing sexual dysfunctions as part of the internalizing spectrum, and explores avenues for future research. PMID:28121167

A Place for Sexual Dysfunctions in an Empirical Taxonomy of Psychopathology.

PubMed

Forbes, Miriam K; Baillie, Andrew J; Eaton, Nicholas R; Krueger, Robert F

Sexual dysfunctions commonly co-occur with various depressive and anxiety disorders. An emerging framework for understanding the classification of mental disorders suggests that such comorbidity is a manifestation of underlying dimensions of psychopathology (or "spectra"). In this review, we synthesize the evidence that sexual dysfunctions should be included in the empirical taxonomy of psychopathology as part of the internalizing spectrum, which accounts for comorbidity among the depressive and anxiety disorders. The review has four parts. Part 1 summarizes the empirical basis and utility of the empirical taxonomy of psychopathology. Part 2 reviews the prima facie evidence for the hypothesis that sexual dysfunctions are part of the internalizing spectrum (i.e., high rates of comorbidity; shared cognitive, affective, and temperament characteristics; common neural substrates and biomarkers; shared course and treatment response; and the lack of causal relationships between them). Part 3 critically analyzes and integrates the results of the eight studies that have addressed this hypothesis. Finally, Part 4 examines the implications of reconceptualizing sexual dysfunctions as part of the internalizing spectrum, and explores avenues for future research.

Review of fall detection techniques: A data availability perspective.

PubMed

Khan, Shehroz S; Hoey, Jesse

2017-01-01

A fall is an abnormal activity that occurs rarely; however, missing to identify falls can have serious health and safety implications on an individual. Due to the rarity of occurrence of falls, there may be insufficient or no training data available for them. Therefore, standard supervised machine learning methods may not be directly applied to handle this problem. In this paper, we present a taxonomy for the study of fall detection from the perspective of availability of fall data. The proposed taxonomy is independent of the type of sensors used and specific feature extraction/selection methods. The taxonomy identifies different categories of classification methods for the study of fall detection based on the availability of their data during training the classifiers. Then, we present a comprehensive literature review within those categories and identify the approach of treating a fall as an abnormal activity to be a plausible research direction. We conclude our paper by discussing several open research problems in the field and pointers for future research. Copyright © 2016 IPEM. Published by Elsevier Ltd. All rights reserved.

History of Soil Survey and Evolution of the Brazilian Soil Classification System - SiBCS

NASA Astrophysics Data System (ADS)

Cunha dos Anjos, Lúcia Helena; Csekö Nolasco de Carvalho, Claudia; Homem Antunes, Mauro Antonio; Muggler, Cristine Carole

2014-05-01

In Brazil soil surveys started around 1940 and the first map with soil information of São Paulo State was published in 1943. The Committee of Soils of the National Service for Agronomic Research was created in 1947 by the Agriculture Ministry and became an historical landmark for soil survey in Brazil. In 1953, the National Program of soil survey was approved and the first soil map and report of Rio de Janeiro State was released in 1958, followed by São Paulo State in 1960. This is also the origin of Embrapa Soil Research institution. Other milestones were the soil surveys published by the Agronomic Institute of Campinas (IAC) and the natural resources studies published within the RADAMBRASIL Project, initially planned for the Amazon region and later covering the whole country. Many soil studies followed and a comprehensive knowledge of tropical soils was achieved resulting in successful technologies for agriculture production, in lands considered by many as of "low fertility and acid soils with limited or no agricultural potential". However, detailed soil surveys are still lacking; only 5% of the country soils are mapped in 1:25.000 scales, and 15-20% in 1:100.000. In the first soil survey reports of Rio de Janeiro (1958) and São Paulo (1960), soil classes were defined according to Baldwin, Kellog & Thorp (Yearbook of Agriculture for 1938), and Thorp & Smith (Soil Science, 67, 1949) publications. It was already clear that the existing classification systems were not adequate to represent the highly weathered tropical soils of the large old landscapes in the cerrado (savanna like) region, or the soils formed on recent hydromorphic conditions at the Amazon Basin and Pantanal region. A national classification system to embody the country's large territory and environmental variation from tropical to subtropical and semiarid conditions, as well as the diversity of soil forming processes in old and new landscapes had to be developed. In 1964, the first attempt of a national soil classification was presented by Marcelo Camargo (Embrapa Soils) and Jacob Bennema (FAO adviser). When Soil Taxonomy was first published in 1975, a field workshop was held in Brazil, and the system was not accepted by the country scientists; one main reason was the usage of climate as a main attribute for suborders. In 1978, the first national soil field correlation meeting was held with the goal of developing the national system, giving origin to the Brazilian Soil Classification System (SiBCS). In 1980, a working group was created by Embrapa Soils and other institutes resulting in four approximations of the system. In 1999, the first edition of the SiBCS was released, followed by a second edition in 2006 and the third in 2013. The SiBCS is a hierarchic system, based on morphogenetic soil attributes, with six categorical levels: order, suborder, great group, subgroup, family, and series. It has 13 soil orders, and it is structured as a key down to subgroup level. Many soil attributes are based on concepts adopted by the Soil Taxonomy (United States) and by the World Reference Base for Soil Resources (WRB - FAO). The development of the SiBCS is supervised by a national executive committee, and information is available at http://www.cnps.embrapa.br/sibcs (in Portuguese).

MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads

PubMed Central

Lukjancenko, Oksana; Thomsen, Martin Christen Frølund; Maddalena Sperotto, Maria; Lund, Ole; Møller Aarestrup, Frank; Sicheritz-Pontén, Thomas

2017-01-01

An increasing amount of species and gene identification studies rely on the use of next generation sequence analysis of either single isolate or metagenomics samples. Several methods are available to perform taxonomic annotations and a previous metagenomics benchmark study has shown that a vast number of false positive species annotations are a problem unless thresholds or post-processing are applied to differentiate between correct and false annotations. MGmapper is a package to process raw next generation sequence data and perform reference based sequence assignment, followed by a post-processing analysis to produce reliable taxonomy annotation at species and strain level resolution. An in-vitro bacterial mock community sample comprised of 8 genuses, 11 species and 12 strains was previously used to benchmark metagenomics classification methods. After applying a post-processing filter, we obtained 100% correct taxonomy assignments at species and genus level. A sensitivity and precision at 75% was obtained for strain level annotations. A comparison between MGmapper and Kraken at species level, shows MGmapper assigns taxonomy at species level using 84.8% of the sequence reads, compared to 70.5% for Kraken and both methods identified all species with no false positives. Extensive read count statistics are provided in plain text and excel sheets for both rejected and accepted taxonomy annotations. The use of custom databases is possible for the command-line version of MGmapper, and the complete pipeline is freely available as a bitbucked package (https://bitbucket.org/genomicepidemiology/mgmapper). A web-version (https://cge.cbs.dtu.dk/services/MGmapper) provides the basic functionality for analysis of small fastq datasets. PMID:28467460

MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads.

PubMed

Petersen, Thomas Nordahl; Lukjancenko, Oksana; Thomsen, Martin Christen Frølund; Maddalena Sperotto, Maria; Lund, Ole; Møller Aarestrup, Frank; Sicheritz-Pontén, Thomas

2017-01-01

An increasing amount of species and gene identification studies rely on the use of next generation sequence analysis of either single isolate or metagenomics samples. Several methods are available to perform taxonomic annotations and a previous metagenomics benchmark study has shown that a vast number of false positive species annotations are a problem unless thresholds or post-processing are applied to differentiate between correct and false annotations. MGmapper is a package to process raw next generation sequence data and perform reference based sequence assignment, followed by a post-processing analysis to produce reliable taxonomy annotation at species and strain level resolution. An in-vitro bacterial mock community sample comprised of 8 genuses, 11 species and 12 strains was previously used to benchmark metagenomics classification methods. After applying a post-processing filter, we obtained 100% correct taxonomy assignments at species and genus level. A sensitivity and precision at 75% was obtained for strain level annotations. A comparison between MGmapper and Kraken at species level, shows MGmapper assigns taxonomy at species level using 84.8% of the sequence reads, compared to 70.5% for Kraken and both methods identified all species with no false positives. Extensive read count statistics are provided in plain text and excel sheets for both rejected and accepted taxonomy annotations. The use of custom databases is possible for the command-line version of MGmapper, and the complete pipeline is freely available as a bitbucked package (https://bitbucket.org/genomicepidemiology/mgmapper). A web-version (https://cge.cbs.dtu.dk/services/MGmapper) provides the basic functionality for analysis of small fastq datasets.

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.

Human Capital Development - Resilient Cyber Physical Systems

DTIC Science & Technology

2017-09-29

Human Capital Development – Resilient Cyber Physical Systems Technical Report SERC-2017-TR-113 September 29, 2017 Principal Investigator...4.2.2 Cyber Attack Taxonomy for Cyber Physical Systems .............................................................................. 43 4.2.3...Cyber- physical System Attack Taxonomy ................................................................................................ 44 4.2.4

Mothe-Diniz Asteroid Dynamical Families V1.0

NASA Astrophysics Data System (ADS)

Mothe-Diniz, T.; Roig, F.; Carvano, J. M.

2006-03-01

This dataset contains an updated compilation of asteroid families and clusters, resulting from the application of the Hierarchical Clustering Method (HCM) on a set of around 120,000 asteroids with available proper elements. Whenever available, the classification in the Bus taxonomy is provided for family members, based on spectra from the SMASS, SMASS2 and S3OS2 spectroscopic surveys.

Construct Validity of Fluency and Implications for the Factorial Structure of Memory

ERIC Educational Resources Information Center

Jewsbury, Paul A.; Bowden, Stephen C.

2017-01-01

Fluency is an important construct in clinical assessment and in cognitive taxonomies. In the Cattell-Horn-Carroll (CHC) model, Fluency is represented by several narrow factors that form a subset of the long-term memory encoding and retrieval (Glr) broad factor. The CHC broad classification of Fluency was evaluated in five data sets, and the CHC…

Relating practitioner needs to research activities

NASA Technical Reports Server (NTRS)

Feather, M. S.; Menzies, T.; Connelly, J. R.

2003-01-01

We present an approach to matching needs (practioner requirements) to solutions (researcher activities). A taxonomical classification scheme acts as intermediary between needs and activities. Expert practitioners exprss their needs in terms of this taxonomy. Researchers express their activities in the same terms. A decision support tool is used to assist in the combination and study of their expressions of needs and activities.

Taxonomy of Challenges for Digital Forensics.

PubMed

Karie, Nickson M; Venter, Hein S

2015-07-01

Since its inception, over a decade ago, the field of digital forensics has faced numerous challenges. Despite different researchers and digital forensic practitioners having studied and analysed various known digital forensic challenges, as of 2013, there still exists a need for a formal classification of these challenges. This article therefore reviews existing research literature and highlights the various challenges that digital forensics has faced for the last 10 years. In conducting this research study, however, it was difficult for the authors to review all the existing research literature in the digital forensic domain; hence, sampling and randomization techniques were employed to facilitate the review of the gathered literature. Taxonomy of the various challenges is subsequently proposed in this paper based on our review of the literature. The taxonomy classifies the large number of digital forensic challenges into four well-defined and easily understood categories. The proposed taxonomy can be useful, for example, in future developments of automated digital forensic tools by explicitly describing processes and procedures that focus on addressing specific challenges identified in this paper. However, it should also be noted that the purpose of this paper was not to propose any solutions to the individual challenges that digital forensics face, but to serve as a survey of the state of the art of the research area. © 2015 American Academy of Forensic Sciences.

The classification systems of nursing practice--the historical and practical perspective.

PubMed

Górajek-Jóźwik, Jolanta

2003-01-01

The contribution into activities connected with the development of the quality of nursing care is closely combined with the process of systematic recording of accumulated data, of undertaken activities and achieved results. This in turn constitutes the essence of the 31st Aim of WHO which speaks not only about the need to continue the rational contribution towards the increase in the nursing care quality but also the application of adequate computer technologies to improve this quality. The aim of this work is to demonstrate the scope and character of the activities that have been over years undertaken by the nursing community towards the development of the classification systems which are comparable with those used in medicine. The focus has been specifically put on the taxonomy of diagnosis used by the North American Nursing Diagnosis Association (NANDA) and the European International Classification of Nursing Practice (ICNP). The analysis of the reference sources constitutes the methodological foundation applied in this work. It has allowed to show the pioneering contribution of the American Nursing Association (ANA) into the process of recording and coding of the data that are essential in care delivery as well as their value for the development of ICNP. The latter one is a systematic and multi-axial structure which uses unified terminology and numeric codes for the three categories of variables: the recognized conditions, the undertaken activities and the achieved results.

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.

Towards a new taxonomy of idiopathic orofacial pain.

PubMed

Woda, Alain; Tubert-Jeannin, Stéphanie; Bouhassira, Didier; Attal, Nadine; Fleiter, Bernard; Goulet, Jean-Paul; Gremeau-Richard, Christelle; Navez, Marie Louise; Picard, Pascale; Pionchon, Paul; Albuisson, Eliane

2005-08-01

There is no current consensus on the taxonomy of the different forms of idiopathic orofacial pain (stomatodynia, atypical odontalgia, atypical facial pain, facial arthromyalgia), which are sometimes considered as separate entities and sometimes grouped together. In the present prospective multicentric study, we used a systematic approach to help to place these different painful syndromes in the general classification of chronic facial pain. This multicenter study was carried out on 245 consecutive patients presenting with chronic facial pain (>4 months duration). Each patient was seen by two experts who proposed a diagnosis, administered a 111-item questionnaire and filled out a standardized 68-item examination form. Statistical processing included univariate analysis and several forms of multidimensional analysis. Migraines (n=37), tension-type headache (n=26), post-traumatic neuralgia (n=20) and trigeminal neuralgia (n=13) tended to cluster independently. When signs and symptoms describing topographic features were not included in the list of variables, the idiopathic orofacial pain patients tended to cluster in a single group. Inside this large cluster, only stomatodynia (n=42) emerged as a distinct homogenous subgroup. In contrast, facial arthromyalgia (n=46) and an entity formed with atypical facial pain (n=25) and atypical odontalgia (n=13) could only be individualised by variables reflecting topographical characteristics. These data provide grounds for an evidence-based classification of idiopathic facial pain entities and indicate that the current sub-classification of these syndromes relies primarily on the topography of the symptoms.

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.

Folk taxonomy and use of mushrooms in communities around Ngorongoro and Serengeti National Park, Tanzania

PubMed Central

2012-01-01

Background Maasai and Kurya form two main communities around the Serengeti National Park in Tanzania which are mainly pastoralists. Changing climate to excessive drought, have recently forced them to start practicing subsistence farming which is severely affected by wild animals. This study explored status of the folk taxonomy and uses of mushrooms in the two communities as a pave way for possibilities of introducing mushroom cultivation, an alternative crop which is hardly affected by wild animals. Methods Folk taxonomy and use mushrooms by the Kurya and Maasai communities were investigated. Information was collected by face to face interviews with 150 individuals in 6 selected villages. Using descriptive statistics by Statistic Package for the Social Science (SPSS) version 17.0, the demographic characteristics of informants were evaluated and cross relationships with the recorded data were analysed. Results Kurya are mycophilic with 94% of the informants recognizing utilization of the wild mushroom either as foodstuff or as tonics while the Maasai are mycophobic with 99% being unaware of the edibility of mushroom although 28% recognized mushrooms as tonic. For both communities, the knowledge of mushroom utilization and folk taxonomy increased with age of the informants, while it decreases with formal education level of the informants which imply that the basis of knowledge is mainly traditional. Comparing the two communities, the Maasai use mushrooms only for medicinal purposes and never sought them for food while the Kurya were well knowledgeable on the edibility and folk classification especially the Termitomyces species. Characters used in folkal taxonomy included color and size of the basidiomata, shape and size of the pseudorrhiza, habitats and edibility information. A new use of ascospores whereby they anaesthaesia bees during honey harvesting was discovered, and mushroom cultivation was widely welcomed (94.7%) as an alternative crop which is rarely affected by wild animals. Conclusion In order to salvage a noted tremendous decrease of knowledge in mushroom utilization and folk taxonomy from vanishing, there is a need to document it throughout, and incorporate it in lower levels of our education system. Mushroom cultivation may possibly be the best alternative crop for the two communities thus should be advocated for improving livelihood and reduce human wildlife conflicts. The new recorded use of ascospores to anaesthaesia the bees during honey harvesting should be exploited and scaled up for sustainable integrated bee keeping and mushroom farming. PMID:22999253

Recommendations for the classification of group A rotaviruses using all 11 genomic RNA segments.

PubMed

Matthijnssens, Jelle; Ciarlet, Max; Rahman, Mustafizur; Attoui, Houssam; Bányai, Krisztián; Estes, Mary K; Gentsch, Jon R; Iturriza-Gómara, Miren; Kirkwood, Carl D; Martella, Vito; Mertens, Peter P C; Nakagomi, Osamu; Patton, John T; Ruggeri, Franco M; Saif, Linda J; Santos, Norma; Steyer, Andrej; Taniguchi, Koki; Desselberger, Ulrich; Van Ranst, Marc

2008-01-01

Recently, a classification system was proposed for rotaviruses in which all the 11 genomic RNA segments are used (Matthijnssens et al. in J Virol 82:3204-3219, 2008). Based on nucleotide identity cut-off percentages, different genotypes were defined for each genome segment. A nomenclature for the comparison of complete rotavirus genomes was considered in which the notations Gx-P[x]-Ix-Rx-Cx-Mx-Ax-Nx-Tx-Ex-Hx are used for the VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5/6 encoding genes, respectively. This classification system is an extension of the previously applied genotype-based system which made use of the rotavirus gene segments encoding VP4, VP7, VP6, and NSP4. In order to assign rotavirus strains to one of the established genotypes or a new genotype, a standard procedure is proposed in this report. As more human and animal rotavirus genomes will be completely sequenced, new genotypes for each of the 11 gene segments may be identified. A Rotavirus Classification Working Group (RCWG) including specialists in molecular virology, infectious diseases, epidemiology, and public health was formed, which can assist in the appropriate delineation of new genotypes, thus avoiding duplications and helping minimize errors. Scientists discovering a potentially new rotavirus genotype for any of the 11 gene segments are invited to send the novel sequence to the RCWG, where the sequence will be analyzed, and a new nomenclature will be advised as appropriate. The RCWG will update the list of classified strains regularly and make this accessible on a website. Close collaboration with the Study Group Reoviridae of the International Committee on the Taxonomy of Viruses will be maintained.

Adipose Tissue Quantification by Imaging Methods: A Proposed Classification

PubMed Central

Shen, Wei; Wang, ZiMian; Punyanita, Mark; Lei, Jianbo; Sinav, Ahmet; Kral, John G.; Imielinska, Celina; Ross, Robert; Heymsfield, Steven B.

2007-01-01

Recent advances in imaging techniques and understanding of differences in the molecular biology of adipose tissue has rendered classical anatomy obsolete, requiring a new classification of the topography of adipose tissue. Adipose tissue is one of the largest body compartments, yet a classification that defines specific adipose tissue depots based on their anatomic location and related functions is lacking. The absence of an accepted taxonomy poses problems for investigators studying adipose tissue topography and its functional correlates. The aim of this review was to critically examine the literature on imaging of whole body and regional adipose tissue and to create the first systematic classification of adipose tissue topography. Adipose tissue terminology was examined in over 100 original publications. Our analysis revealed inconsistencies in the use of specific definitions, especially for the compartment termed “visceral” adipose tissue. This analysis leads us to propose an updated classification of total body and regional adipose tissue, providing a well-defined basis for correlating imaging studies of specific adipose tissue depots with molecular processes. PMID:12529479

Toward extending terrestrial laser scanning applications in forestry: a case study of broad- and needle-leaf tree classification

NASA Astrophysics Data System (ADS)

Lin, Yi; Jiang, Miao

2017-01-01

Tree species information is essential for forest research and management purposes, which in turn require approaches for accurate and precise classification of tree species. One such remote sensing technology, terrestrial laser scanning (TLS), has proved to be capable of characterizing detailed tree structures, such as tree stem geometry. Can TLS further differentiate between broad- and needle-leaves? If the answer is positive, TLS data can be used for classification of taxonomic tree groups by directly examining their differences in leaf morphology. An analysis was proposed to assess TLS-represented broad- and needle-leaf structures, followed by a Bayes classifier to perform the classification. Tests indicated that the proposed method can basically implement the task, with an overall accuracy of 77.78%. This study indicates a way of implementing the classification of the two major broad- and needle-leaf taxonomies measured by TLS in accordance to their literal definitions, and manifests the potential of extending TLS applications in forestry.

The normative structure of mathematization in systematic biology.

PubMed

Sterner, Beckett; Lidgard, Scott

2014-06-01

We argue that the mathematization of science should be understood as a normative activity of advocating for a particular methodology with its own criteria for evaluating good research. As a case study, we examine the mathematization of taxonomic classification in systematic biology. We show how mathematization is a normative activity by contrasting its distinctive features in numerical taxonomy in the 1960s with an earlier reform advocated by Ernst Mayr starting in the 1940s. Both Mayr and the numerical taxonomists sought to formalize the work of classification, but Mayr introduced a qualitative formalism based on human judgment for determining the taxonomic rank of populations, while the numerical taxonomists introduced a quantitative formalism based on automated procedures for computing classifications. The key contrast between Mayr and the numerical taxonomists is how they conceptualized the temporal structure of the workflow of classification, specifically where they allowed meta-level discourse about difficulties in producing the classification. Copyright © 2014. Published by Elsevier Ltd.

Towards A Taxonomy Of Attacks Against Energy Control Systems

NASA Astrophysics Data System (ADS)

Fleury, Terry; Khurana, Himanshu; Welch, Von

Control systems in the energy sector (e.g., supervisory control and data acquisition (SCADA) systems) involve a hierarchy of sensing, monitoring and control devices connected to centralized control stations or centers. The incorporation of commercial off-the-shelf technologies in energy control systems makes them vulnerable to cyber attacks. A taxonomy of cyber attacks against control systems can assist the energy sector in managing the cyber threat. This paper takes the first step towards a taxonomy by presenting a comprehensive model of attacks, vulnerabilities and damage related to control systems. The model is populated based on a survey of the technical literature from industry, academia and national laboratories.

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.

A survey of transposable element classification systems--a call for a fundamental update to meet the challenge of their diversity and complexity.

PubMed

Piégu, Benoît; Bire, Solenne; Arensburger, Peter; Bigot, Yves

2015-05-01

The increase of publicly available sequencing data has allowed for rapid progress in our understanding of genome composition. As new information becomes available we should constantly be updating and reanalyzing existing and newly acquired data. In this report we focus on transposable elements (TEs) which make up a significant portion of nearly all sequenced genomes. Our ability to accurately identify and classify these sequences is critical to understanding their impact on host genomes. At the same time, as we demonstrate in this report, problems with existing classification schemes have led to significant misunderstandings of the evolution of both TE sequences and their host genomes. In a pioneering publication Finnegan (1989) proposed classifying all TE sequences into two classes based on transposition mechanisms and structural features: the retrotransposons (class I) and the DNA transposons (class II). We have retraced how ideas regarding TE classification and annotation in both prokaryotic and eukaryotic scientific communities have changed over time. This has led us to observe that: (1) a number of TEs have convergent structural features and/or transposition mechanisms that have led to misleading conclusions regarding their classification, (2) the evolution of TEs is similar to that of viruses by having several unrelated origins, (3) there might be at least 8 classes and 12 orders of TEs including 10 novel orders. In an effort to address these classification issues we propose: (1) the outline of a universal TE classification, (2) a set of methods and classification rules that could be used by all scientific communities involved in the study of TEs, and (3) a 5-year schedule for the establishment of an International Committee for Taxonomy of Transposable Elements (ICTTE). Copyright © 2015 Elsevier Inc. All rights reserved.

Taxonomy and clustering in collaborative systems: The case of the on-line encyclopedia Wikipedia

NASA Astrophysics Data System (ADS)

Capocci, A.; Rao, F.; Caldarelli, G.

2008-01-01

In this paper we investigate the nature and structure of the relation between imposed classifications and real clustering in a particular case of a scale-free network given by the on-line encyclopedia Wikipedia. We find a statistical similarity in the distributions of community sizes both by using the top-down approach of the categories division present in the archive and in the bottom-up procedure of community detection given by an algorithm based on the spectral properties of the graph. Regardless of the statistically similar behaviour, the two methods provide a rather different division of the articles, thereby signaling that the nature and presence of power laws is a general feature for these systems and cannot be used as a benchmark to evaluate the suitability of a clustering method.

Communication technologies through an etymological lens: looking for a classification, reflections about health, medicine and care.

PubMed

Colucci, Massimiliano

2015-11-01

Information and communication technologies are widely used in healthcare. However, there is not still a unified taxonomy for them. The lack of understanding of this phenomenon implies theoretical and ethical issues. This paper attempts to find out the basis for a classification, starting from a new perspective: the structural elements are obtained from the etymologies of the lexicon commonly used, that is words like telemedicine, telehealth, telecare and telecure. This will promote a better understanding of communication technologies; at the same time, it will allow to draw some reflection about health, medicine and care, and their semantic and relational nature.

Version Condensada de la Clasificacion de los Objectivos de la Educacion (A Condensed, Translated Version of the Taxonomy of Educational Objectives).

ERIC Educational Resources Information Center

Castro, Margarita, Ed.; Forero, Fanny, Ed.

This document provides a classification of educational objectives in the cognitive and affective domains, defines each objective, and offers examples. Special emphasis is not given to any particular objective; it is left to the teachers in a given program to determine the specific objectives to be derived in each learning experience within the…

78 FR 23533 - Endangered and Threatened Wildlife and Plants; 90-Day Finding on a Petition To Delist the Wood Bison

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-19

... classification and our rationale for accepting wood bison as a valid subspecies below. Taxonomy is the theory and... groups of animals should be lumped together or split apart. Such is the case for wood bison. We recognize... separated by a great distance, led Boyd et al. (2010, p. 16 (American Bison Specialist Group)) to conclude...

Taxonomy of segmental myocardial systolic dysfunction

PubMed Central

McDiarmid, Adam K.; Pellicori, Pierpaolo; Cleland, John G.; Plein, Sven

2017-01-01

The terms used to describe different states of myocardial health and disease are poorly defined. Imprecision and inconsistency in nomenclature can lead to difficulty in interpreting and applying trial outcomes to clinical practice. In particular, the terms ‘viable’ and ‘hibernating’ are commonly applied interchangeably and incorrectly to myocardium that exhibits chronic contractile dysfunction in patients with ischaemic heart disease. The range of inherent differences amongst imaging modalities used to define myocardial health and disease add further challenges to consistent definitions. The results of several large trials have led to renewed discussion about the classification of dysfunctional myocardial segments. This article aims to describe the diverse myocardial pathologies that may affect the myocardium in ischaemic heart disease and cardiomyopathy, and how they may be assessed with non-invasive imaging techniques in order to provide a taxonomy of myocardial dysfunction. PMID:27147609

Diversity in action: exchange of perspectives and reflections on taxonomies of individual differences.

PubMed

Uher, Jana; Trofimova, Irina; Sulis, William; Netter, Petra; Pessoa, Luiz; Posner, Michael I; Rothbart, Mary K; Rusalov, Vladimir; Peterson, Isaac T; Schmidt, Louis A

2018-04-19

Throughout the last 2500 years, the classification of individual differences in healthy people and their extreme expressions in mental disorders has remained one of the most difficult challenges in science that affects our ability to explore individuals' functioning, underlying psychobiological processes and pathways of development. To facilitate analyses of the principles required for studying individual differences, this theme issue brought together prominent scholars from diverse backgrounds of which many bring unique combinations of cross-disciplinary experiences and perspectives that help establish connections and promote exchange across disciplines. This final paper presents brief commentaries of some of our authors and further scholars exchanging perspectives and reflecting on the contributions of this theme issue.This article is part of the theme issue 'Diverse perspectives on diversity: multi-disciplinary approaches to taxonomies of individual differences'. © 2018 The Author(s).

Identification of Candida lusitaniae as an opportunistic yeast in humans.

PubMed

Holzschu, D L; Presley, H L; Miranda, M; Phaff, H J

1979-08-01

Four yeast strains, causally associated with infection in a patient with acute myelogenous leukemia, were identified by standard methods currently used in yeast taxonomy as representatives of Candida lusitania van Uden et do Carmo-Sousa. Because this species has not been recognized previously as an opportunistic yeast in humans, molecular taxonomic methods were applied to confirm its identity. The nuclear deoxyribonucleic acid (DNA) base composition of two clinical isolates was shown to be 45.1 mol% guanine plus cytosine as compared to 44.7 mol% guanine plus cytosine for the type strain of this species. DNA/DNA reassociation experiments revealed more than 95% complementarity between the DNAs from the clinical isolates and that of the type strain of C. lusitaniae, thus confirming their classification by conventional taxonomy. A key is provided to differentiate C. lusitaniae from two phenotypically similar Candida species.

A Taxonomy-Based Approach to Shed Light on the Babel of Mathematical Models for Rice Simulation

NASA Technical Reports Server (NTRS)

Confalonieri, Roberto; Bregaglio, Simone; Adam, Myriam; Ruget, Francoise; Li, Tao; Hasegawa, Toshihiro; Yin, Xinyou; Zhu, Yan; Boote, Kenneth; Buis, Samuel;

Synthesis of phylogeny and taxonomy into a comprehensive tree of life

PubMed Central

Hinchliff, Cody E.; Smith, Stephen A.; Allman, James F.; Burleigh, J. Gordon; Chaudhary, Ruchi; Coghill, Lyndon M.; Crandall, Keith A.; Deng, Jiabin; Drew, Bryan T.; Gazis, Romina; Gude, Karl; Hibbett, David S.; Katz, Laura A.; Laughinghouse, H. Dail; McTavish, Emily Jane; Midford, Peter E.; Owen, Christopher L.; Ree, Richard H.; Rees, Jonathan A.; Soltis, Douglas E.; Williams, Tiffani; Cranston, Karen A.

2015-01-01

Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips—the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: (i) a comprehensive global reference taxonomy and (ii) a database of published phylogenetic trees mapped to this taxonomy. Our open source framework facilitates community comment and contribution, enabling the tree to be continuously updated when new phylogenetic and taxonomic data become digitally available. Although data coverage and phylogenetic conflict across the Open Tree of Life illuminate gaps in both the underlying data available for phylogenetic reconstruction and the publication of trees as digital objects, the tree provides a compelling starting point for community contribution. This comprehensive tree will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate change, agriculture, and genomics. PMID:26385966

Synthesis of phylogeny and taxonomy into a comprehensive tree of life.

PubMed

Hinchliff, Cody E; Smith, Stephen A; Allman, James F; Burleigh, J Gordon; Chaudhary, Ruchi; Coghill, Lyndon M; Crandall, Keith A; Deng, Jiabin; Drew, Bryan T; Gazis, Romina; Gude, Karl; Hibbett, David S; Katz, Laura A; Laughinghouse, H Dail; McTavish, Emily Jane; Midford, Peter E; Owen, Christopher L; Ree, Richard H; Rees, Jonathan A; Soltis, Douglas E; Williams, Tiffani; Cranston, Karen A

2015-10-13

Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips-the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: (i) a comprehensive global reference taxonomy and (ii) a database of published phylogenetic trees mapped to this taxonomy. Our open source framework facilitates community comment and contribution, enabling the tree to be continuously updated when new phylogenetic and taxonomic data become digitally available. Although data coverage and phylogenetic conflict across the Open Tree of Life illuminate gaps in both the underlying data available for phylogenetic reconstruction and the publication of trees as digital objects, the tree provides a compelling starting point for community contribution. This comprehensive tree will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate change, agriculture, and genomics.

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

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

Influence Map Methodology for Evaluating Systemic Safety Issues

NASA Technical Reports Server (NTRS)

2008-01-01

"Raising the bar" in safety performance is a critical challenge for many organizations, including Kennedy Space Center. Contributing-factor taxonomies organize information about the reasons accidents occur and therefore are essential elements of accident investigations and safety reporting systems. Organizations must balance efforts to identify causes of specific accidents with efforts to evaluate systemic safety issues in order to become more proactive about improving safety. This project successfully addressed the following two problems: (1) methods and metrics to support the design of effective taxonomies are limited and (2) influence relationships among contributing factors are not explicitly modeled within a taxonomy.

An error taxonomy system for analysis of haemodialysis incidents.

PubMed

Gu, Xiuzhu; Itoh, Kenji; Suzuki, Satoshi

2014-12-01

This paper describes the development of a haemodialysis error taxonomy system for analysing incidents and predicting the safety status of a dialysis organisation. The error taxonomy system was developed by adapting an error taxonomy system which assumed no specific specialty to haemodialysis situations. Its application was conducted with 1,909 incident reports collected from two dialysis facilities in Japan. Over 70% of haemodialysis incidents were reported as problems or complications related to dialyser, circuit, medication and setting of dialysis condition. Approximately 70% of errors took place immediately before and after the four hours of haemodialysis therapy. Error types most frequently made in the dialysis unit were omission and qualitative errors. Failures or complications classified to staff human factors, communication, task and organisational factors were found in most dialysis incidents. Device/equipment/materials, medicine and clinical documents were most likely to be involved in errors. Haemodialysis nurses were involved in more incidents related to medicine and documents, whereas dialysis technologists made more errors with device/equipment/materials. This error taxonomy system is able to investigate incidents and adverse events occurring in the dialysis setting but is also able to estimate safety-related status of an organisation, such as reporting culture. © 2014 European Dialysis and Transplant Nurses Association/European Renal Care Association.

A Classification and Analysis of Contracting Literature

DTIC Science & Technology

1989-12-01

Pricing Model ( CAPM . This is a model designed by investment analysts to determine required rates of return given the systematic risk of a company. The...For the amount of risk they take, these profit margins were not excessively high. The author examined profitability in terms of the Capital Asset ...taxonomy was applied was limited , the results were necessarily qualified. However, at the least this application provided areas for further research

Wireless Emergency Alerts (WEA) Cybersecurity Risk Management Strategy for Alert Originators

DTIC Science & Technology

2014-03-01

formerly known as the Commercial Mobile Alert Service ( CMAS ) RDT&E program, is a collaborative partnership that includes the cellular industry, the...Examples illustrate a STRIDE analysis of the generic mission 1 The CMAS Alerting Pipeline Taxonomy describes in detail a hierarchical classification...SEI-2013-SR-018 | 1 1 Introduction The Wireless Emergency Alerts (WEA) service, formerly known as the Commercial Mobile Alert Service ( CMAS ), is a

vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria.

PubMed

Bolduc, Benjamin; Jang, Ho Bin; Doulcier, Guilhem; You, Zhi-Qiang; Roux, Simon; Sullivan, Matthew B

2017-01-01

Taxonomic classification of archaeal and bacterial viruses is challenging, yet also fundamental for developing a predictive understanding of microbial ecosystems. Recent identification of hundreds of thousands of new viral genomes and genome fragments, whose hosts remain unknown, requires a paradigm shift away from traditional classification approaches and towards the use of genomes for taxonomy. Here we revisited the use of genomes and their protein content as a means for developing a viral taxonomy for bacterial and archaeal viruses. A network-based analytic was evaluated and benchmarked against authority-accepted taxonomic assignments and found to be largely concordant. Exceptions were manually examined and found to represent areas of viral genome 'sequence space' that are under-sampled or prone to excessive genetic exchange. While both cases are poorly resolved by genome-based taxonomic approaches, the former will improve as viral sequence space is better sampled and the latter are uncommon. Finally, given the largely robust taxonomic capabilities of this approach, we sought to enable researchers to easily and systematically classify new viruses. Thus, we established a tool, vConTACT, as an app at iVirus, where it operates as a fast, highly scalable, user-friendly app within the free and powerful CyVerse cyberinfrastructure.

vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria

PubMed Central

Doulcier, Guilhem; You, Zhi-Qiang; Roux, Simon

2017-01-01

Taxonomic classification of archaeal and bacterial viruses is challenging, yet also fundamental for developing a predictive understanding of microbial ecosystems. Recent identification of hundreds of thousands of new viral genomes and genome fragments, whose hosts remain unknown, requires a paradigm shift away from traditional classification approaches and towards the use of genomes for taxonomy. Here we revisited the use of genomes and their protein content as a means for developing a viral taxonomy for bacterial and archaeal viruses. A network-based analytic was evaluated and benchmarked against authority-accepted taxonomic assignments and found to be largely concordant. Exceptions were manually examined and found to represent areas of viral genome ‘sequence space’ that are under-sampled or prone to excessive genetic exchange. While both cases are poorly resolved by genome-based taxonomic approaches, the former will improve as viral sequence space is better sampled and the latter are uncommon. Finally, given the largely robust taxonomic capabilities of this approach, we sought to enable researchers to easily and systematically classify new viruses. Thus, we established a tool, vConTACT, as an app at iVirus, where it operates as a fast, highly scalable, user-friendly app within the free and powerful CyVerse cyberinfrastructure. PMID:28480138

vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria

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

Bolduc, Benjamin; Jang, Ho Bin; Doulcier, Guilhem

Taxonomic classification of archaeal and bacterial viruses is challenging, yet also fundamental for developing a predictive understanding of microbial ecosystems. Recent identification of hundreds of thousands of new viral genomes and genome fragments, whose hosts remain unknown, requires a paradigm shift away from traditional classification approaches and towards the use of genomes for taxonomy. Here we revisited the use of genomes and their protein content as a means for developing a viral taxonomy for bacterial and archaeal viruses. A network-based analytic was evaluated and benchmarked against authority-accepted taxonomic assignments and found to be largely concordant. Exceptions were manually examined andmore » found to represent areas of viral genome ‘sequence space’ that are under-sampled or prone to excessive genetic exchange. While both cases are poorly resolved by genome-based taxonomic approaches, the former will improve as viral sequence space is better sampled and the latter are uncommon. Finally, given the largely robust taxonomic capabilities of this approach, we sought to enable researchers to easily and systematically classify new viruses. Thus, we established a tool, vConTACT, as an app at iVirus, where it operates as a fast, highly scalable, user-friendly app within the free and powerful CyVerse cyberinfrastructure.« less

vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria

DOE PAGES

Bolduc, Benjamin; Jang, Ho Bin; Doulcier, Guilhem; ...

2017-05-03

Taxonomic classification of archaeal and bacterial viruses is challenging, yet also fundamental for developing a predictive understanding of microbial ecosystems. Recent identification of hundreds of thousands of new viral genomes and genome fragments, whose hosts remain unknown, requires a paradigm shift away from traditional classification approaches and towards the use of genomes for taxonomy. Here we revisited the use of genomes and their protein content as a means for developing a viral taxonomy for bacterial and archaeal viruses. A network-based analytic was evaluated and benchmarked against authority-accepted taxonomic assignments and found to be largely concordant. Exceptions were manually examined andmore » found to represent areas of viral genome ‘sequence space’ that are under-sampled or prone to excessive genetic exchange. While both cases are poorly resolved by genome-based taxonomic approaches, the former will improve as viral sequence space is better sampled and the latter are uncommon. Finally, given the largely robust taxonomic capabilities of this approach, we sought to enable researchers to easily and systematically classify new viruses. Thus, we established a tool, vConTACT, as an app at iVirus, where it operates as a fast, highly scalable, user-friendly app within the free and powerful CyVerse cyberinfrastructure.« less

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

Australian sea-floor survey data, with images and expert annotations.

PubMed

Bewley, Michael; Friedman, Ariell; Ferrari, Renata; Hill, Nicole; Hovey, Renae; Barrett, Neville; Marzinelli, Ezequiel M; Pizarro, Oscar; Figueira, Will; Meyer, Lisa; Babcock, Russ; Bellchambers, Lynda; Byrne, Maria; Williams, Stefan B

2015-01-01

This Australian benthic data set (BENTHOZ-2015) consists of an expert-annotated set of georeferenced benthic images and associated sensor data, captured by an autonomous underwater vehicle (AUV) around Australia. This type of data is of interest to marine scientists studying benthic habitats and organisms. AUVs collect georeferenced images over an area with consistent illumination and altitude, and make it possible to generate broad scale, photo-realistic 3D maps. Marine scientists then typically spend several minutes on each of thousands of images, labeling substratum type and biota at a subset of points. Labels from four Australian research groups were combined using the CATAMI classification scheme, a hierarchical classification scheme based on taxonomy and morphology for scoring marine imagery. This data set consists of 407,968 expert labeled points from around the Australian coast, with associated images, geolocation and other sensor data. The robotic surveys that collected this data form part of Australia's Integrated Marine Observing System (IMOS) ongoing benthic monitoring program. There is reuse potential in marine science, robotics, and computer vision research.

Australian sea-floor survey data, with images and expert annotations

PubMed Central

Bewley, Michael; Friedman, Ariell; Ferrari, Renata; Hill, Nicole; Hovey, Renae; Barrett, Neville; Pizarro, Oscar; Figueira, Will; Meyer, Lisa; Babcock, Russ; Bellchambers, Lynda; Byrne, Maria; Williams, Stefan B.

2015-01-01

This Australian benthic data set (BENTHOZ-2015) consists of an expert-annotated set of georeferenced benthic images and associated sensor data, captured by an autonomous underwater vehicle (AUV) around Australia. This type of data is of interest to marine scientists studying benthic habitats and organisms. AUVs collect georeferenced images over an area with consistent illumination and altitude, and make it possible to generate broad scale, photo-realistic 3D maps. Marine scientists then typically spend several minutes on each of thousands of images, labeling substratum type and biota at a subset of points. Labels from four Australian research groups were combined using the CATAMI classification scheme, a hierarchical classification scheme based on taxonomy and morphology for scoring marine imagery. This data set consists of 407,968 expert labeled points from around the Australian coast, with associated images, geolocation and other sensor data. The robotic surveys that collected this data form part of Australia's Integrated Marine Observing System (IMOS) ongoing benthic monitoring program. There is reuse potential in marine science, robotics, and computer vision research. PMID:26528396

Australian sea-floor survey data, with images and expert annotations

NASA Astrophysics Data System (ADS)

Bewley, Michael; Friedman, Ariell; Ferrari, Renata; Hill, Nicole; Hovey, Renae; Barrett, Neville; Pizarro, Oscar; Figueira, Will; Meyer, Lisa; Babcock, Russ; Bellchambers, Lynda; Byrne, Maria; Williams, Stefan B.

2015-10-01

This Australian benthic data set (BENTHOZ-2015) consists of an expert-annotated set of georeferenced benthic images and associated sensor data, captured by an autonomous underwater vehicle (AUV) around Australia. This type of data is of interest to marine scientists studying benthic habitats and organisms. AUVs collect georeferenced images over an area with consistent illumination and altitude, and make it possible to generate broad scale, photo-realistic 3D maps. Marine scientists then typically spend several minutes on each of thousands of images, labeling substratum type and biota at a subset of points. Labels from four Australian research groups were combined using the CATAMI classification scheme, a hierarchical classification scheme based on taxonomy and morphology for scoring marine imagery. This data set consists of 407,968 expert labeled points from around the Australian coast, with associated images, geolocation and other sensor data. The robotic surveys that collected this data form part of Australia's Integrated Marine Observing System (IMOS) ongoing benthic monitoring program. There is reuse potential in marine science, robotics, and computer vision research.

PGIS (Project Grant Information System) Taxonomy [Rough Draft].

ERIC Educational Resources Information Center

North American Rockwell Information Systems Co., Arlington, VA.

The Project Grant Information System (PGIS) is a computerized information indexing and retrieval system which supports the U.S. Office of Education. Its purpose is to provide OE officials with up-to-date information about the Office's discretionary grant programs and projects. The purpose of the Taxonomy is to provide: (1) those individuals who…

Development of Systems Engineering Competency Career Development Model: An Analytical Approach using Blooms Taxonomy

DTIC Science & Technology

2014-06-01

4 E .   PURPOSE/BENEFIT ..................................................................................... 4   F.   SCOPE...INCORPORATING DAU SPRDE CL/POS & ELOS .............................. 29   E .   MAPPING TO FIT BLOOM’S TAXONOMY .......................................... 32...Description PSE Program Systems Engineering RDT& E Research, Development, Test and Engineering SE systems engineering SME Subject Matter Expert SPAWAR

Knowledge Management in Taxonomy and Biostratigraphy using TaxonConcept Software

NASA Astrophysics Data System (ADS)

Klump, J.; Huber, R.; Goetz, S.

2005-12-01

The use of fossils to constrain age models for geological samples is not as straightforward as it might seem. Even though index fossils have been defined as biostratigraphic time markers ambiguity arises from the synonymous use of taxonomic names. Progress in our understanding of the origin of certain species have sometimes lead to substantial changes in the taxonomic classification of these organisms. TaxonConcept was created as part of the Stratigraphy.net initiative as a tool to manage taxonomic information and complex knowledge networks to help resolve taxonomic ambiguities in biostratigraphy. Its workflow is based on the principles of open nomenclature. Open nomenclature allows researchers to comment on the identification of a specimen which cannot exactly be determined and is frequently used in synonymy lists. The use of such synonymy lists in TaxonConcept allows to work with taxonomic classifications that are uncertain, or where several versions exist. Every single taxonomic entity in TaxonConcept is recorded with its relevant citations in the literature. This allows to manage information on taxonomy. The members of working groups using TaxonConcept can record their opinion on the taxonomic classification of each taxon in the framework of open nomenclature and annotate it in free text. This managed and structured collection of taxonomic opinions is an example of knowledge management. Taxonomic opinions are otherwise dispersed throughout the literature, if recorded at all, and are only available to the specialist. Assembled as a collection, they represent our knowledge on the taxonomy of a certain group of organisms. In the terminology of computer science, the semantic relationships between taxonomic terms are an ontology. Open nomenclature offers a formal framework that lends itself very well to describe the nature of the relations between taxonomic terms. The use of such synonymy lists in a taxonomic information system allows interesting search options, ranging from tracking name changes to the investigation of complex taxonomic topologies. In addition to its synonymy and literature management, TaxonConcept allows to store many other information categories such as textual descriptions (e.g. diagnoses and comments), images, bioevents and specimen and collection data. Ecological information is scheduled for a later stage of the project. Already now TaxonConcept is linked to taxon names in paleoenvironmental data of the World Data Center for Marine Environmental Sciences (WDC-MARE), interfaces to other databases are planned. WDC-MARE stores environmental, marine and geological research data and frequently uses taxon names in its parameters. By linking TaxonConcept and WDC-MARE, synonymous names can be included in queries, e.g. when researching for stable isotope data measured on microfossils. TaxonConcept is not a project on authoritative taxonomic information, but is a tool for taxonomic projects to use to find a taxonomic consensus, e.g. to define a taxonomic framework for biostratigraphic studies. Both, the project specific hierarchical classification of selected taxa, as well as a project specific selection of any other information categories is supported by TaxonConcept. The results of such a taxonomic consensus can be used to create Fossilium Catalogus style summaries in various output formats which can later be used to create online or print publications.

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…

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.

Development and classification of a robust inventory of near real-time outcome measurements for assessing information technology interventions in health care.

PubMed

Colicchio, Tiago K; Del Fiol, Guilherme; Scammon, Debra L; Bowes, Watson A; Facelli, Julio C; Narus, Scott P

2017-09-01

To develop and classify an inventory of near real-time outcome measures for assessing information technology (IT) interventions in health care and assess their relevance as perceived by experts in the field. To verify the robustness and coverage of a previously published inventory of measures and taxonomy, we conducted semi-structured interviews with clinical and administrative leaders from a large care delivery system to collect suggestions of outcome measures that can be calculated with data available in electronic format for near real-time monitoring of EHR implementations. We combined these measures with the most commonly reported in the literature. We then conducted two online surveys with subject-matter experts to collect their perceptions of the relevance of the measures, and identify other potentially relevant measures. With input from experienced health care leaders and informaticists, we developed an inventory of 102 outcome measures. These measures were classified into a taxonomy of commonly used measures around the categories of quality, productivity, and safety. Safety measures were rated as most relevant by subject-matter experts, especially those measuring medication processes. Clinician satisfaction and measures assessing mean time to complete tasks and time spent on electronic documentation were also rated as highly relevant. By expanding the coverage of our previously published inventory and taxonomy, we expect to help providers, health IT vendors and researchers to more effectively and consistently monitor the impact of EHR implementations in near real-time, and report more standardized outcomes in future studies. We identified several measures not commonly assessed by previous studies of IT implementations, especially those of safety and productivity, which deserve more attention from the broader informatics community. Our inventory of measures and taxonomy will help researchers identify gaps in their measurement approaches and report more standardized measurements of IT interventions that could be shared among researchers, hopefully facilitating comparison across future studies and increasing our understanding of the impact of IT interventions in health care. Copyright © 2017 Elsevier Inc. All rights reserved.

Sponge systematics facing new challenges.

PubMed

Cárdenas, P; Pérez, T; Boury-Esnault, N

2012-01-01

Systematics is nowadays facing new challenges with the introduction of new concepts and new techniques. Compared to most other phyla, phylogenetic relationships among sponges are still largely unresolved. In the past 10 years, the classical taxonomy has been completely overturned and a review of the state of the art appears necessary. The field of taxonomy remains a prominent discipline of sponge research and studies related to sponge systematics were in greater number in the Eighth World Sponge Conference (Girona, Spain, September 2010) than in any previous world sponge conferences. To understand the state of this rapidly growing field, this chapter proposes to review studies, mainly from the past decade, in sponge taxonomy, nomenclature and phylogeny. In a first part, we analyse the reasons of the current success of this field. In a second part, we establish the current sponge systematics theoretical framework, with the use of (1) cladistics, (2) different codes of nomenclature (PhyloCode vs. Linnaean system) and (3) integrative taxonomy. Sponges are infamous for their lack of characters. However, by listing and discussing in a third part all characters available to taxonomists, we show how diverse characters are and that new ones are being used and tested, while old ones should be revisited. We then review the systematics of the four main classes of sponges (Hexactinellida, Calcispongiae, Homoscleromorpha and Demospongiae), each time focusing on current issues and case studies. We present a review of the taxonomic changes since the publication of the Systema Porifera (2002), and point to problems a sponge taxonomist is still faced with nowadays. To conclude, we make a series of proposals for the future of sponge systematics. In the light of recent studies, we establish a series of taxonomic changes that the sponge community may be ready to accept. We also propose a series of sponge new names and definitions following the PhyloCode. The issue of phantom species (potential new species revealed by molecular studies) is raised, and we show how they could be dealt with. Finally, we present a general strategy to help us succeed in building a Porifera tree along with the corresponding revised Porifera classification. Copyright © 2012 Elsevier Ltd. All rights reserved.

Taxonomy of segmental myocardial systolic dysfunction.

PubMed

McDiarmid, Adam K; Pellicori, Pierpaolo; Cleland, John G; Plein, Sven

2017-04-01

The terms used to describe different states of myocardial health and disease are poorly defined. Imprecision and inconsistency in nomenclature can lead to difficulty in interpreting and applying trial outcomes to clinical practice. In particular, the terms 'viable' and 'hibernating' are commonly applied interchangeably and incorrectly to myocardium that exhibits chronic contractile dysfunction in patients with ischaemic heart disease. The range of inherent differences amongst imaging modalities used to define myocardial health and disease add further challenges to consistent definitions. The results of several large trials have led to renewed discussion about the classification of dysfunctional myocardial segments. This article aims to describe the diverse myocardial pathologies that may affect the myocardium in ischaemic heart disease and cardiomyopathy, and how they may be assessed with non-invasive imaging techniques in order to provide a taxonomy of myocardial dysfunction. © The Author 2016. Published by Oxford University Press on behalf of the European Society of Cardiology.

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.

Identification of Candida lusitaniae as an opportunistic yeast in humans.

PubMed Central

Holzschu, D L; Presley, H L; Miranda, M; Phaff, H J

1979-01-01

Four yeast strains, causally associated with infection in a patient with acute myelogenous leukemia, were identified by standard methods currently used in yeast taxonomy as representatives of Candida lusitania van Uden et do Carmo-Sousa. Because this species has not been recognized previously as an opportunistic yeast in humans, molecular taxonomic methods were applied to confirm its identity. The nuclear deoxyribonucleic acid (DNA) base composition of two clinical isolates was shown to be 45.1 mol% guanine plus cytosine as compared to 44.7 mol% guanine plus cytosine for the type strain of this species. DNA/DNA reassociation experiments revealed more than 95% complementarity between the DNAs from the clinical isolates and that of the type strain of C. lusitaniae, thus confirming their classification by conventional taxonomy. A key is provided to differentiate C. lusitaniae from two phenotypically similar Candida species. PMID:292646

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.

Enzyme Mini-Test for Field Identification of Leishmania Isolates from U.S. Military Personnel.

DTIC Science & Technology

1985-08-15

8217.*". .. , 00 ENZYME MINI-TEST FOR FIELD IDENTIFICATION OF ’ r LEISHMANIA ISOLATES FROM U.S. MILITARY la ...No 0704-0188% __REPORTDOCUMENTATION__PAGEExp Date Jun30, 1986 la REPORT SECURITY CLASSIFICATION lb RESTRICTIVE MARKINGS Unclassified 2a SECURITY...Soc. Trop. Med. ’* Mcreevy, P. B., P. D. Kreutzer, E. D. Frank-, H. A. Stim- son , C. N. Oster and L. D. H-ndricks. 1983. Taxonomy, clinical pathology

Development and Effectiveness Analysis of a Personalized Ubiquitous Multi-Device Certification Tutoring System Based on Bloom's Taxonomy of Educational Objectives

ERIC Educational Resources Information Center

Hwang, Gwo-Haur; Chen, Beyin; Huang, Cin-Wei

2016-01-01

In recent years, with the gradual increase in the importance of professional certificates, improvement in certification tutoring systems has become more important. In this study, we have developed a personalized ubiquitous multi-device certification tutoring system (PUMDCTS) based on "Bloom's Taxonomy of Educational Objectives," and…

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

Statistical text classifier to detect specific type of medical incidents.

PubMed

Wong, Zoie Shui-Yee; Akiyama, Masanori

2013-01-01

WHO Patient Safety has put focus to increase the coherence and expressiveness of patient safety classification with the foundation of International Classification for Patient Safety (ICPS). Text classification and statistical approaches has showed to be successful to identifysafety problems in the Aviation industryusing incident text information. It has been challenging to comprehend the taxonomy of medical incidents in a structured manner. Independent reporting mechanisms for patient safety incidents have been established in the UK, Canada, Australia, Japan, Hong Kong etc. This research demonstrates the potential to construct statistical text classifiers to detect specific type of medical incidents using incident text data. An illustrative example for classifying look-alike sound-alike (LASA) medication incidents using structured text from 227 advisories related to medication errors from Global Patient Safety Alerts (GPSA) is shown in this poster presentation. The classifier was built using logistic regression model. ROC curve and the AUC value indicated that this is a satisfactory good model.

Towards a controlled vocabulary on software engineering education

NASA Astrophysics Data System (ADS)

Pizard, Sebastián; Vallespir, Diego

2017-11-01

Software engineering is the discipline that develops all the aspects of the production of software. Although there are guidelines about what topics to include in a software engineering curricula, it is usually unclear which are the best methods to teach them. In any science discipline the construction of a classification schema is a common approach to understand a thematic area. This study examines previous publications in software engineering education to obtain a first controlled vocabulary (a more formal definition of a classification schema) in the field. Publications from 1988 to 2014 were collected and processed using automatic clustering techniques and the outcomes were analysed manually. The result is an initial controlled vocabulary with a taxonomy form with 43 concepts that were identified as the most used in the research publications. We present the classification of the concepts in three facets: 'what to teach', 'how to teach' and 'where to teach' and the evolution of concepts over time.

A Proposed Genus Boundary for the Prokaryotes Based on Genomic Insights

PubMed Central

Qin, Qi-Long; Xie, Bin-Bin; Zhang, Xi-Ying; Chen, Xiu-Lan; Zhou, Bai-Cheng; Zhou, Jizhong; Oren, Aharon

2014-01-01

Genomic information has already been applied to prokaryotic species definition and classification. However, the contribution of the genome sequence to prokaryotic genus delimitation has been less studied. To gain insights into genus definition for the prokaryotes, we attempted to reveal the genus-level genomic differences in the current prokaryotic classification system and to delineate the boundary of a genus on the basis of genomic information. The average nucleotide sequence identity between two genomes can be used for prokaryotic species delineation, but it is not suitable for genus demarcation. We used the percentage of conserved proteins (POCP) between two strains to estimate their evolutionary and phenotypic distance. A comprehensive genomic survey indicated that the POCP can serve as a robust genomic index for establishing the genus boundary for prokaryotic groups. Basically, two species belonging to the same genus would share at least half of their proteins. In a specific lineage, the genus and family/order ranks showed slight or no overlap in terms of POCP values. A prokaryotic genus can be defined as a group of species with all pairwise POCP values higher than 50%. Integration of whole-genome data into the current taxonomy system can provide comprehensive information for prokaryotic genus definition and delimitation. PMID:24706738

A Software Safety Risk Taxonomy for Use in Retrospective Safety Cases

NASA Technical Reports Server (NTRS)

Hill, Janice L.

2007-01-01

Safety standards contain technical and process-oriented safely requirements. The best time to include these requirements is early in the development lifecycle of the system. When software safety requirements are levied on a legacy system after the fact, a retrospective safety case will need to be constructed for the software in the system. This can be a difficult task because there may be few to no art facts available to show compliance to the software safely requirements. The risks associated with not meeting safely requirements in a legacy safely-critical computer system must be addressed to give confidence for reuse. This paper introduces a proposal for a software safely risk taxonomy for legacy safely-critical computer systems, by specializing the Software Engineering Institute's 'Software Development Risk Taxonomy' with safely elements and attributes.

The development of a computer assisted instruction and assessment system in pharmacology.

PubMed

Madsen, B W; Bell, R C

1977-01-01

We describe the construction of a computer based system for instruction and assessment in pharmacology, utilizing a large bank of multiple choice questions. Items were collected from many sources, edited and coded for student suitability, topic, taxonomy and difficulty and text references. Students reserve a time during the day, specify the type of test desired and questions are presented randomly from the subset satisfying their criteria. Answers are scored after each question and a summary given at the end of every test; details on item performance are recorded automatically. The biggest hurdle in implementation was the assembly, review, classification and editing of items, while the programming was relatively straight-forward. A number of modifications had to be made to the initial plans and changes will undoubtedly continue with further experience. When fully operational the system will possess a number of advantages including: elimination of test preparation, editing and marking; facilitated item review opportunities; increased objectivity, feedback, flexibility and descreased anxiety in students.

Meta-Analysis of the Effects of Computerized Cognitive Training on Executive Functions: a Cross-Disciplinary Taxonomy for Classifying Outcome Cognitive Factors.

PubMed

Webb, Shannon L; Loh, Vanessa; Lampit, Amit; Bateman, Joel E; Birney, Damian P

2018-06-01

The growing prevalence of neurodegenerative disorders associated with aging and cognitive decline has generated increasing cross-disciplinary interest in non-pharmacological interventions, such as computerized cognitive training (CCT), which may prevent or slow cognitive decline. However, inconsistent findings across meta-analytic reviews in the field suggest a lack of cross-disciplinary consensus and on-going debate regarding the benefits of CCT. We posit that a contributing factor is the lack of a theoretically-based taxonomy of constructs and representative tasks typically used. An integration of the Cattell-Horn-Carroll (CHC) taxonomy of broad and narrow cognitive factors and the Miyake unity-diversity theory of executive functions (EF) is proposed (CHC-M) as an attempt to clarify this issue through representing and integrating the disciplines contributing to CCT research. The present study assessed the utility of this taxonomy by reanalyzing the Lampit et al. (2014) meta-analysis of CCT in healthy older adults using the CHC-M framework. Results suggest that: 1) substantively different statistical effects are observed when CHC-M is applied to the Lampit et al. meta-analytic review, leading to importantly different interpretations of the data; 2) typically-used classification practices conflate Executive Function (EF) tasks with fluid reasoning (Gf) and retrieval fluency (Gr), and Attention with sensory perception; and 3) there is theoretical and practical advantage in differentiating attention and working-memory tasks into the narrow shifting, inhibition, and updating EF domains. Implications for clinical practice, particularly for our understanding of EF are discussed.

Hitting the right target: taxonomic challenges for, and of, plant invasions

PubMed Central

Pyšek, Petr; Hulme, Philip E.; Meyerson, Laura A.; Smith, Gideon F.; Boatwright, James S.; Crouch, Neil R.; Figueiredo, Estrela; Foxcroft, Llewellyn C.; Jarošík, Vojtěch; Richardson, David M.; Suda, Jan; Wilson, John R. U.

2013-01-01

This paper explores how a lack of taxonomic expertise, and by implication a dearth of taxonomic products such as identification tools, has hindered progress in understanding and managing biological invasions. It also explores how the taxonomic endeavour could benefit from studies of invasive species. We review the literature on the current situation in taxonomy with a focus on the challenges of identifying alien plant species and explore how this has affected the study of biological invasions. Biosecurity strategies, legislation dealing with invasive species, quarantine, weed surveillance and monitoring all depend on accurate and rapid identification of non-native taxa. However, such identification can be challenging because the taxonomic skill base in most countries is diffuse and lacks critical mass. Taxonomic resources are essential for the effective management of invasive plants and incorrect identifications can impede ecological studies. On the other hand, biological invasions have provided important tests of basic theories about species concepts. Better integration of classical alpha taxonomy and modern genetic taxonomic approaches will improve the accuracy of species identification and further refine taxonomic classification at the level of populations and genotypes in the field and laboratory. Modern taxonomy therefore needs to integrate both classical and new concepts and approaches. In particular, differing points of view between the proponents of morphological and molecular approaches should be negotiated because a narrow taxonomic perspective is harmful; the rigour of taxonomic decision-making clearly increases if insights from a variety of different complementary disciplines are combined and confronted. Taxonomy plays a critical role in the study of plant invasions and in turn benefits from the insights gained from these studies.

Making Mosquito Taxonomy Useful: A Stable Classification of Tribe Aedini that Balances Utility with Current Knowledge of Evolutionary Relationships.

PubMed

Wilkerson, Richard C; Linton, Yvonne-Marie; Fonseca, Dina M; Schultz, Ted R; Price, Dana C; Strickman, Daniel A

2015-01-01

The tribe Aedini (Family Culicidae) contains approximately one-quarter of the known species of mosquitoes, including vectors of deadly or debilitating disease agents. This tribe contains the genus Aedes, which is one of the three most familiar genera of mosquitoes. During the past decade, Aedini has been the focus of a series of extensive morphology-based phylogenetic studies published by Reinert, Harbach, and Kitching (RH&K). Those authors created 74 new, elevated or resurrected genera from what had been the single genus Aedes, almost tripling the number of genera in the entire family Culicidae. The proposed classification is based on subjective assessments of the "number and nature of the characters that support the branches" subtending particular monophyletic groups in the results of cladistic analyses of a large set of morphological characters of representative species. To gauge the stability of RH&K's generic groupings we reanalyzed their data with unweighted parsimony jackknife and maximum-parsimony analyses, with and without ordering 14 of the characters as in RH&K. We found that their phylogeny was largely weakly supported and their taxonomic rankings failed priority and other useful taxon-naming criteria. Consequently, we propose simplified aedine generic designations that 1) restore a classification system that is useful for the operational community; 2) enhance the ability of taxonomists to accurately place new species into genera; 3) maintain the progress toward a natural classification based on monophyletic groups of species; and 4) correct the current classification system that is subject to instability as new species are described and existing species more thoroughly defined. We do not challenge the phylogenetic hypotheses generated by the above-mentioned series of morphological studies. However, we reduce the ranks of the genera and subgenera of RH&K to subgenera or informal species groups, respectively, to preserve stability as new data become available.

Making Mosquito Taxonomy Useful: A Stable Classification of Tribe Aedini that Balances Utility with Current Knowledge of Evolutionary Relationships

PubMed Central

Wilkerson, Richard C.; Linton, Yvonne-Marie; Fonseca, Dina M.; Schultz, Ted R.; Price, Dana C.; Strickman, Daniel A.

2015-01-01

The tribe Aedini (Family Culicidae) contains approximately one-quarter of the known species of mosquitoes, including vectors of deadly or debilitating disease agents. This tribe contains the genus Aedes, which is one of the three most familiar genera of mosquitoes. During the past decade, Aedini has been the focus of a series of extensive morphology-based phylogenetic studies published by Reinert, Harbach, and Kitching (RH&K). Those authors created 74 new, elevated or resurrected genera from what had been the single genus Aedes, almost tripling the number of genera in the entire family Culicidae. The proposed classification is based on subjective assessments of the “number and nature of the characters that support the branches” subtending particular monophyletic groups in the results of cladistic analyses of a large set of morphological characters of representative species. To gauge the stability of RH&K’s generic groupings we reanalyzed their data with unweighted parsimony jackknife and maximum-parsimony analyses, with and without ordering 14 of the characters as in RH&K. We found that their phylogeny was largely weakly supported and their taxonomic rankings failed priority and other useful taxon-naming criteria. Consequently, we propose simplified aedine generic designations that 1) restore a classification system that is useful for the operational community; 2) enhance the ability of taxonomists to accurately place new species into genera; 3) maintain the progress toward a natural classification based on monophyletic groups of species; and 4) correct the current classification system that is subject to instability as new species are described and existing species more thoroughly defined. We do not challenge the phylogenetic hypotheses generated by the above-mentioned series of morphological studies. However, we reduce the ranks of the genera and subgenera of RH&K to subgenera or informal species groups, respectively, to preserve stability as new data become available. PMID:26226613

Evaluating a Bilingual Text-Mining System with a Taxonomy of Key Words and Hierarchical Visualization for Understanding Learner-Generated Text

ERIC Educational Resources Information Center

Kong, Siu Cheung; Li, Ping; Song, Yanjie

2018-01-01

This study evaluated a bilingual text-mining system, which incorporated a bilingual taxonomy of key words and provided hierarchical visualization, for understanding learner-generated text in the learning management systems through automatic identification and counting of matching key words. A class of 27 in-service teachers studied a course…

Effects of the Original Versus Revised Bloom's Taxonomy on Lesson Planning Skills: A Turkish Study Among Pre-Service Teachers

NASA Astrophysics Data System (ADS)

Bümen, Nilay T.

2007-07-01

The original taxonomy of educational objectives, developed by Benjamin S.␣Bloom and his associates in the 1950s, was revised several decades later by a group of educationists and cognitive psychologists, who developed a revised taxonomy (RT). This article describes a Turkish study carried out among a group of pre-service teachers in order to compare the influence of the two systems on lesson planning skills. The results confirmed other studies that have indicated a number of advantages of the revised system over the earlier one.

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.;

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.

Discovering Beaten Paths in Collaborative Ontology-Engineering Projects using Markov Chains

PubMed Central

Walk, Simon; Singer, Philipp; Strohmaier, Markus; Tudorache, Tania; Musen, Mark A.; Noy, Natalya F.

2014-01-01

Biomedical taxonomies, thesauri and ontologies in the form of the International Classification of Diseases as a taxonomy or the National Cancer Institute Thesaurus as an OWL-based ontology, play a critical role in acquiring, representing and processing information about human health. With increasing adoption and relevance, biomedical ontologies have also significantly increased in size. For example, the 11th revision of the International Classification of Diseases, which is currently under active development by the World Health Organization contains nearly 50, 000 classes representing a vast variety of different diseases and causes of death. This evolution in terms of size was accompanied by an evolution in the way ontologies are engineered. Because no single individual has the expertise to develop such large-scale ontologies, ontology-engineering projects have evolved from small-scale efforts involving just a few domain experts to large-scale projects that require effective collaboration between dozens or even hundreds of experts, practitioners and other stakeholders. Understanding the way these different stakeholders collaborate will enable us to improve editing environments that support such collaborations. In this paper, we uncover how large ontology-engineering projects, such as the International Classification of Diseases in its 11th revision, unfold by analyzing usage logs of five different biomedical ontology-engineering projects of varying sizes and scopes using Markov chains. We discover intriguing interaction patterns (e.g., which properties users frequently change after specific given ones) that suggest that large collaborative ontology-engineering projects are governed by a few general principles that determine and drive development. From our analysis, we identify commonalities and differences between different projects that have implications for project managers, ontology editors, developers and contributors working on collaborative ontology-engineering projects and tools in the biomedical domain. PMID:24953242

Whales, dolphins or fishes? The ethnotaxonomy of cetaceans in São Sebastião, Brazil

PubMed Central

Souza, Shirley P; Begossi, Alpina

2007-01-01

The local knowledge of human populations about the natural world has been addressed through ethnobiological studies, especially concerning resources uses and their management. Several criteria, such as morphology, ecology, behavior, utility and salience, have been used by local communities to classify plants and animals. Studies regarding fishers' knowledge on cetaceans in the world, especially in Brazil, began in the last decade. Our objective is to investigate the folk classification by fishers concerning cetaceans, and the contribution of fishers' local knowledge to the conservation of that group. In particular, we aim to record fishers' knowledge in relation to cetaceans, with emphasis on folk taxonomy. The studied area is São Sebastião, located in the southeastern coast of Brazil, where 70 fishers from 14 communities were selected according to their fishing experience and interviewed through questionnaires about classification, nomenclature and ecological aspects of local cetaceans' species. Our results indicated that most fishers classified cetaceans as belonging to the life-form 'fish'. Fishers' citations for the nomenclature of the 11 biological species (10 biological genera), resulted in 14 folk species (3 generic names). Fishers' taxonomy was influenced mostly by the phenotypic and cultural salience of the studied cetaceans. Cultural transmission, vertical and horizontal, was intimately linked to fishers' classification process. The most salient species, therefore well recognized and named, were those most often caught by gillnets, in addition to the biggest ones and those most exposed by media, through TV programs, which were watched and mentioned by fishers. Our results showed that fishers' ecological knowledge could be a valuable contribution to cetaceans' conservation, helping to determine areas and periods for their protection, indicating priority topics for research and participating in alternative management related to the gillnet fisheries. PMID:17311681

Discovering beaten paths in collaborative ontology-engineering projects using Markov chains.

PubMed

Walk, Simon; Singer, Philipp; Strohmaier, Markus; Tudorache, Tania; Musen, Mark A; Noy, Natalya F

2014-10-01

Biomedical taxonomies, thesauri and ontologies in the form of the International Classification of Diseases as a taxonomy or the National Cancer Institute Thesaurus as an OWL-based ontology, play a critical role in acquiring, representing and processing information about human health. With increasing adoption and relevance, biomedical ontologies have also significantly increased in size. For example, the 11th revision of the International Classification of Diseases, which is currently under active development by the World Health Organization contains nearly 50,000 classes representing a vast variety of different diseases and causes of death. This evolution in terms of size was accompanied by an evolution in the way ontologies are engineered. Because no single individual has the expertise to develop such large-scale ontologies, ontology-engineering projects have evolved from small-scale efforts involving just a few domain experts to large-scale projects that require effective collaboration between dozens or even hundreds of experts, practitioners and other stakeholders. Understanding the way these different stakeholders collaborate will enable us to improve editing environments that support such collaborations. In this paper, we uncover how large ontology-engineering projects, such as the International Classification of Diseases in its 11th revision, unfold by analyzing usage logs of five different biomedical ontology-engineering projects of varying sizes and scopes using Markov chains. We discover intriguing interaction patterns (e.g., which properties users frequently change after specific given ones) that suggest that large collaborative ontology-engineering projects are governed by a few general principles that determine and drive development. From our analysis, we identify commonalities and differences between different projects that have implications for project managers, ontology editors, developers and contributors working on collaborative ontology-engineering projects and tools in the biomedical domain. Copyright © 2014 Elsevier Inc. All rights reserved.

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.

E&V Guidebook, Version 1.1

DTIC Science & Technology

1989-08-15

checklist 14.1] Chapter 3, Language-related issues, extracts from the Ada language reference manua! [,_D 1982] those features exp!icitly a!owcd to vay...welcome. Please send comments electronically (preferred) to szymansk~aja;po.sei.cmu.edu, or by regular mail to Mr. Raymond Szymanski , AFWAL/AAAF, Wright...of Tool Features for the Ada Programming Support Environment (APSE) 4-3 4.3 E&V Report: DoD APSE Analysis 4-4 4.4 Classification Schema/E&V Taxonomy

In my experience: Mitochondrial DNA in wildlife taxonomy and conservation biology: Cautionary notes

USGS Publications Warehouse

Cronin, Matthew A.

1993-01-01

Several recently published papers discussed the importance of systematics (the study of evolutionary and genetic relationships among organisms) and taxonomy (the naming and classification of organisms) for managing wildlife (Ryder 1986, Avise 1989, Amato 1991, O'Brien and Mayr 1991, Dowling et al. 1992), Often, classification below the species level is needed; for example, the Endangered Species Act of 1973 applies to local populations and subspecies as well as species. Conservation efforts may focus below the species level because of concerns about the fitness, evolutionary potentials, and locally adapted gene pools of natural populations (Soulé 1986, Hedrick and Milller 1992). This can be considered the genetic component of biodiversity.Recent systematic studies with wildlife management applications have used modern molecular genetic methods. Analyses of a specific molecular marker, mitochondrial DNA (mtDNA), have been used in many of these studies (e.g., Shields and Wilson 1987, Avise and Nelson 1989, O'Brien et al. 1990, Wayne and Jenks 1991, Cronin 1992), However, there are limitations to the use of mtDNA in systematics (e.g., Overden et al., 1987, Pamilo and Nei 1988, Dowling et al. 1992). In my experience as a geneticist working with wildlife biologists, I have found a need for clarification of the use and limitations of modern molecular genetics. I specifically discuss the limitations of mtDNA data in systematic assessments of wildlife at and below the species level.

A review of the automated detection and classification of acute leukaemia: Coherent taxonomy, datasets, validation and performance measurements, motivation, open challenges and recommendations.

PubMed

Alsalem, M A; Zaidan, A A; Zaidan, B B; Hashim, M; Madhloom, H T; Azeez, N D; Alsyisuf, S

2018-05-01

Acute leukaemia diagnosis is a field requiring automated solutions, tools and methods and the ability to facilitate early detection and even prediction. Many studies have focused on the automatic detection and classification of acute leukaemia and their subtypes to promote enable highly accurate diagnosis. This study aimed to review and analyse literature related to the detection and classification of acute leukaemia. The factors that were considered to improve understanding on the field's various contextual aspects in published studies and characteristics were motivation, open challenges that confronted researchers and recommendations presented to researchers to enhance this vital research area. We systematically searched all articles about the classification and detection of acute leukaemia, as well as their evaluation and benchmarking, in three main databases: ScienceDirect, Web of Science and IEEE Xplore from 2007 to 2017. These indices were considered to be sufficiently extensive to encompass our field of literature. Based on our inclusion and exclusion criteria, 89 articles were selected. Most studies (58/89) focused on the methods or algorithms of acute leukaemia classification, a number of papers (22/89) covered the developed systems for the detection or diagnosis of acute leukaemia and few papers (5/89) presented evaluation and comparative studies. The smallest portion (4/89) of articles comprised reviews and surveys. Acute leukaemia diagnosis, which is a field requiring automated solutions, tools and methods, entails the ability to facilitate early detection or even prediction. Many studies have been performed on the automatic detection and classification of acute leukaemia and their subtypes to promote accurate diagnosis. Research areas on medical-image classification vary, but they are all equally vital. We expect this systematic review to help emphasise current research opportunities and thus extend and create additional research fields. Copyright © 2018 Elsevier B.V. All rights reserved.

Engineering derivatives from biological systems for advanced aerospace applications

NASA Technical Reports Server (NTRS)

Winfield, Daniel L.; Hering, Dean H.; Cole, David

1991-01-01

The present study consisted of a literature survey, a survey of researchers, and a workshop on bionics. These tasks produced an extensive annotated bibliography of bionics research (282 citations), a directory of bionics researchers, and a workshop report on specific bionics research topics applicable to space technology. These deliverables are included as Appendix A, Appendix B, and Section 5.0, respectively. To provide organization to this highly interdisciplinary field and to serve as a guide for interested researchers, we have also prepared a taxonomy or classification of the various subelements of natural engineering systems. Finally, we have synthesized the results of the various components of this study into a discussion of the most promising opportunities for accelerated research, seeking solutions which apply engineering principles from natural systems to advanced aerospace problems. A discussion of opportunities within the areas of materials, structures, sensors, information processing, robotics, autonomous systems, life support systems, and aeronautics is given. Following the conclusions are six discipline summaries that highlight the potential benefits of research in these areas for NASA's space technology programs.

Looking forward and back to relapse: implications for research and practice.

PubMed

Connors, G J; Longabaugh, R; Miller, W R

1996-12-01

In this commentary, the three principal investigators of the Relapse Replication and Extension Project (RREP) reflect on clinical and research implications of study findings from the three collaborating sites. A primary purpose of RREP was to study the reliability and validity of a taxonomy of relapse antecedents originally proposed by Marlatt two decades ago. Under the best of research conditions, with extensive training and practice, it was difficult to achieve reliability of coding with the original three-level system, although with only two levels of classification more reasonable albeit variable reliability was found. Modifications may improve the taxonomy's reliability, but RREP data indicate that a more appropriate strategy is to measure possible antecedents of relapse by continuous scales such as those provided by Annis, Heather and Litman. There is reasonably consistent evidence for two common antecedents of relapse: negative emotional states, and positive emotional states in a social context. Antecedents of relapse show only modest consistency within individuals from one occasion to the next. The causes to which clients attribute relapses may exert a significant effect on future drinking episodes. Stable and internal attributions, such as are commonly associated with a dispositional disease model, may serve to perpetuate relapse. From the RREP studies, the availability of coping skills appears to be a potent protective factor, and ineffective coping a consistent predictor of relapse. Implications for clinical research and practice are considered.

Doha agreement meeting on terminology and definitions in groin pain in athletes

PubMed Central

Weir, Adam; Brukner, Peter; Delahunt, Eamonn; Ekstrand, Jan; Griffin, Damian; Khan, Karim M; Lovell, Greg; Meyers, William C; Muschaweck, Ulrike; Orchard, John; Paajanen, Hannu; Philippon, Marc; Reboul, Gilles; Robinson, Philip; Schache, Anthony G; Schilders, Ernest; Serner, Andreas; Silvers, Holly; Thorborg, Kristian; Tyler, Timothy; Verrall, Geoffrey; de Vos, Robert-Jan; Vuckovic, Zarko; Hölmich, Per

2015-01-01

Background Heterogeneous taxonomy of groin injuries in athletes adds confusion to this complicated area. Aim The ‘Doha agreement meeting on terminology and definitions in groin pain in athletes’ was convened to attempt to resolve this problem. Our aim was to agree on a standard terminology, along with accompanying definitions. Methods A one-day agreement meeting was held on 4 November 2014. Twenty-four international experts from 14 different countries participated. Systematic reviews were performed to give an up-to-date synthesis of the current evidence on major topics concerning groin pain in athletes. All members participated in a Delphi questionnaire prior to the meeting. Results Unanimous agreement was reached on the following terminology. The classification system has three major subheadings of groin pain in athletes: 1. Defined clinical entities for groin pain: Adductor-related, iliopsoas-related, inguinal-related and pubic-related groin pain. 2. Hip-related groin pain. 3. Other causes of groin pain in athletes. The definitions are included in this paper. Conclusions The Doha agreement meeting on terminology and definitions in groin pain in athletes reached a consensus on a clinically based taxonomy using three major categories. These definitions and terminology are based on history and physical examination to categorise athletes, making it simple and suitable for both clinical practice and research. PMID:26031643

Confidential reporting of patient safety events in primary care: results from a multilevel classification of cognitive and system factors.

PubMed

Kostopoulou, Olga; Delaney, Brendan

2007-04-01

To classify events of actual or potential harm to primary care patients using a multilevel taxonomy of cognitive and system factors. Observational study of patient safety events obtained via a confidential but not anonymous reporting system. Reports were followed up with interviews where necessary. Events were analysed for their causes and contributing factors using causal trees and were classified using the taxonomy. Five general medical practices in the West Midlands were selected to represent a range of sizes and types of patient population. All practice staff were invited to report patient safety events. Main outcome measures were frequencies of clinical types of events reported, cognitive types of error, types of detection and contributing factors; and relationship between types of error, practice size, patient consequences and detection. 78 reports were relevant to patient safety and analysable. They included 21 (27%) adverse events and 50 (64%) near misses. 16.7% (13/71) had serious patient consequences, including one death. 75.7% (59/78) had the potential for serious patient harm. Most reports referred to administrative errors (25.6%, 20/78). 60% (47/78) of the reports contained sufficient information to characterise cognition: "situation assessment and response selection" was involved in 45% (21/47) of these reports and was often linked to serious potential consequences. The most frequent contributing factor was work organisation, identified in 71 events. This included excessive task demands (47%, 37/71) and fragmentation (28%, 22/71). Even though most reported events were near misses, events with serious patient consequences were also reported. Failures in situation assessment and response selection, a cognitive activity that occurs in both clinical and administrative tasks, was related to serious potential harm.

Confidential reporting of patient safety events in primary care: results from a multilevel classification of cognitive and system factors

PubMed Central

Kostopoulou, Olga; Delaney, Brendan

2007-01-01

Objective To classify events of actual or potential harm to primary care patients using a multilevel taxonomy of cognitive and system factors. Methods Observational study of patient safety events obtained via a confidential but not anonymous reporting system. Reports were followed up with interviews where necessary. Events were analysed for their causes and contributing factors using causal trees and were classified using the taxonomy. Five general medical practices in the West Midlands were selected to represent a range of sizes and types of patient population. All practice staff were invited to report patient safety events. Main outcome measures were frequencies of clinical types of events reported, cognitive types of error, types of detection and contributing factors; and relationship between types of error, practice size, patient consequences and detection. Results 78 reports were relevant to patient safety and analysable. They included 21 (27%) adverse events and 50 (64%) near misses. 16.7% (13/71) had serious patient consequences, including one death. 75.7% (59/78) had the potential for serious patient harm. Most reports referred to administrative errors (25.6%, 20/78). 60% (47/78) of the reports contained sufficient information to characterise cognition: “situation assessment and response selection” was involved in 45% (21/47) of these reports and was often linked to serious potential consequences. The most frequent contributing factor was work organisation, identified in 71 events. This included excessive task demands (47%, 37/71) and fragmentation (28%, 22/71). Conclusions Even though most reported events were near misses, events with serious patient consequences were also reported. Failures in situation assessment and response selection, a cognitive activity that occurs in both clinical and administrative tasks, was related to serious potential harm. PMID:17403753

A knowledge engineering taxonomy for intelligent tutoring system development

NASA Technical Reports Server (NTRS)

Fink, Pamela K.; Herren, L. Tandy

1993-01-01

This paper describes a study addressing the issue of developing an appropriate mapping of knowledge acquisition methods to problem types for intelligent tutoring system development. Recent research has recognized that knowledge acquisition methodologies are not general across problem domains; the effectiveness of a method for obtaining knowledge depends on the characteristics of the domain and problem solving task. Southwest Research Institute developed a taxonomy of problem types by evaluating the characteristics that discriminate between problems and grouping problems that share critical characteristics. Along with the problem taxonomy, heuristics that guide the knowledge acquisition process based on the characteristics of the class are provided.

Multilocus resolution of Mugilidae phylogeny (Teleostei: Mugiliformes): Implications for the family's taxonomy.

PubMed

Xia, Rong; Durand, Jean-Dominique; Fu, Cuizhang

2016-03-01

The interrelationships among mugilids (Mugiliformes: Mugilidae) remain highly debated. Using a mitochondrial gene-based phylogeny as criterion, a revised classification with 25 genera in the Mugilidae has recently been proposed. However, phylogenetic relationships of major mitochondrial lineages remain unresolved and to gain a general acceptance the classification requires confirmation based on multilocus evidence and diagnostic morphological characters. Here, we construct a species-tree using twelve nuclear and three mitochondrial loci and infer the evolution of 71 morphological characters. Our multilocus phylogeny does not agree with previous morphology-based hypotheses for the relationships within Mugilidae, confirms the revised classification with 25 genera and further resolves their phylogenetic relationships. Using the well-resolved multilocus phylogeny as the criterion, we reclassify Mugilidae genera into three new subfamilies (Myxinae, Rhinomugilinae, and Cheloninae) and one new, recombined, subfamily (Mugilinae). The Rhinomugilinae subfamily is further divided into four tribes. The revised classification of Mugilidae is supported by morpho-anatomical synapomorphies or a combination of characters. These characters are used to erect a key to the subfamilies and genera. Copyright © 2015 Elsevier Inc. All rights reserved.

Periodontal profile classes predict periodontal disease progression and tooth loss.

PubMed

Morelli, Thiago; Moss, Kevin L; Preisser, John S; Beck, James D; Divaris, Kimon; Wu, Di; Offenbacher, Steven

2018-02-01

Current periodontal disease taxonomies have limited utility for predicting disease progression and tooth loss; in fact, tooth loss itself can undermine precise person-level periodontal disease classifications. To overcome this limitation, the current group recently introduced a novel patient stratification system using latent class analyses of clinical parameters, including patterns of missing teeth. This investigation sought to determine the clinical utility of the Periodontal Profile Classes and Tooth Profile Classes (PPC/TPC) taxonomy for risk assessment, specifically for predicting periodontal disease progression and incident tooth loss. The analytic sample comprised 4,682 adult participants of two prospective cohort studies (Dental Atherosclerosis Risk in Communities Study and Piedmont Dental Study) with information on periodontal disease progression and incident tooth loss. The PPC/TPC taxonomy includes seven distinct PPCs (person-level disease pattern and severity) and seven TPCs (tooth-level disease). Logistic regression modeling was used to estimate relative risks (RR) and 95% confidence intervals (CI) for the association of these latent classes with disease progression and incident tooth loss, adjusting for examination center, race, sex, age, diabetes, and smoking. To obtain personalized outcome propensities, risk estimates associated with each participant's PPC and TPC were combined into person-level composite risk scores (Index of Periodontal Risk [IPR]). Individuals in two PPCs (PPC-G: Severe Disease and PPC-D: Tooth Loss) had the highest tooth loss risk (RR = 3.6; 95% CI = 2.6 to 5.0 and RR = 3.8; 95% CI = 2.9 to 5.1, respectively). PPC-G also had the highest risk for periodontitis progression (RR = 5.7; 95% CI = 2.2 to 14.7). Personalized IPR scores were positively associated with both periodontitis progression and tooth loss. These findings, upon additional validation, suggest that the periodontal/tooth profile classes and the derived personalized propensity scores provide clinical periodontal definitions that reflect disease patterns in the population and offer a useful system for patient stratification that is predictive for disease progression and tooth loss. © 2018 American Academy of Periodontology.

A Report Card for Risk Management in Higher Education for Two-Year Colleges in Minnesota, Wisconsin, and Michigan: A Study to Assess Gaps Regarding Risk Management in Higher Education

ERIC Educational Resources Information Center

Centko, John David

2017-01-01

The purpose of this study was to organize the identified risks into one of the five classifications in order to establish a taxonomy created by peers and to measure the variances in the level of risk at two-year colleges. A universal problem for colleges and universities is the difficulty of finding peer groups that have and are willing to share…

The order Zoantharia Rafinesque, 1815 (Cnidaria, Anthozoa: Hexacorallia): supraspecific classification and nomenclature

PubMed Central

Low, Martyn E. Y.; Sinniger, Frederic; Reimer, James Davis

2016-01-01

Abstract Many supraspecific zoantharian names have long and complicated histories. The present list is provided to advise researchers on the current state of supraspecific nomenclature of the zoantharians, particularly given the recent attention paid to the taxonomy, phylogeny, and biodiversity of this order. At the same time, several taxonomic issues brought to light by recent research are resolved. Details on the taxonomic and nomenclatural history of most groups are provided, along with appendices of invalid supraspecific names. PMID:28138291

Molecular classification of breast cancer: what the pathologist needs to know.

PubMed

Rakha, Emad A; Green, Andrew R

2017-02-01

Breast cancer is a heterogeneous disease featuring distinct histological, molecular and clinical phenotypes. Although traditional classification systems utilising clinicopathological and few molecular markers are well established and validated, they remain insufficient to reflect the diverse biological and clinical heterogeneity of breast cancer. Advancements in high-throughput molecular techniques and bioinformatics have contributed to the improved understanding of breast cancer biology, refinement of molecular taxonomies and the development of novel prognostic and predictive molecular assays. Application of such technologies is already underway, and is expected to change the way we manage breast cancer. Despite the enormous amount of work that has been carried out to develop and refine breast cancer molecular prognostic and predictive assays, molecular testing is still in evolution. Pathologists should be aware of the new technology and be ready for the challenge. In this review, we provide an update on the application of molecular techniques with regard to breast cancer diagnosis, prognosis and outcome prediction. The current contribution of emerging technology to our understanding of breast cancer is also highlighted. Copyright © 2016 Royal College of Pathologists of Australasia. Published by Elsevier B.V. All rights reserved.

Bridging Theory with Practice: An Exploratory Study of Visualization Use and Design for Climate Model Comparison

DOE PAGES

Dasgupta, Aritra; Poco, Jorge; Wei, Yaxing; ...

2015-03-16

Evaluation methodologies in visualization have mostly focused on how well the tools and techniques cater to the analytical needs of the user. While this is important in determining the effectiveness of the tools and advancing the state-of-the-art in visualization research, a key area that has mostly been overlooked is how well established visualization theories and principles are instantiated in practice. This is especially relevant when domain experts, and not visualization researchers, design visualizations for analysis of their data or for broader dissemination of scientific knowledge. There is very little research on exploring the synergistic capabilities of cross-domain collaboration between domainmore » experts and visualization researchers. To fill this gap, in this paper we describe the results of an exploratory study of climate data visualizations conducted in tight collaboration with a pool of climate scientists. The study analyzes a large set of static climate data visualizations for identifying their shortcomings in terms of visualization design. The outcome of the study is a classification scheme that categorizes the design problems in the form of a descriptive taxonomy. The taxonomy is a first attempt for systematically categorizing the types, causes, and consequences of design problems in visualizations created by domain experts. We demonstrate the use of the taxonomy for a number of purposes, such as, improving the existing climate data visualizations, reflecting on the impact of the problems for enabling domain experts in designing better visualizations, and also learning about the gaps and opportunities for future visualization research. We demonstrate the applicability of our taxonomy through a number of examples and discuss the lessons learnt and implications of our findings.« less

Bridging Theory with Practice: An Exploratory Study of Visualization Use and Design for Climate Model Comparison

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

Dasgupta, Aritra; Poco, Jorge; Wei, Yaxing

Evaluation methodologies in visualization have mostly focused on how well the tools and techniques cater to the analytical needs of the user. While this is important in determining the effectiveness of the tools and advancing the state-of-the-art in visualization research, a key area that has mostly been overlooked is how well established visualization theories and principles are instantiated in practice. This is especially relevant when domain experts, and not visualization researchers, design visualizations for analysis of their data or for broader dissemination of scientific knowledge. There is very little research on exploring the synergistic capabilities of cross-domain collaboration between domainmore » experts and visualization researchers. To fill this gap, in this paper we describe the results of an exploratory study of climate data visualizations conducted in tight collaboration with a pool of climate scientists. The study analyzes a large set of static climate data visualizations for identifying their shortcomings in terms of visualization design. The outcome of the study is a classification scheme that categorizes the design problems in the form of a descriptive taxonomy. The taxonomy is a first attempt for systematically categorizing the types, causes, and consequences of design problems in visualizations created by domain experts. We demonstrate the use of the taxonomy for a number of purposes, such as, improving the existing climate data visualizations, reflecting on the impact of the problems for enabling domain experts in designing better visualizations, and also learning about the gaps and opportunities for future visualization research. We demonstrate the applicability of our taxonomy through a number of examples and discuss the lessons learnt and implications of our findings.« less

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

Charles Darwin, beetles and phylogenetics.

PubMed

Beutel, Rolf G; Friedrich, Frank; Leschen, Richard A B

2009-11-01

Here, we review Charles Darwin's relation to beetles and developments in coleopteran systematics in the last two centuries. Darwin was an enthusiastic beetle collector. He used beetles to illustrate different evolutionary phenomena in his major works, and astonishingly, an entire sub-chapter is dedicated to beetles in "The Descent of Man". During his voyage on the Beagle, Darwin was impressed by the high diversity of beetles in the tropics, and he remarked that, to his surprise, the majority of species were small and inconspicuous. However, despite his obvious interest in the group, he did not get involved in beetle taxonomy, and his theoretical work had little immediate impact on beetle classification. The development of taxonomy and classification in the late nineteenth and earlier twentieth century was mainly characterised by the exploration of new character systems (e.g. larval features and wing venation). In the mid-twentieth century, Hennig's new methodology to group lineages by derived characters revolutionised systematics of Coleoptera and other organisms. As envisioned by Darwin and Ernst Haeckel, the new Hennigian approach enabled systematists to establish classifications truly reflecting evolution. Roy A. Crowson and Howard E. Hinton, who both made tremendous contributions to coleopterology, had an ambivalent attitude towards the Hennigian ideas. The Mickoleit school combined detailed anatomical work with a classical Hennigian character evaluation, with stepwise tree building, comparatively few characters and a priori polarity assessment without explicit use of the outgroup comparison method. The rise of cladistic methods in the 1970s had a strong impact on beetle systematics. Cladistic computer programs facilitated parsimony analyses of large data matrices, mostly morphological characters not requiring detailed anatomical investigations. Molecular studies on beetle phylogeny started in the 1990s with modest taxon sampling and limited DNA data. This has changed dramatically. With very large data sets and high throughput sampling, phylogenetic questions can be addressed without prior knowledge of morphological characters. Nevertheless, molecular studies have not lead to the great breakthrough in beetle systematics--yet. Especially the phylogeny of the extremely species rich suborder Polyphaga remains incompletely resolved. Coordinated efforts of molecular workers and of morphologists using innovative techniques may lead to more profound insights in the near future. The final aim is to develop a well-founded phylogeny, which truly reflects the evolution of this immensely species rich group of organisms.

Charles Darwin, beetles and phylogenetics

NASA Astrophysics Data System (ADS)

Beutel, Rolf G.; Friedrich, Frank; Leschen, Richard A. B.

2009-11-01

Here, we review Charles Darwin’s relation to beetles and developments in coleopteran systematics in the last two centuries. Darwin was an enthusiastic beetle collector. He used beetles to illustrate different evolutionary phenomena in his major works, and astonishingly, an entire sub-chapter is dedicated to beetles in “The Descent of Man”. During his voyage on the Beagle, Darwin was impressed by the high diversity of beetles in the tropics, and he remarked that, to his surprise, the majority of species were small and inconspicuous. However, despite his obvious interest in the group, he did not get involved in beetle taxonomy, and his theoretical work had little immediate impact on beetle classification. The development of taxonomy and classification in the late nineteenth and earlier twentieth century was mainly characterised by the exploration of new character systems (e.g. larval features and wing venation). In the mid-twentieth century, Hennig’s new methodology to group lineages by derived characters revolutionised systematics of Coleoptera and other organisms. As envisioned by Darwin and Ernst Haeckel, the new Hennigian approach enabled systematists to establish classifications truly reflecting evolution. Roy A. Crowson and Howard E. Hinton, who both made tremendous contributions to coleopterology, had an ambivalent attitude towards the Hennigian ideas. The Mickoleit school combined detailed anatomical work with a classical Hennigian character evaluation, with stepwise tree building, comparatively few characters and a priori polarity assessment without explicit use of the outgroup comparison method. The rise of cladistic methods in the 1970s had a strong impact on beetle systematics. Cladistic computer programs facilitated parsimony analyses of large data matrices, mostly morphological characters not requiring detailed anatomical investigations. Molecular studies on beetle phylogeny started in the 1990s with modest taxon sampling and limited DNA data. This has changed dramatically. With very large data sets and high throughput sampling, phylogenetic questions can be addressed without prior knowledge of morphological characters. Nevertheless, molecular studies have not lead to the great breakthrough in beetle systematics—yet. Especially the phylogeny of the extremely species rich suborder Polyphaga remains incompletely resolved. Coordinated efforts of molecular workers and of morphologists using innovative techniques may lead to more profound insights in the near future. The final aim is to develop a well-founded phylogeny, which truly reflects the evolution of this immensely species rich group of organisms.

Towards a taxonomy for integrated care: a mixed-methods study

PubMed Central

Valentijn, Pim P.; Boesveld, Inge C.; van der Klauw, Denise M.; Ruwaard, Dirk; Struijs, Jeroen N.; Molema, Johanna J.W.; Bruijnzeels, Marc A.; Vrijhoef, Hubertus JM.

2015-01-01

Introduction Building integrated services in a primary care setting is considered an essential important strategy for establishing a high-quality and affordable health care system. The theoretical foundations of such integrated service models are described by the Rainbow Model of Integrated Care, which distinguishes six integration dimensions (clinical, professional, organisational, system, functional and normative integration). The aim of the present study is to refine the Rainbow Model of Integrated Care by developing a taxonomy that specifies the underlying key features of the six dimensions. Methods First, a literature review was conducted to identify features for achieving integrated service delivery. Second, a thematic analysis method was used to develop a taxonomy of key features organised into the dimensions of the Rainbow Model of Integrated Care. Finally, the appropriateness of the key features was tested in a Delphi study among Dutch experts. Results The taxonomy consists of 59 key features distributed across the six integration dimensions of the Rainbow Model of Integrated Care. Key features associated with the clinical, professional, organisational and normative dimensions were considered appropriate by the experts. Key features linked to the functional and system dimensions were considered less appropriate. Discussion This study contributes to the ongoing debate of defining the concept and typology of integrated care. This taxonomy provides a development agenda for establishing an accepted scientific framework of integrated care from an end-user, professional, managerial and policy perspective. PMID:25759607

Towards a taxonomy for integrated care: a mixed-methods study.

PubMed

Valentijn, Pim P; Boesveld, Inge C; van der Klauw, Denise M; Ruwaard, Dirk; Struijs, Jeroen N; Molema, Johanna J W; Bruijnzeels, Marc A; Vrijhoef, Hubertus Jm

2015-01-01

Building integrated services in a primary care setting is considered an essential important strategy for establishing a high-quality and affordable health care system. The theoretical foundations of such integrated service models are described by the Rainbow Model of Integrated Care, which distinguishes six integration dimensions (clinical, professional, organisational, system, functional and normative integration). The aim of the present study is to refine the Rainbow Model of Integrated Care by developing a taxonomy that specifies the underlying key features of the six dimensions. First, a literature review was conducted to identify features for achieving integrated service delivery. Second, a thematic analysis method was used to develop a taxonomy of key features organised into the dimensions of the Rainbow Model of Integrated Care. Finally, the appropriateness of the key features was tested in a Delphi study among Dutch experts. The taxonomy consists of 59 key features distributed across the six integration dimensions of the Rainbow Model of Integrated Care. Key features associated with the clinical, professional, organisational and normative dimensions were considered appropriate by the experts. Key features linked to the functional and system dimensions were considered less appropriate. This study contributes to the ongoing debate of defining the concept and typology of integrated care. This taxonomy provides a development agenda for establishing an accepted scientific framework of integrated care from an end-user, professional, managerial and policy perspective.

Paradigm lost: race, ethnicity, and the search for a new population taxonomy.

PubMed

Oppenheimer, G M

2001-07-01

The Institute of Medicine (IOM) recently recommended that the National Institutes of Health (NIH) reevaluate its employment of "race," a concept lacking scientific or anthropological justification, in cancer surveillance and other population research. The IOM advised the NIH to use a different population classification, that of "ethnic group," instead of "race." A relatively new term, according to the IOM, "ethnic group" would turn research attention away from biological determinism and toward a focus on culture and behavior. This article examines the historically central role of racial categorization and its relationship to racism in the United States and questions whether dropping "race" from population taxonomies is either possible or, at least in the short run, preferable. In addition, a historical examination of "ethnicity" and "ethnic group" finds that these concepts, as used in the United States, derive in part from race and immigration and are not neutral terms; instead, they carry their own burden of political, social, and ideological meaning.

Improved data retrieval from TreeBASE via taxonomic and linguistic data enrichment

PubMed Central

Anwar, Nadia; Hunt, Ela

2009-01-01

Background TreeBASE, the only data repository for phylogenetic studies, is not being used effectively since it does not meet the taxonomic data retrieval requirements of the systematics community. We show, through an examination of the queries performed on TreeBASE, that data retrieval using taxon names is unsatisfactory. Results We report on a new wrapper supporting taxon queries on TreeBASE by utilising a Taxonomy and Classification Database (TCl-Db) we created. TCl-Db holds merged and consolidated taxonomic names from multiple data sources and can be used to translate hierarchical, vernacular and synonym queries into specific query terms in TreeBASE. The query expansion supported by TCl-Db shows very significant information retrieval quality improvement. The wrapper can be accessed at the URL The methodology we developed is scalable and can be applied to new data, as those become available in the future. Conclusion Significantly improved data retrieval quality is shown for all queries, and additional flexibility is achieved via user-driven taxonomy selection. PMID:19426482

Taxonomy of Fungi Causing Mucormycosis and Entomophthoramycosis (Zygomycosis) and Nomenclature of the Disease: Molecular Mycologic Perspectives

PubMed Central

2012-01-01

Molecular phylogenetic analysis confirmed the phylum Zygomycota to be polyphyletic, and the taxa conventionally classified in Zygomycota are now distributed among the new phylum Glomeromycota and 4 subphyla incertae sedis (uncertain placement). Because the nomenclature of the disease zygomycosis was based on the phylum Zygomycota (Zygomycetes) in which the etiologic agents had been classified, the new classification profoundly affects the name of the disease. Zygomycosis was originally described as a convenient and inclusive name for 2 clinicopathologically different diseases, mucormycosis caused by members of Mucorales and entomophthoramycosis caused by species in the order Entomophthorales of Zygomycota. Without revision of original definition, the name “zygomycosis,” however, has more often been used as a synonym only for mucormycosis. This article reviews the progress and changes in taxonomy and nomenclature of Zygomycota and the disease zygomycosis. The article also reiterates the reasons why the classic names “mucormycosis” and “entomophthoramycosis” are more appropriate than “zygomycosis.” PMID:22247451

[An approach to bacteriological taxonomy by application of Immanuel Kant's transcendental dialectics (author's transl)].

PubMed

Habs, H

1981-01-01

After having altered the name of International Committee for Bacteriological Nomenclature in International Committee on Systematic Bacteriology in 1970, the latter will also have to reflect upon the objects of taxonomy. An approach thereto is recognizable in the revision of the International Code of Nomenclature of Bacteria in 1975. Considerations are being made whether a classification of bacteria does justice to the laws of homogenicity, specification and continuity as laid down by Kant in his transcendental dialectic. Most important of all are definition and determination of the taxon species. As far as contents go the latter is not possible from the biological point of view but applicable to its range in application of the regulations of the code. Within the priorities of taxa the species adopts a preferential position because conceptions of applied bacteriology are contained therein. The variety of infra-subspecific subdivisions is taken into consideration; as far as the formae speciales are concerned considerations as made with regard to species apply.

Paradigm lost: race, ethnicity, and the search for a new population taxonomy.

PubMed Central

Oppenheimer, G M

2001-01-01

The Institute of Medicine (IOM) recently recommended that the National Institutes of Health (NIH) reevaluate its employment of "race," a concept lacking scientific or anthropological justification, in cancer surveillance and other population research. The IOM advised the NIH to use a different population classification, that of "ethnic group," instead of "race." A relatively new term, according to the IOM, "ethnic group" would turn research attention away from biological determinism and toward a focus on culture and behavior. This article examines the historically central role of racial categorization and its relationship to racism in the United States and questions whether dropping "race" from population taxonomies is either possible or, at least in the short run, preferable. In addition, a historical examination of "ethnicity" and "ethnic group" finds that these concepts, as used in the United States, derive in part from race and immigration and are not neutral terms; instead, they carry their own burden of political, social, and ideological meaning. PMID:11441730

Taxonomy of multi-focal nematode image stacks by a CNN based image fusion approach.

PubMed

Liu, Min; Wang, Xueping; Zhang, Hongzhong

2018-03-01

In the biomedical field, digital multi-focal images are very important for documentation and communication of specimen data, because the morphological information for a transparent specimen can be captured in form of a stack of high-quality images. Given biomedical image stacks containing multi-focal images, how to efficiently extract effective features from all layers to classify the image stacks is still an open question. We present to use a deep convolutional neural network (CNN) image fusion based multilinear approach for the taxonomy of multi-focal image stacks. A deep CNN based image fusion technique is used to combine relevant information of multi-focal images within a given image stack into a single image, which is more informative and complete than any single image in the given stack. Besides, multi-focal images within a stack are fused along 3 orthogonal directions, and multiple features extracted from the fused images along different directions are combined by canonical correlation analysis (CCA). Because multi-focal image stacks represent the effect of different factors - texture, shape, different instances within the same class and different classes of objects, we embed the deep CNN based image fusion method within a multilinear framework to propose an image fusion based multilinear classifier. The experimental results on nematode multi-focal image stacks demonstrated that the deep CNN image fusion based multilinear classifier can reach a higher classification rate (95.7%) than that by the previous multilinear based approach (88.7%), even we only use the texture feature instead of the combination of texture and shape features as in the previous work. The proposed deep CNN image fusion based multilinear approach shows great potential in building an automated nematode taxonomy system for nematologists. It is effective to classify multi-focal image stacks. Copyright © 2018 Elsevier B.V. All rights reserved.

[Program about therapeutics education. Roll-playing exercise].

PubMed

Salinas, Carmen Martín

2011-05-01

This article presents a program about therapeutics education aimed at a patient with diabetes mellitus type 2, associated with hypertension, dyslipidemia and obesity The association of these factors constitutes the so-called metabolic syndrome, which entails an increase in the risk of heart disease. This roll-playing exercise is used in the subject Nutrition and Dietetics, given in the second academic year of the Nursing University School La Paz of Madrid, Spain, in order to strengthen self-directed learning. Solving the case comprises evaluation of the patient's self-care agency identification of the self-care deficit and those nurse interventions which are considered necessary to treat that deficit. Both three Diagnosis Taxonomy by the North American Nursing Diagnosis Association, Nursing Intervention Classification and Nursing Result Classification were used to solve it.

Development and content validity testing of a comprehensive classification of diagnoses for pediatric nurse practitioners.

PubMed

Burns, C

1991-01-01

Pediatric nurse practitioners (PNPs) need an integrated, comprehensive classification that includes nursing, disease, and developmental diagnoses to effectively describe their practice. No such classification exists. Further, methodologic studies to help evaluate the content validity of any nursing taxonomy are unavailable. A conceptual framework was derived. Then 178 diagnoses from the North American Nursing Diagnosis Association (NANDA) 1986 list, selected diagnoses from the International Classification of Diseases, the Diagnostic and Statistical Manual, Third Revision, and others were selected. This framework identified and listed, with definitions, three domains of diagnoses: Developmental Problems, Diseases, and Daily Living Problems. The diagnoses were ranked using a 4-point scale (4 = highly related to 1 = not related) and were placed into the three domains. The rating scale was assigned by a panel of eight expert pediatric nurses. Diagnoses that were assigned to the Daily Living Problems domain were then sorted into the 11 Functional Health patterns described by Gordon (1987). Reliability was measured using proportions of agreement and Kappas. Content validity of the groups created was measured using indices of content validity and average congruency percentages. The experts used a new method to sort the diagnoses in a new way that decreased overlaps among the domains. The Developmental and Disease domains were judged reliable and valid. The Daily Living domain of nursing diagnoses showed marginally acceptable validity with acceptable reliability. Six Functional Health Patterns were judged reliable and valid, mixed results were determined for four categories, and the Coping/Stress Tolerance category was judged reliable but not valid using either test. There were considerable differences between the panel's, Gordon's (1987), and NANDA's clustering of NANDA diagnoses. This study defines the diagnostic practice of nurses from a holistic, patient-centered perspective. It is the first study to use quantitative methods to test a diagnostic classification system for nursing. The classification model could also be adapted for other nurse specialties.

Construction of a Calibrated Probabilistic Classification Catalog: Application to 50k Variable Sources in the All-Sky Automated Survey

NASA Astrophysics Data System (ADS)

Richards, Joseph W.; Starr, Dan L.; Miller, Adam A.; Bloom, Joshua S.; Butler, Nathaniel R.; Brink, Henrik; Crellin-Quick, Arien

2012-12-01

With growing data volumes from synoptic surveys, astronomers necessarily must become more abstracted from the discovery and introspection processes. Given the scarcity of follow-up resources, there is a particularly sharp onus on the frameworks that replace these human roles to provide accurate and well-calibrated probabilistic classification catalogs. Such catalogs inform the subsequent follow-up, allowing consumers to optimize the selection of specific sources for further study and permitting rigorous treatment of classification purities and efficiencies for population studies. Here, we describe a process to produce a probabilistic classification catalog of variability with machine learning from a multi-epoch photometric survey. In addition to producing accurate classifications, we show how to estimate calibrated class probabilities and motivate the importance of probability calibration. We also introduce a methodology for feature-based anomaly detection, which allows discovery of objects in the survey that do not fit within the predefined class taxonomy. Finally, we apply these methods to sources observed by the All-Sky Automated Survey (ASAS), and release the Machine-learned ASAS Classification Catalog (MACC), a 28 class probabilistic classification catalog of 50,124 ASAS sources in the ASAS Catalog of Variable Stars. We estimate that MACC achieves a sub-20% classification error rate and demonstrate that the class posterior probabilities are reasonably calibrated. MACC classifications compare favorably to the classifications of several previous domain-specific ASAS papers and to the ASAS Catalog of Variable Stars, which had classified only 24% of those sources into one of 12 science classes.

CONSTRUCTION OF A CALIBRATED PROBABILISTIC CLASSIFICATION CATALOG: APPLICATION TO 50k VARIABLE SOURCES IN THE ALL-SKY AUTOMATED SURVEY

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

Richards, Joseph W.; Starr, Dan L.; Miller, Adam A.

2012-12-15

With growing data volumes from synoptic surveys, astronomers necessarily must become more abstracted from the discovery and introspection processes. Given the scarcity of follow-up resources, there is a particularly sharp onus on the frameworks that replace these human roles to provide accurate and well-calibrated probabilistic classification catalogs. Such catalogs inform the subsequent follow-up, allowing consumers to optimize the selection of specific sources for further study and permitting rigorous treatment of classification purities and efficiencies for population studies. Here, we describe a process to produce a probabilistic classification catalog of variability with machine learning from a multi-epoch photometric survey. In additionmore » to producing accurate classifications, we show how to estimate calibrated class probabilities and motivate the importance of probability calibration. We also introduce a methodology for feature-based anomaly detection, which allows discovery of objects in the survey that do not fit within the predefined class taxonomy. Finally, we apply these methods to sources observed by the All-Sky Automated Survey (ASAS), and release the Machine-learned ASAS Classification Catalog (MACC), a 28 class probabilistic classification catalog of 50,124 ASAS sources in the ASAS Catalog of Variable Stars. We estimate that MACC achieves a sub-20% classification error rate and demonstrate that the class posterior probabilities are reasonably calibrated. MACC classifications compare favorably to the classifications of several previous domain-specific ASAS papers and to the ASAS Catalog of Variable Stars, which had classified only 24% of those sources into one of 12 science classes.« less

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.

Revision of the characters of Centrolenidae (Amphibia : Anura : Athesphatanura), with comments on its taxonomy and the description of new taxa of glassfrogs

USGS Publications Warehouse

Cisneros-Heredia, D.F.; McDiarmid, Roy W.

2007-01-01

Anurans of the family Centrolenidae are a diverse clade of arboreal frogs distributed across tropical America. Knowledge of their taxonomy, systematics, ecology, behavior, morphology, and other evolutionary aspects of their biology is deficient. Relationships among centrolenid species remain largely unresolved, with no satisfactory phylogenetic hypothesis, and none of the current genera has compelling evidence of monophyly. Further, understanding the phylogeny of glassfrogs is constrained by species-level taxonomic problems, including incorrect description of characters, incomplete analyses of intraspecific variation, and lack of appreciation of species diversity. Herein, we define and analyze the 23 characters that are useful, in combination, in diagnosing centrolenid species, and thereby provide a reference for the use of future workers. We propose revised classifications for the parietal and visceral peritoneal pigmentation, liver form and coloration of its associated hepatic peritoneum, nuptial excrescences, and hand ornamentation. We comment on the generic and species-level taxonomy of Centrolenidae, proposing the recognition of a new genus and describing a new species from Ecuador. We treat Hyla ocellifera Boulenger as a synonym of Centrolene prosoblepon (Boettger), Hyalinobatrachium cardiacalyptum McCranie & Wilson as a synonym of Hyalinobatrachium chirripoi (Taylor), and Hyalinobatrachium crybetes McCranie and Wilson as a synonym of Hyalinobatrachium colymbiphyllum (Taylor). We also present an annotated list of the species of glassfrogs from the Republic of Ecuador with some distributional remarks.

There is more to mental illness than negative affect: comprehensive temperament profiles in depression and generalized anxiety.

PubMed

Trofimova, Irina; Sulis, William

2018-05-10

Temperament and mental illness are thought to represent varying degrees along the same continuum of neurotransmitter imbalances. A taxonomy of temperament could provide the basis for a new taxonomy of mental illness. Most popular models of temperament, being based heavily on emotionality traits, show very poor ability to discriminate between mental disorders. The main goal of this study was to examine whether a temperament model based on modern neurophysiology and possessing an extensive set of non-emotionality traits provides better discrimination between Major Depression (MD), Generalized Anxiety (GAD) and Comorbid MD and GAD, in comparison to emotionality-based temperament models. Using the Structure of Temperament Questionnaire, the temperament profiles of 687 individuals (396 clients of private psychiatric and psychological practice, and 291 control subjects) were compared across four adult age groups (18-24, 25-45, 46-65, 66-84). MD and GAD appear to be accurately distinguished by the traits of Motor Endurance and Motor Tempo (much lower values in depression), and Neuroticism (much higher value in anxiety). Comorbids can be distinguished based on a significant decrease in the traits of Plasticity, Intellectual Endurance, Sensitivity to Probabilities, and increased Impulsivity. These effects seemed independent of age and gender. The results suggest the benefits of including non-emotionality-related traits and the usefulness of a functional approach to both taxonomy of temperament and classification of mental disorders.

Identification and classification of silks using infrared spectroscopy

PubMed Central

Boulet-Audet, Maxime; Vollrath, Fritz; Holland, Chris

2015-01-01

ABSTRACT Lepidopteran silks number in the thousands and display a vast diversity of structures, properties and industrial potential. To map this remarkable biochemical diversity, we present an identification and screening method based on the infrared spectra of native silk feedstock and cocoons. Multivariate analysis of over 1214 infrared spectra obtained from 35 species allowed us to group silks into distinct hierarchies and a classification that agrees well with current phylogenetic data and taxonomies. This approach also provides information on the relative content of sericin, calcium oxalate, phenolic compounds, poly-alanine and poly(alanine-glycine) β-sheets. It emerged that the domesticated mulberry silkmoth Bombyx mori represents an outlier compared with other silkmoth taxa in terms of spectral properties. Interestingly, Epiphora bauhiniae was found to contain the highest amount of β-sheets reported to date for any wild silkmoth. We conclude that our approach provides a new route to determine cocoon chemical composition and in turn a novel, biological as well as material, classification of silks. PMID:26347557

A Review on Human Activity Recognition Using Vision-Based Method.

PubMed

Zhang, Shugang; Wei, Zhiqiang; Nie, Jie; Huang, Lei; Wang, Shuang; Li, Zhen

2017-01-01

Human activity recognition (HAR) aims to recognize activities from a series of observations on the actions of subjects and the environmental conditions. The vision-based HAR research is the basis of many applications including video surveillance, health care, and human-computer interaction (HCI). This review highlights the advances of state-of-the-art activity recognition approaches, especially for the activity representation and classification methods. For the representation methods, we sort out a chronological research trajectory from global representations to local representations, and recent depth-based representations. For the classification methods, we conform to the categorization of template-based methods, discriminative models, and generative models and review several prevalent methods. Next, representative and available datasets are introduced. Aiming to provide an overview of those methods and a convenient way of comparing them, we classify existing literatures with a detailed taxonomy including representation and classification methods, as well as the datasets they used. Finally, we investigate the directions for future research.

A Review on Human Activity Recognition Using Vision-Based Method

PubMed Central

Nie, Jie

2017-01-01

Human activity recognition (HAR) aims to recognize activities from a series of observations on the actions of subjects and the environmental conditions. The vision-based HAR research is the basis of many applications including video surveillance, health care, and human-computer interaction (HCI). This review highlights the advances of state-of-the-art activity recognition approaches, especially for the activity representation and classification methods. For the representation methods, we sort out a chronological research trajectory from global representations to local representations, and recent depth-based representations. For the classification methods, we conform to the categorization of template-based methods, discriminative models, and generative models and review several prevalent methods. Next, representative and available datasets are introduced. Aiming to provide an overview of those methods and a convenient way of comparing them, we classify existing literatures with a detailed taxonomy including representation and classification methods, as well as the datasets they used. Finally, we investigate the directions for future research. PMID:29065585

Phylogenetic classification and the universal tree.

PubMed

Doolittle, W F

1999-06-25

From comparative analyses of the nucleotide sequences of genes encoding ribosomal RNAs and several proteins, molecular phylogeneticists have constructed a "universal tree of life," taking it as the basis for a "natural" hierarchical classification of all living things. Although confidence in some of the tree's early branches has recently been shaken, new approaches could still resolve many methodological uncertainties. More challenging is evidence that most archaeal and bacterial genomes (and the inferred ancestral eukaryotic nuclear genome) contain genes from multiple sources. If "chimerism" or "lateral gene transfer" cannot be dismissed as trivial in extent or limited to special categories of genes, then no hierarchical universal classification can be taken as natural. Molecular phylogeneticists will have failed to find the "true tree," not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree. However, taxonomies based on molecular sequences will remain indispensable, and understanding of the evolutionary process will ultimately be enriched, not impoverished.

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.

Enabling knowledge discovery: taxonomy development for NASA

NASA Technical Reports Server (NTRS)

Dutra, J.; Busch, J.

2003-01-01

This white paper provides the background for why it is important to take the next steps with the NASA taxonomy including test and validation, XML schema development, integration with the FirstGov federal search engine, the OneNASA portal and its supporting web content management system.

Resolving prokaryotic taxonomy without rRNA: longer oligonucleotide word lengths improve genome and metagenome taxonomic classification.

PubMed

Alsop, Eric B; Raymond, Jason

2013-01-01

Oligonucleotide signatures, especially tetranucleotide signatures, have been used as method for homology binning by exploiting an organism's inherent biases towards the use of specific oligonucleotide words. Tetranucleotide signatures have been especially useful in environmental metagenomics samples as many of these samples contain organisms from poorly classified phyla which cannot be easily identified using traditional homology methods, including NCBI BLAST. This study examines oligonucleotide signatures across 1,424 completed genomes from across the tree of life, substantially expanding upon previous work. A comprehensive analysis of mononucleotide through nonanucleotide word lengths suggests that longer word lengths substantially improve the classification of DNA fragments across a range of sizes of relevance to high throughput sequencing. We find that, at present, heptanucleotide signatures represent an optimal balance between prediction accuracy and computational time for resolving taxonomy using both genomic and metagenomic fragments. We directly compare the ability of tetranucleotide and heptanucleotide world lengths (tetranucleotide signatures are the current standard for oligonucleotide word usage analyses) for taxonomic binning of metagenome reads. We present evidence that heptanucleotide word lengths consistently provide more taxonomic resolving power, particularly in distinguishing between closely related organisms that are often present in metagenomic samples. This implies that longer oligonucleotide word lengths should replace tetranucleotide signatures for most analyses. Finally, we show that the application of longer word lengths to metagenomic datasets leads to more accurate taxonomic binning of DNA scaffolds and have the potential to substantially improve taxonomic assignment and assembly of metagenomic data.

OpenBiodiv-O: ontology of the OpenBiodiv knowledge management system.

PubMed

Senderov, Viktor; Simov, Kiril; Franz, Nico; Stoev, Pavel; Catapano, Terry; Agosti, Donat; Sautter, Guido; Morris, Robert A; Penev, Lyubomir

2018-01-18

The biodiversity domain, and in particular biological taxonomy, is moving in the direction of semantization of its research outputs. The present work introduces OpenBiodiv-O, the ontology that serves as the basis of the OpenBiodiv Knowledge Management System. Our intent is to provide an ontology that fills the gaps between ontologies for biodiversity resources, such as DarwinCore-based ontologies, and semantic publishing ontologies, such as the SPAR Ontologies. We bridge this gap by providing an ontology focusing on biological taxonomy. OpenBiodiv-O introduces classes, properties, and axioms in the domains of scholarly biodiversity publishing and biological taxonomy and aligns them with several important domain ontologies (FaBiO, DoCO, DwC, Darwin-SW, NOMEN, ENVO). By doing so, it bridges the ontological gap across scholarly biodiversity publishing and biological taxonomy and allows for the creation of a Linked Open Dataset (LOD) of biodiversity information (a biodiversity knowledge graph) and enables the creation of the OpenBiodiv Knowledge Management System. A key feature of the ontology is that it is an ontology of the scientific process of biological taxonomy and not of any particular state of knowledge. This feature allows it to express a multiplicity of scientific opinions. The resulting OpenBiodiv knowledge system may gain a high level of trust in the scientific community as it does not force a scientific opinion on its users (e.g. practicing taxonomists, library researchers, etc.), but rather provides the tools for experts to encode different views as science progresses. OpenBiodiv-O provides a conceptual model of the structure of a biodiversity publication and the development of related taxonomic concepts. It also serves as the basis for the OpenBiodiv Knowledge Management System.

Application of taxonomy theory, Volume 1: Computing a Hopf bifurcation-related segment of the feasibility boundary. Final report

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

Zaborszky, J.; Venkatasubramanian, V.

1995-10-01

Taxonomy Theory is the first precise comprehensive theory for large power system dynamics modeled in any detail. The motivation for this project is to show that it can be used, practically, for analyzing a disturbance that actually occurred on a large system, which affected a sizable portion of the Midwest with supercritical Hopf type oscillations. This event is well documented and studied. The report first summarizes Taxonomy Theory with an engineering flavor. Then various computational approaches are sighted and analyzed for desirability to use with Taxonomy Theory. Then working equations are developed for computing a segment of the feasibility boundarymore » that bounds the region of (operating) parameters throughout which the operating point can be moved without losing stability. Then experimental software incorporating large EPRI software packages PSAPAC is developed. After a summary of the events during the subject disturbance, numerous large scale computations, up to 7600 buses, are reported. These results are reduced into graphical and tabular forms, which then are analyzed and discussed. The report is divided into two volumes. This volume illustrates the use of the Taxonomy Theory for computing the feasibility boundary and presents evidence that the event indeed led to a Hopf type oscillation on the system. Furthermore it proves that the Feasibility Theory can indeed be used for practical computation work with very large systems. Volume 2, a separate volume, will show that the disturbance has led to a supercritical (that is stable oscillation) Hopf bifurcation.« less

Situation Awareness and Levels of Automation

NASA Technical Reports Server (NTRS)

Kaber, David B.

1999-01-01

During the first year of this project, a taxonomy of theoretical levels of automation (LOAs) was applied to the advanced commercial aircraft by categorizing actual modes of McDonald Douglas MD-11 autoflight system operation in terms of the taxonomy. As well, high LOAs included in the taxonomy (e.g., supervisory control) were modeled in the context of MD-11 autoflight systems through development of a virtual flight simulator. The flight simulator was an integration of a re-configurable simulator developed by the Georgia Institute Technology and new software prototypes of autoflight system modules found in the MD-11 cockpit. In addition to this work, a version of the Situation Awareness Global Assessment Technique (SAGAT) was developed for application to commercial piloting tasks. A software package was developed to deliver the SAGAT and was integrated with the virtual flight simulator.

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.

The Evaluation of the Cognitive Learning Process of the Renewed Bloom Taxonomy Using a Web Based Expert System

ERIC Educational Resources Information Center

Goksu, Idris

2016-01-01

The aim of this study is to develop the Web Based Expert System (WBES) which provides analyses and reports based on the cognitive processes of Renewed Bloom Taxonomy (RBT), and to put forward the impact of the supportive education provided in line with these reports, on the academic achievement and mastery learning state of the students. The study…

[Classification of organisms and structuralism in biology].

PubMed

Vasil'eva, L I

2001-01-01

Structuralism in biology is the oldest trend oriented to the search for natural "laws of forms" comparable with laws of growth of crystal, was revived at the end of 20th century on the basis of structuralist thought in socio-humanitarian sciences. The development of principal ideas of the linguistic structuralism in some aspects is similar to that of biological systematics, especially concerning the relationships between "system" and "evolution". However, apart from this general similarity, biological structuralism is strongly focused on familiar problems of the origin of diversity in nature. In their striving for the renovation of existing views, biological structuralists oppose the neo-darwinism emphasizing the existence of "law of forms", that are independent on heredity and genetic "determinism". The trend to develop so-called "rational taxonomy" is also characteristic of biological structuralism but this attempt failed being connected neither with Darwin's historicism nor with Plato's typology.

Understanding the local public health workforce: labels versus substance.

PubMed

Merrill, Jacqueline A; Keeling, Jonathan W

2014-11-01

The workforce is a key component of the nation's public health (PH) infrastructure, but little is known about the skills of local health department (LHD) workers to guide policy and planning. To profile a sample of LHD workers using classification schemes for PH work (the substance of what is done) and PH job titles (the labeling of what is done) to determine if work content is consistent with job classifications. A secondary analysis was conducted on data collected from 2,734 employees from 19 LHDs using a taxonomy of 151 essential tasks performed, knowledge possessed, and resources available. Each employee was classified by job title using a schema developed by PH experts. The inter-rater agreement was calculated within job classes and congruence on tasks, knowledge, and resources for five exemplar classes was examined. The average response rate was 89%. Overall, workers exhibited moderate agreement on tasks and poor agreement on knowledge and resources. Job classes with higher agreement included agency directors and community workers; those with lower agreement were mid-level managers such as program directors. Findings suggest that local PH workers within a job class perform similar tasks but vary in training and access to resources. Job classes that are specific and focused have higher agreement whereas job classes that perform in many roles show less agreement. The PH worker classification may not match employees' skill sets or how LHDs allocate resources, which may be a contributor to unexplained fluctuation in public health system performance. Copyright © 2014. Published by Elsevier Inc.

Electromagnetic pulse (EMP) coupling codes for use with the vulnerability/lethality (VIL) taxonomy. Final report, June-October 1984

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

Mar, M.H.

1995-07-01

Based on the vulnerability Lethality (V/L) taxonomy developed by the Ballistic Vulnerability Lethality Division (BVLD) of the Survivability Lethality Analysis Directorate (SLAD), a nuclear electromagnetic pulse (EMP) coupling V/L analysis taxonomy has been developed. A nuclear EMP threat to a military system can be divided into two levels: (1) coupling to a system level through a cable, antenna, or aperture; and (2) the component level. This report will focus on the initial condition, which includes threat definition and target description, as well as the mapping process from the initial condition to damaged components state. EMP coupling analysis at a systemmore » level is used to accomplish this. This report introduces the nature of EMP threat, interaction between the threat and target, and how the output of EMP coupling analysis at a system level becomes the input to the component level analysis. Many different tools (EMP coupling codes) will be discussed for the mapping process, which correponds to the physics of phenomenology. This EMP coupling V/L taxonomy and the models identified in this report will provide the tools necessary to conduct basic V/L analysis of EMP coupling.« less

Genetics-Based Classification of Filoviruses Calls for Expanded Sampling of Genomic Sequences

PubMed Central

Lauber, Chris; Gorbalenya, Alexander E.

2012-01-01

We have recently developed a computational approach for hierarchical, genome-based classification of viruses of a family (DEmARC). In DEmARC, virus clusters are delimited objectively by devising a universal family-wide threshold on intra-cluster genetic divergence of viruses that is specific for each level of the classification. Here, we apply DEmARC to a set of 56 filoviruses with complete genome sequences and compare the resulting classification to the ICTV taxonomy of the family Filoviridae. We find in total six candidate taxon levels two of which correspond to the species and genus ranks of the family. At these two levels, the six filovirus species and two genera officially recognized by ICTV, as well as a seventh tentative species for Lloviu virus and prototyping a third genus, are reproduced. DEmARC lends the highest possible support for these two as well as the four other levels, implying that the actual number of valid taxon levels remains uncertain and the choice of levels for filovirus species and genera is arbitrary. Based on our experience with other virus families, we conclude that the current sampling of filovirus genomic sequences needs to be considerably expanded in order to resolve these uncertainties in the framework of genetics-based classification. PMID:23170166

Genetics-based classification of filoviruses calls for expanded sampling of genomic sequences.

PubMed

Lauber, Chris; Gorbalenya, Alexander E

2012-09-01

We have recently developed a computational approach for hierarchical, genome-based classification of viruses of a family (DEmARC). In DEmARC, virus clusters are delimited objectively by devising a universal family-wide threshold on intra-cluster genetic divergence of viruses that is specific for each level of the classification. Here, we apply DEmARC to a set of 56 filoviruses with complete genome sequences and compare the resulting classification to the ICTV taxonomy of the family Filoviridae. We find in total six candidate taxon levels two of which correspond to the species and genus ranks of the family. At these two levels, the six filovirus species and two genera officially recognized by ICTV, as well as a seventh tentative species for Lloviu virus and prototyping a third genus, are reproduced. DEmARC lends the highest possible support for these two as well as the four other levels, implying that the actual number of valid taxon levels remains uncertain and the choice of levels for filovirus species and genera is arbitrary. Based on our experience with other virus families, we conclude that the current sampling of filovirus genomic sequences needs to be considerably expanded in order to resolve these uncertainties in the framework of genetics-based classification.

A Taxonomy of Technical Assistance Skills.

ERIC Educational Resources Information Center

Ogden, Evelyn; Musumeci, Marilyn

To operationalize the Technical Assistance Brokerage System, the first major task called for the development of a taxonomy of training and technical assistance services specifying requisite skills and skill clusters by the dimensions of client type, stages of dissemination, and levels of experience. From a literature search approximately 400…

A subgeneric classification of Selaginella (Selaginellaceae).

PubMed

Weststrand, Stina; Korall, Petra

2016-12-01

The lycophyte family Selaginellaceae includes approximately 750 herbaceous species worldwide, with the main species richness in the tropics and subtropics. We recently presented a phylogenetic analysis of Selaginellaceae based on DNA sequence data and, with the phylogeny as a framework, the study discussed the character evolution of the group focusing on gross morphology. Here we translate these findings into a new classification. To present a robust and useful classification, we identified well-supported monophyletic groups from our previous phylogenetic analysis of 223 species, which together represent the diversity of the family with respect to morphology, taxonomy, and geographical distribution. Care was taken to choose groups with supporting morphology. In this classification, we recognize a single genus Selaginella and seven subgenera: Selaginella, Rupestrae, Lepidophyllae, Gymnogynum, Exaltatae, Ericetorum, and Stachygynandrum. The subgenera are all well supported based on analysis of DNA sequence data and morphology. A key to the subgenera is presented. Our new classification is based on a well-founded hypothesis of the evolutionary relationships of Selaginella, and each subgenus can be identified by a suite of morphological features, most of them possible to study in the field. Our intention is that the classification will be useful not only to experts in the field, but also to a broader audience. © 2016 Weststrand and Korall. Published by the Botanical Society of America. This work is licensed under a Creative Commons Attribution License (CC-BY 4.0).

Problems of classification in the family Paramyxoviridae.

PubMed

Rima, Bert; Collins, Peter; Easton, Andrew; Fouchier, Ron; Kurath, Gael; Lamb, Robert A; Lee, Benhur; Maisner, Andrea; Rota, Paul; Wang, Lin-Fa

2018-05-01

A number of unassigned viruses in the family Paramyxoviridae need to be classified either as a new genus or placed into one of the seven genera currently recognized in this family. Furthermore, numerous new paramyxoviruses continue to be discovered. However, attempts at classification have highlighted the difficulties that arise by applying historic criteria or criteria based on sequence alone to the classification of the viruses in this family. While the recent taxonomic change that elevated the previous subfamily Pneumovirinae into a separate family Pneumoviridae is readily justified on the basis of RNA dependent -RNA polymerase (RdRp or L protein) sequence motifs, using RdRp sequence comparisons for assignment to lower level taxa raises problems that would require an overhaul of the current criteria for assignment into genera in the family Paramyxoviridae. Arbitrary cut off points to delineate genera and species would have to be set if classification was based on the amino acid sequence of the RdRp alone or on pairwise analysis of sequence complementarity (PASC) of all open reading frames (ORFs). While these cut-offs cannot be made consistent with the current classification in this family, resorting to genus-level demarcation criteria with additional input from the biological context may afford a way forward. Such criteria would reflect the increasingly dynamic nature of virus taxonomy even if it would require a complete revision of the current classification.

An automatic taxonomy of galaxy morphology using unsupervised machine learning

NASA Astrophysics Data System (ADS)

Hocking, Alex; Geach, James E.; Sun, Yi; Davey, Neil

2018-01-01

We present an unsupervised machine learning technique that automatically segments and labels galaxies in astronomical imaging surveys using only pixel data. Distinct from previous unsupervised machine learning approaches used in astronomy we use no pre-selection or pre-filtering of target galaxy type to identify galaxies that are similar. We demonstrate the technique on the Hubble Space Telescope (HST) Frontier Fields. By training the algorithm using galaxies from one field (Abell 2744) and applying the result to another (MACS 0416.1-2403), we show how the algorithm can cleanly separate early and late type galaxies without any form of pre-directed training for what an 'early' or 'late' type galaxy is. We then apply the technique to the HST Cosmic Assembly Near-infrared Deep Extragalactic Legacy Survey (CANDELS) fields, creating a catalogue of approximately 60 000 classifications. We show how the automatic classification groups galaxies of similar morphological (and photometric) type and make the classifications public via a catalogue, a visual catalogue and galaxy similarity search. We compare the CANDELS machine-based classifications to human-classifications from the Galaxy Zoo: CANDELS project. Although there is not a direct mapping between Galaxy Zoo and our hierarchical labelling, we demonstrate a good level of concordance between human and machine classifications. Finally, we show how the technique can be used to identify rarer objects and present lensed galaxy candidates from the CANDELS imaging.

The effects of explicit visual cues in reading biological diagrams

NASA Astrophysics Data System (ADS)

Ge, Yun-Ping; Unsworth, Len; Wang, Kuo-Hua

2017-03-01

Drawing on cognitive theories, this study intends to investigate the effects of explicit visual cues which have been proposed as a critical factor in facilitating understanding of biological images. Three diagrams from Taiwanese textbooks with implicit visual cues, involving the concepts of biological classification systems, fish taxonomy, and energy pyramid, were selected as the reading materials for the control group and reformatted in tree structure or with additional arrows as the diagrams for the treatment group. A quasi-experiment with an online reading test was conducted to examine the effect of the different image conditions on reading comprehension of the two groups. In total, 192 Taiwanese participants from year 7 were assigned randomly into either control group or treatment group according to the pre-test of relevant prior knowledge. The results indicated that not all explicit visual cues were significantly efficient. Only the explicit tree-structured diagrams cued significantly the key concepts of qualitative class-inclusion, parallel relations, and fish taxonomy. Meanwhile the effect of indexical arrows was not significant. The inconsistent effect of tree structure and arrows might be related to the extent of image reformation in which the tree-structured diagrams had undergone radical change of knowledge representation; meanwhile, the arrows had not changed the diagram structure of energy pyramid. The factor of prior knowledge was essential in considering the influence of image design as the effect of diagrams was very different for low and high prior knowledge students. Implications are drawn for the importance of visual design in textbooks.

Doha agreement meeting on terminology and definitions in groin pain in athletes.

PubMed

Weir, Adam; Brukner, Peter; Delahunt, Eamonn; Ekstrand, Jan; Griffin, Damian; Khan, Karim M; Lovell, Greg; Meyers, William C; Muschaweck, Ulrike; Orchard, John; Paajanen, Hannu; Philippon, Marc; Reboul, Gilles; Robinson, Philip; Schache, Anthony G; Schilders, Ernest; Serner, Andreas; Silvers, Holly; Thorborg, Kristian; Tyler, Timothy; Verrall, Geoffrey; de Vos, Robert-Jan; Vuckovic, Zarko; Hölmich, Per

2015-06-01

Heterogeneous taxonomy of groin injuries in athletes adds confusion to this complicated area. The 'Doha agreement meeting on terminology and definitions in groin pain in athletes' was convened to attempt to resolve this problem. Our aim was to agree on a standard terminology, along with accompanying definitions. A one-day agreement meeting was held on 4 November 2014. Twenty-four international experts from 14 different countries participated. Systematic reviews were performed to give an up-to-date synthesis of the current evidence on major topics concerning groin pain in athletes. All members participated in a Delphi questionnaire prior to the meeting. Unanimous agreement was reached on the following terminology. The classification system has three major subheadings of groin pain in athletes: 1. Defined clinical entities for groin pain: Adductor-related, iliopsoas-related, inguinal-related and pubic-related groin pain. 2. Hip-related groin pain. 3. Other causes of groin pain in athletes. The definitions are included in this paper. The Doha agreement meeting on terminology and definitions in groin pain in athletes reached a consensus on a clinically based taxonomy using three major categories. These definitions and terminology are based on history and physical examination to categorise athletes, making it simple and suitable for both clinical practice and research. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Poster - 27: Incident Learning Practices in Ontario

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

Angers, Crystal; Medlam, Gaylene; Liszewski, Brian

Purpose: The Radiation Incident and Safety Committee (RISC), established and supported by Cancer Care Ontario (CCO), is responsible for advising the Provincial Head of the Radiation Treatment program on matters relating to provincial reporting of radiation incidents with the goal of improved risk mitigation. Methods: The committee is made up of Radiation Incident Leads (RILs) with representation from each of the 14 radiation medicine programs in the province. RISC routinely meets to review recent critical incidents and to discuss provincial reporting processes and future directions of the committee. Regular face to face meetings have provided an excellent venue for sharingmore » incident learning practices. A summary of the incident learning practices across Ontario has been compiled. Results: Almost all programs in Ontario employ an incident learning committee to review incidents and identify corrective actions or process improvements. Tools used for incident reporting include: paper based reporting, a number of different commercial products and software solutions developed in-house. A wide range of classification schema (data taxonomies) are employed, although most have been influenced by national guidance documents. The majority of clinics perform root cause analyses but utilized methodologies vary significantly. Conclusions: Most programs in Ontario employ a committee approach to incident learning. However, the reporting tools and taxonomies in use vary greatly which represents a significant challenge to provincial reporting. RISC is preparing to adopt the National System for Incident Reporting – Radiation Therapy (NSIR-RT) which will standardize incident reporting and facilitate data analyses aimed at identifying targeted improvement initiatives.« less

Equating an expert system to a classifier in order to evaluate the expert system

NASA Technical Reports Server (NTRS)

Odell, Patrick L.

1989-01-01

A strategy to evaluate an expert system is formulated. The strategy proposed is based on finding an equivalent classifier to an expert system and evaluate that classifier with respect to an optimal classifier, a Bayes classifier. Here it is shown that for the rules considered an equivalent classifier exists. Also, a brief consideration of meta and meta-meta rules is included. Also, a taxonomy of expert systems is presented and an assertion made that an equivalent classifier exists for each type of expert system in the taxonomy with associated sets of underlying assumptions.

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

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.

[Nursing care in fluorescein angiography].

PubMed

Santos-Blanco, Feliciano

2008-01-01

Fluoresceinic angiography of the ocular fundus is a diagnostic technique to study retinal and choroidal circulation. This technique consists of parenteral administration of 500 mg of sodium fluorescein 10% and photographing the fluorescence in the eye vessels. Although this substance is fairly safe, it may also produce mild, moderate or severe local and/or general adverse reactions. The nursing process is routinely used in hospital units but not always in outpatient clinics, even through the use of invasive procedures with intravenous medication administration is common. Therefore, nurses, as those reponsible for intravenous administration, should use the nursing process to guarantee the quality of care required by the patient. To do this, we describe an individualized care plan based on evaluation by Marjorie Gordon's functional health patterns, NANDA's nursing diagnoses Taxonomy II, Nursing Outcomes Classification (NOC), Nursing Interventions Classifications (NIC) and potential complications of the procedure.

Classification of Pelteobagrus fish in Poyang Lake based on mitochondrial COI gene sequence.

PubMed

Zhong, Bin; Chen, Ting-Ting; Gong, Rui-Yue; Zhao, Zhe-Xia; Wang, Binhua; Fang, Chunlin; Mao, Hui-Ling

2016-11-01

We use DNA molecular marker technology to correct the deficiency of traditional morphological taxonomy. Totality 770 Pelteobagrus fish from Poyang Lake were collected. After preliminary morphological classification, random selected eight samples in each species for DNA extraction. Mitochondrial COI gene sequence was cloned with universal primers and sequenced. The results showed that there are four species of Pelteobagrus living in Poyang Lake. The average of intraspecific genetic distance value was 0.003, while the average interspecific genetic distance was 0.128. The interspecific genetic distance is far more than intraspecific genetic distance. Besides, phylogenetic tree analysis revealed that molecular systematics was in accord with morphological classification. It indicated that COI gene is an effective DNA molecular marker in Pelteobagrus classification. Surprisingly, the intraspecific difference of some individuals (P. e6, P. n6, P. e5, and P. v4) from their original named exceeded species threshold (2%), which should be renewedly classified into Pelteobagrus fulvidraco. However, another individual P. v3 was very different, because its genetic distance was over 8.4% difference from original named Pelteobagrus vachelli. Its taxonomic status remained to be further studied.

Taxonomy, genetic organization, and life cycle of Pneumocystis carinii.

PubMed

Cushion, M T

1998-12-01

Pneumocystis carinii was initially misidentified as a protozoan parasite. Recent molecular and biochemical analyses provide unequivocal evidence for placement of P. carinii with the fungi, and that P. carinii is most likely an ascomycete. Genetic investigations further show that P. carinii derived from different mammalian hosts (human, rat, mouse, and ferret) exhibit considerable chromosomal and gene sequence divergence indicating that they are likely of different species. The life cycle of P. carinii has not been definitively established, but available evidence is reviewed in light of classification of this organism as a fungus.

Guide to the Correct Use of Filoviral Nomenclature.

PubMed

Kuhn, Jens H

2017-01-01

The International Committee on Taxonomy of Viruses (ICTV) currently recognizes three genera and seven species as part of the mononegaviral family Filoviridae. Eight distinct filoviruses (Bundibugyo virus, Ebola virus, Lloviu virus, Marburg virus, Ravn virus, Reston virus, Sudan virus, and Taï Forest virus) have been assigned to these seven species. This chapter briefly summarizes the status quo of filovirus classification and focuses on the importance of differentiating between filoviral species and filoviruses and the correct use of taxonomic and vernacular filovirus names and abbreviations in written and oral discourse.

Resilience in Utility Technologies

NASA Astrophysics Data System (ADS)

Seaton, Roger

The following sections are included: * Scope of paper * Preamble * Background to the case-study projects * Source projects * Resilience * Case study 1: Electricity generation * Context * Model * Case study 2: Water recycling * Context * Model * Case study 3: Ecotechnology and water treatment * Context * The problem of classification: Finding a classificatory solution * Application of the new taxonomy to water treatment * Concluding comments and questions * Conclusions * Questions and issues * Purposive or Purposeful? * Resilience: Flexibility and adaptivity? * Resilience: With respect of what? * Risk, uncertainty, surprise, emergence - What sort of shock, and who says so? * Co-evolutionary friction * References

Folk classification of the crabs and swimming crabs (Crustacea – Brachyura) of the Mamanguape river estuary, Northeastern – Brazil

PubMed Central

Ferreira, Emmanoela N; da S Mourão, José; Rocha, Pollyana D; Nascimento, Douglas M; da S Q Bezerra, Dandara Monalisa Mariz

2009-01-01

Background Folk taxonomy is a sub-area of ethnobiology that study the way of how traditional communities classify, identify and name their natural resources. The work present was undertaken in two traditional communities (Barra de Mamanguape and Tramataia). The objective of this study was investigate the ethnobiological classification of the local crabs and swimming crabs used by the crustaceous gatherers of the Mamanguape River Estuary (MRE), Paraíba State, Brazil. Methods The methodology used here involved a combination of qualitative methods (open interviews, semi-structured interviews, direct observations, guided tours, surveys, and interviews in synchronic and diachronic situations that crossed-checked and repeated identifications) and quantitative methods (Venn diagram). A total of 32 men and women were interviewed in the two communities. Specimens of the local crustaceans were collected and identified by the harvesters themselves, subsequently fixed in formalin, conserved in 70% ethyl alcohol, identified using appropriate specialized literature, and then deposited in the laboratory of the Zoology Department of the University State of Paraiba. Results The crustaceous gatherers we studied were observed to group crustaceans according to their similarities and differences, producing a hierarchical classification system containing four levels of decreasing taxonomic order: unique beginner, life-form, generic, and specific. A sequential and/or semantic system classification system that is used to classify the ontogeny of the female swimming crab was also identified. Of the nine folk generics identified, 44.5% were monotypic. 55.5% were polytypic and were subdivided into 15 folk specifics. An identification key was elaborated with the data obtained about the folk polytypics generics. Conclusion The detailed knowledge concerning the crabs and swimming crabs revealed by the MRE crustaceous gatherers demonstrates that these people detain a vast knowledge concerning these marine resources. This local knowledge provides a rich but little-known source of information that will aid future ecological and/or zoological studies in the region that will be indispensable for producing management plans to help guarantee the sustainability of these local natural resources. PMID:19671153

LacSubPred: predicting subtypes of Laccases, an important lignin metabolism-related enzyme class, using in silico approaches

PubMed Central

2014-01-01

Background Laccases (E.C. 1.10.3.2) are multi-copper oxidases that have gained importance in many industries such as biofuels, pulp production, textile dye bleaching, bioremediation, and food production. Their usefulness stems from the ability to act on a diverse range of phenolic compounds such as o-/p-quinols, aminophenols, polyphenols, polyamines, aryl diamines, and aromatic thiols. Despite acting on a wide range of compounds as a family, individual Laccases often exhibit distinctive and varied substrate ranges. This is likely due to Laccases involvement in many metabolic roles across diverse taxa. Classification systems for multi-copper oxidases have been developed using multiple sequence alignments, however, these systems seem to largely follow species taxonomy rather than substrate ranges, enzyme properties, or specific function. It has been suggested that the roles and substrates of various Laccases are related to their optimal pH. This is consistent with the observation that fungal Laccases usually prefer acidic conditions, whereas plant and bacterial Laccases prefer basic conditions. Based on these observations, we hypothesize that a descriptor-based unsupervised learning system could generate homology independent classification system for better describing the functional properties of Laccases. Results In this study, we first utilized unsupervised learning approach to develop a novel homology independent Laccase classification system. From the descriptors considered, physicochemical properties showed the best performance. Physicochemical properties divided the Laccases into twelve subtypes. Analysis of the clusters using a t-test revealed that the majority of the physicochemical descriptors had statistically significant differences between the classes. Feature selection identified the most important features as negatively charges residues, the peptide isoelectric point, and acidic or amidic residues. Secondly, to allow for classification of new Laccases, a supervised learning system was developed from the clusters. The models showed high performance with an overall accuracy of 99.03%, error of 0.49%, MCC of 0.9367, precision of 94.20%, sensitivity of 94.20%, and specificity of 99.47% in a 5-fold cross-validation test. In an independent test, our models still provide a high accuracy of 97.98%, error rate of 1.02%, MCC of 0.8678, precision of 87.88%, sensitivity of 87.88% and specificity of 98.90%. Conclusion This study provides a useful classification system for better understanding of Laccases from their physicochemical properties perspective. We also developed a publically available web tool for the characterization of Laccase protein sequences (http://lacsubpred.bioinfo.ucr.edu/). Finally, the programs used in the study are made available for researchers interested in applying the system to other enzyme classes (https://github.com/tweirick/SubClPred). PMID:25350584

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.

Development and Validation of the Behavioral Tendencies Questionnaire

PubMed Central

Van Dam, Nicholas T.; Brown, Anna; Mole, Tom B.; Davis, Jake H.; Britton, Willoughby B.; Brewer, Judson A.

2015-01-01

At a fundamental level, taxonomy of behavior and behavioral tendencies can be described in terms of approach, avoid, or equivocate (i.e., neither approach nor avoid). While there are numerous theories of personality, temperament, and character, few seem to take advantage of parsimonious taxonomy. The present study sought to implement this taxonomy by creating a questionnaire based on a categorization of behavioral temperaments/tendencies first identified in Buddhist accounts over fifteen hundred years ago. Items were developed using historical and contemporary texts of the behavioral temperaments, described as “Greedy/Faithful”, “Aversive/Discerning”, and “Deluded/Speculative”. To both maintain this categorical typology and benefit from the advantageous properties of forced-choice response format (e.g., reduction of response biases), binary pairwise preferences for items were modeled using Latent Class Analysis (LCA). One sample (n1 = 394) was used to estimate the item parameters, and the second sample (n2 = 504) was used to classify the participants using the established parameters and cross-validate the classification against multiple other measures. The cross-validated measure exhibited good nomothetic span (construct-consistent relationships with related measures) that seemed to corroborate the ideas present in the original Buddhist source documents. The final 13-block questionnaire created from the best performing items (the Behavioral Tendencies Questionnaire or BTQ) is a psychometrically valid questionnaire that is historically consistent, based in behavioral tendencies, and promises practical and clinical utility particularly in settings that teach and study meditation practices such as Mindfulness Based Stress Reduction (MBSR). PMID:26535904

Reasoning over taxonomic change: exploring alignments for the Perelleschus use case.

PubMed

Franz, Nico M; Chen, Mingmin; Yu, Shizhuo; Kianmajd, Parisa; Bowers, Shawn; Ludäscher, Bertram

2015-01-01

Classifications and phylogenetic inferences of organismal groups change in light of new insights. Over time these changes can result in an imperfect tracking of taxonomic perspectives through the re-/use of Code-compliant or informal names. To mitigate these limitations, we introduce a novel approach for aligning taxonomies through the interaction of human experts and logic reasoners. We explore the performance of this approach with the Perelleschus use case of Franz & Cardona-Duque (2013). The use case includes six taxonomies published from 1936 to 2013, 54 taxonomic concepts (i.e., circumscriptions of names individuated according to their respective source publications), and 75 expert-asserted Region Connection Calculus articulations (e.g., congruence, proper inclusion, overlap, or exclusion). An Open Source reasoning toolkit is used to analyze 13 paired Perelleschus taxonomy alignments under heterogeneous constraints and interpretations. The reasoning workflow optimizes the logical consistency and expressiveness of the input and infers the set of maximally informative relations among the entailed taxonomic concepts. The latter are then used to produce merge visualizations that represent all congruent and non-congruent taxonomic elements among the aligned input trees. In this small use case with 6-53 input concepts per alignment, the information gained through the reasoning process is on average one order of magnitude greater than in the input. The approach offers scalable solutions for tracking provenance among succeeding taxonomic perspectives that may have differential biases in naming conventions, phylogenetic resolution, ingroup and outgroup sampling, or ostensive (member-referencing) versus intensional (property-referencing) concepts and articulations.

Development and Validation of the Behavioral Tendencies Questionnaire.

PubMed

Van Dam, Nicholas T; Brown, Anna; Mole, Tom B; Davis, Jake H; Britton, Willoughby B; Brewer, Judson A

2015-01-01

At a fundamental level, taxonomy of behavior and behavioral tendencies can be described in terms of approach, avoid, or equivocate (i.e., neither approach nor avoid). While there are numerous theories of personality, temperament, and character, few seem to take advantage of parsimonious taxonomy. The present study sought to implement this taxonomy by creating a questionnaire based on a categorization of behavioral temperaments/tendencies first identified in Buddhist accounts over fifteen hundred years ago. Items were developed using historical and contemporary texts of the behavioral temperaments, described as "Greedy/Faithful", "Aversive/Discerning", and "Deluded/Speculative". To both maintain this categorical typology and benefit from the advantageous properties of forced-choice response format (e.g., reduction of response biases), binary pairwise preferences for items were modeled using Latent Class Analysis (LCA). One sample (n1 = 394) was used to estimate the item parameters, and the second sample (n2 = 504) was used to classify the participants using the established parameters and cross-validate the classification against multiple other measures. The cross-validated measure exhibited good nomothetic span (construct-consistent relationships with related measures) that seemed to corroborate the ideas present in the original Buddhist source documents. The final 13-block questionnaire created from the best performing items (the Behavioral Tendencies Questionnaire or BTQ) is a psychometrically valid questionnaire that is historically consistent, based in behavioral tendencies, and promises practical and clinical utility particularly in settings that teach and study meditation practices such as Mindfulness Based Stress Reduction (MBSR).

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

Pain after spinal cord injury: a review of classification, treatment approaches, and treatment assessment.

PubMed

Cardenas, Diana D; Felix, Elizabeth R

2009-12-01

Pain is a prevalent consequence of spinal cord injury (SCI) that can persist for years after the injury and can have a significant impact on physical and emotional function and quality of life. There are a variety of types of pain that may develop after a SCI, including those of primarily nociceptive origin and those of primarily neuropathic origin. Recommendations for diagnostic and treatment strategies have been varied in part because of the lack of a universal classification system and in part because of the biopsychosocial nature of pain. The most recent taxonomy for pain after SCI is described herein. Pain-management strategies, including pharmacological, interventional, and psychological treatments, also are described. For neuropathic pain in SCI, anticonvulsant agents and tricyclic antidepressants often are tried, but these treatments have had limited success in many patients, and alternative interventions (eg, massage therapy, acupuncture, meditation) often are just as successful. Treatment of nociceptive pain after SCI often includes nonsteroidal antiinflammatory agents and acetaminophen, but correction of underlying etiologies and behavior adjustments also should be implemented if possible. An overview of self-report pain questionnaires and scales is also presented to provide the clinician and researcher with a set of tools to evaluate the efficacy of pain interventions.

Comparison of Actual Costs to Integrate Commercial Buildings with the Grid

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

Piette, Mary Ann; Black, Doug; Yin, Rongxin

During the past decade, the technology to automate demand response (DR) in buildings and industrial facilities has advanced significantly. Automation allows rapid, repeatable, reliable operation. This study focuses on costs for DR automation in commercial buildings with some discussion on residential buildings and industrial facilities. DR automation technology relies on numerous components, including communication systems, hardware and software gateways, standards-based messaging protocols, controls and integration platforms, and measurement and telemetry systems. This paper discusses the impact factors that contribute to the costs of automated DR systems, with a focus on OpenADR 1.0 and 2.0 systems. In addition, this report comparesmore » cost data from several DR automation programs and pilot projects, evaluates trends in the cost per unit of DR and kilowatts (kW) available from automated systems, and applies a standard naming convention and classification or taxonomy for system elements. In summary, median costs for the 56 installed automated DR systems studied here are about $200/kW. The deviation around this median is large with costs in some cases being an order of magnitude greater or less than median. Costs to automate fast DR systems for ancillary services are not fully analyzed in this report because additional research is needed to determine the total such costs.« less

Culicoides Latreille (Diptera: Ceratopogonidae) taxonomy: Current challenges and future directions

PubMed Central

Harrup, L.E.; Bellis, G.A.; Balenghien, T.; Garros, C.

2015-01-01

Culicoides Latreille biting midges (Diptera: Ceratopogonidae) cause a significant biting nuisance to humans, livestock and equines, and are the biological vectors of a range of internationally important pathogens of both veterinary and medical importance. Despite their economic significance, the delimitation and identification of species and evolutionary relationships between species within this genus remains at best problematic. To date no phylogenetic study has attempted to validate the subgeneric classification of the genus and the monophyly of many of the subgenera remains doubtful. Many informal species groupings are also known to exist but few are adequately described, further complicating accurate identification. Recent contributions to Culicoides taxonomy at the species level have revealed a high correlation between morphological and molecular analyses although molecular analyses are revealing the existence of cryptic species. This review considers the methods for studying the systematics of Culicoides using both morphological and genetic techniques, with a view to understanding the factors limiting our current understanding of Culicoides biology and hence arbovirus epidemiology. In addition, we examine the global status of Culicoides identification, highlighting areas that are poorly addressed, including the potential implementation of emerging technologies. PMID:25535946

Neuropathic orofacial pain: Facts and fiction.

PubMed

Baad-Hansen, Lene; Benoliel, Rafael

2017-06-01

Definition and taxonomy This review deals with neuropathic pain of traumatic origin affecting the trigeminal nerve, i.e. painful post-traumatic trigeminal neuropathy (PTTN). Symptomatology The clinical characteristics of PTTN vary considerably, partly due to the type and extent of injury. Symptoms involve combinations of spontaneous and evoked pain and of positive and negative somatosensory signs. These patients are at risk of going through unnecessary dental/surgical procedures in the attempt to eradicate the cause of the pain, due to the fact that most dentists only rarely encounter PTTN. Epidemiology Overall, approximately 3% of patients with trigeminal nerve injuries develop PTTN. Patients are most often female above the age of 45 years, and both physical and psychological comorbidities are common. Pathophysiology PTTN shares many pathophysiological mechanisms with other peripheral neuropathic pain conditions. Diagnostic considerations PTTN may be confused with one of the regional neuralgias or other orofacial pain conditions. For intraoral PTTN, early stages are often misdiagnosed as odontogenic pain. Pain management Management of PTTN generally follows recommendations for peripheral neuropathic pain. Expert opinion International consensus on classification and taxonomy is urgently needed in order to advance the field related to this condition.

Contribution of gall microscopic structure to taxonomy of gallicolous aphids on Pistacia.

PubMed

Álvarez, R; Martinez, J-J I; Muñoz-Viveros, A L; Molist, P; Abad-González, J; Nieto Nafría, J M

2016-09-01

Aphids inducing galls on Pistacia plants belong to the tribe Fordini. According to the Heie & Wegierek classification, the genera are grouped into three subtribes. Previous microscopic studies showed that this taxonomy is not consistent with the histological characteristics of the galls. In this paper, galls induced by Aplonerura lentisci, Asiphonella cynodonti, Forda riccobonii, Slavun wertheimae and Smynthurodes betae were analyzed for the first time, as well as nine other galls previously described. Based on histological features three groups of galls can be establish: the first group comprises closed galls, induced by Baizongia pistaciae, Geoica utricularia, Rectinasus buxtoni and Slavun wertheimae; the second group includes two species of Geopemphigus (G. blackmani and G. torsus), and the third one is divided into two subgroups, the first comprises Aplonerura lentisci, Asiphonella cynodonti and Geopemphigus morral, and the second that includes Forda formicaria, F. marginata, F. riccobonii, Paracletus cimiciformis and Smynthurodes betae. An identification key of species based on microscopic features of galls is presented. © 2016 German Botanical Society and The Royal Botanical Society of the Netherlands.

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/

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 classification of components of workplace disability management programs: results from a systematic review.

PubMed

Gensby, U; Labriola, M; Irvin, E; Amick, B C; Lund, T

2014-06-01

This paper presents results from a Campbell systematic review on the nature and effectiveness of workplace disability management programs (WPDM) promoting return to work (RTW), as implemented and practiced by employers. A classification of WPDM program components, based on the review results, is proposed. Twelve databases were searched between 1948 to July 2010 for peer-reviewed studies of WPDM programs provided by employers to re-entering workers with occupational or non-occupational illnesses or injuries. Screening of articles, risk of bias assessment and data extraction were conducted in pairs of reviewers. Studies were clustered around various dimensions of the design and context of programs. 16,932 records were identified by the initial search. 599 papers were assessed for relevance. Thirteen studies met inclusion criteria. Twelve peer reviewed articles (two non-randomized studies, and ten single group experimental before and after studies), including ten different WPDM programs informed the synthesis of results. Narrative descriptions of the included program characteristics provided insight on program scope, components, procedures and human resources involved. However, there were insufficient data on the characteristics of the sample and the effect sizes were uncertain. A taxonomy classifying policies and practices around WPDM programs is proposed. There is insufficient evidence to draw conclusions on the effectiveness of employer provided WPDM programs promoting RTW. It was not possible to determine if specific program components or specific sets of components are driving effectiveness. The proposed taxonomy may guide future WPDM program evaluation and clarify the setup of programs offered to identify gaps in existing company strategies.

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.

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.

2010 College Course Map. Technical Report. NCES 2012-162

ERIC Educational Resources Information Center

Bryan, Michael; Simone, Sean

2012-01-01

The College Course Map (CCM) is a taxonomy system for coding postsecondary education courses in NCES research studies. Originally developed in 1988 in support of the postsecondary transcript study in the National Longitudinal Study of the High School Class of 1972 (NLS-72), the taxonomy was updated in 1993 for the High School and Beyond Study…

Visual classification of very fine-grained sediments: Evaluation through univariate and multivariate statistics

USGS Publications Warehouse

Hohn, M. Ed; Nuhfer, E.B.; Vinopal, R.J.; Klanderman, D.S.

1980-01-01

Classifying very fine-grained rocks through fabric elements provides information about depositional environments, but is subject to the biases of visual taxonomy. To evaluate the statistical significance of an empirical classification of very fine-grained rocks, samples from Devonian shales in four cored wells in West Virginia and Virginia were measured for 15 variables: quartz, illite, pyrite and expandable clays determined by X-ray diffraction; total sulfur, organic content, inorganic carbon, matrix density, bulk density, porosity, silt, as well as density, sonic travel time, resistivity, and ??-ray response measured from well logs. The four lithologic types comprised: (1) sharply banded shale, (2) thinly laminated shale, (3) lenticularly laminated shale, and (4) nonbanded shale. Univariate and multivariate analyses of variance showed that the lithologic classification reflects significant differences for the variables measured, difference that can be detected independently of stratigraphic effects. Little-known statistical methods found useful in this work included: the multivariate analysis of variance with more than one effect, simultaneous plotting of samples and variables on canonical variates, and the use of parametric ANOVA and MANOVA on ranked data. ?? 1980 Plenum Publishing Corporation.

The role of man in flight experiment payload missions. Volume 1: Results

NASA Technical Reports Server (NTRS)

Malone, T. B.

1973-01-01

It is pointed out that a controversy exists concerning the required role of man, and his attendant skills and levels of skills, for Sortie Lab operations. As a result, a study was conducted to generate a taxonomy of candidate crew roles which would: (1) be applicable across all experiments, and (2) be usable for Sortie scientists and engineers in determination of level of skill as well as type of skill. Nine basic roles were identified in the study, and the tasks associated with each were developed from a functional description of a generalized in-flight experiment. The functional analysis comprised the baseline for establishment of crew roles, with roles being defined as combinations of tasks, associated skills, and knowledges. A role classification scheme was developed in which the functions and tasks identified were allocated to each of the nine role types. This classification scheme is presented together with the significant results of the study.

A complete solution classification and unified algorithmic treatment for the one- and two-step asymmetric S-transverse mass event scale statistic

NASA Astrophysics Data System (ADS)

Walker, Joel W.

2014-08-01

The M T2, or "s-transverse mass", statistic was developed to associate a parent mass scale to a missing transverse energy signature, given that escaping particles are generally expected in pairs, while collider experiments are sensitive to just a single transverse momentum vector sum. This document focuses on the generalized extension of that statistic to asymmetric one- and two-step decay chains, with arbitrary child particle masses and upstream missing transverse momentum. It provides a unified theoretical formulation, complete solution classification, taxonomy of critical points, and technical algorithmic prescription for treatment of the event scale. An implementation of the described algorithm is available for download, and is also a deployable component of the author's selection cut software package AEAC uS (Algorithmic Event Arbiter and C ut Selector). appendices address combinatoric event assembly, algorithm validation, and a complete pseudocode.

Population genetics, taxonomy, phylogeny and evolution of Borrelia burgdorferi sensu lato

PubMed Central

Margos, Gabriele; Vollmer, Stephanie A.; Ogden, Nicholas H.; Fish, Durland

2011-01-01

In order to understand the population structure and dynamics of bacterial microorganisms, typing systems that accurately reflect the phylogenetic and evolutionary relationship of the agents are required. Over the past 15 years multilocus sequence typing schemes have replaced single locus approaches, giving novel insights into phylogenetic and evolutionary relationships of many bacterial species and facilitating taxonomy. Since 2004, several schemes using multiple loci have been developed to better understand the taxonomy, phylogeny and evolution of Lyme borreliosis spirochetes and in this paper we have reviewed and summarized the progress that has been made for this important group of vector-borne zoonotic bacteria. PMID:21843658

A Practitioner's Perspective on Taxonomy, Ontology and Findability

NASA Technical Reports Server (NTRS)

Berndt, Sarah

2011-01-01

This slide presentation reviews the presenters perspective on developing a taxonomy for JSC to capitalize on the accomplishments of yesterday, while maintaining the flexibility needed for the evolving information of today. A clear vision and scope for the semantic system is integral to its success. The vision for the JSC Taxonomy is to connect information stovepipes to present a unified view for information and knowledge across the Center, across organizations, and across decades. Semantic search at JSC means seamless integration of disparate information sets into a single interface. Ever increasing use, interest, and organizational participation mark successful integration and provide the framework for future application.

ICTV Virus Taxonomy Profile: Picornaviridae.

PubMed

Zell, R; Delwart, E; Gorbalenya, A E; Hovi, T; King, A M Q; Knowles, N J; Lindberg, A M; Pallansch, M A; Palmenberg, A C; Reuter, G; Simmonds, P; Skern, T; Stanway, G; Yamashita, T; Ictv Report Consortium

2017-10-01

The family Picornaviridae comprises small non-enveloped viruses with RNA genomes of 6.7 to 10.1 kb, and contains >30 genera and >75 species. Most of the known picornaviruses infect mammals and birds, but some have also been detected in reptiles, amphibians and fish. Many picornaviruses are important human and veterinary pathogens and may cause diseases of the central nervous system, heart, liver, skin, gastrointestinal tract or upper respiratory tract. Most picornaviruses are transmitted by the faecal-oral or respiratory routes. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Picornaviridae, which is available at www.ictv.global/report/picornaviridae.

Taxonomy, Ontology and Semantics at Johnson Space Center

NASA Technical Reports Server (NTRS)

Berndt, Sarah Ann

2011-01-01

At NASA Johnson Space Center (JSC), the Chief Knowledge Officer has been developing the JSC Taxonomy to capitalize on the accomplishments of yesterday while maintaining the flexibility needed for the evolving information environment of today. A clear vision and scope for the semantic system is integral to its success. The vision for the JSC Taxonomy is to connect information stovepipes to present a unified view for information and knowledge across the Center, across organizations, and across decades. Semantic search at JSC means seemless integration of disparate information sets into a single interface. Ever increasing use, interest, and organizational participation mark successful integration and provide the framework for future application.

Evaluation of an integrated system for classification, assessment and comparison of services for long-term care in Europe: the eDESDE-LTC study

PubMed Central

2013-01-01

Background The harmonization of European health systems brings with it a need for tools to allow the standardized collection of information about medical care. A common coding system and standards for the description of services are needed to allow local data to be incorporated into evidence-informed policy, and to permit equity and mobility to be assessed. The aim of this project has been to design such a classification and a related tool for the coding of services for Long Term Care (DESDE-LTC), based on the European Service Mapping Schedule (ESMS). Methods The development of DESDE-LTC followed an iterative process using nominal groups in 6 European countries. 54 researchers and stakeholders in health and social services contributed to this process. In order to classify services, we use the minimal organization unit or “Basic Stable Input of Care” (BSIC), coded by its principal function or “Main Type of Care” (MTC). The evaluation of the tool included an analysis of feasibility, consistency, ontology, inter-rater reliability, Boolean Factor Analysis, and a preliminary impact analysis (screening, scoping and appraisal). Results DESDE-LTC includes an alpha-numerical coding system, a glossary and an assessment instrument for mapping and counting LTC. It shows high feasibility, consistency, inter-rater reliability and face, content and construct validity. DESDE-LTC is ontologically consistent. It is regarded by experts as useful and relevant for evidence-informed decision making. Conclusion DESDE-LTC contributes to establishing a common terminology, taxonomy and coding of LTC services in a European context, and a standard procedure for data collection and international comparison. PMID:23768163

What Happened to the Streptococci: Overview of Taxonomic and Nomenclature Changes

PubMed Central

Facklam, Richard

2002-01-01

Since the division of the Streptococcus genus into enterococci, lactococci, and streptococci in 1984, many changes in the nomenclature and taxonomy of the Streptococcus genus have taken place. The application of genetic comparisons has improved the proper classification of the different species. The Lancefield system of serogrouping the streptococci by the expression of beta-hemolysis on blood agar plates is still very useful for the identification of streptococci for patient management. The Lancefield grouping system cannot be used in itself for accurate identification of specific beta-hemolytic species, but it can be a useful part of the identification procedure. Except for identification of the “Streptococcus bovis group” of species and Streptococcus suis, Lancefield grouping is of little value in identification of the non-beta-hemolytic streptococci and related genera. In fact, identification of the non-beta-hemolytic species is problematic for conventional as well as commercially available identification procedures. A combination of conventional tests and specific chromogenic tests suggested by several investigators is presented and discussed. Tables are included that suggest tests and procedures to guide investigators attempting to identify all the species. PMID:12364372

What do primary care practitioners want to know? A content analysis of questions asked at the point of care.

PubMed

Bjerre, Lise M; Paterson, Nicholas R; McGowan, Jessie; Hogg, William; Campbell, Craig M; Viner, Gary; Archibald, Douglas

2013-01-01

Assessing physician needs to develop continuing medical education (CME) activities is an integral part of CME curriculum development. The purpose of the present study was to demonstrate the feasibility of identifying areas of perceived greatest needs for continuing medical education (CME) by using questions collected electronically at the point of care. This study is a secondary analysis of the "Just-in-Time" (JIT) information librarian consultation service database of questions using quantitative content analysis methods. The original JIT project demonstrated the feasibility of a real-time librarian service for answering questions asked by primary care clinicians at the point of care using a Web-based platform or handheld device. Data were collected from 88 primary care practitioners in Ontario, Canada, from October 2005 to April 2006. Questions were answered in less than 15 minutes, enabling clinicians to use the answer during patient encounters. Description of type and frequency of questions asked, including the organ system on which the questions focused, was produced using 2 classification systems, the "taxonomy of generic clinical questions" (TGCQ), and the International Classification for Primary Care version 2 (ICPC-2). Of the original 1889 questions, 1871 (99.0%) were suitable for analysis. A total of 970 (52%) of questions related to therapy; of these, 671 (69.2%) addressed questions about drug therapy, representing 36% of all questions. Questions related to diagnosis (24.8%) and epidemiology (13.5%) were also common. Organ systems questions concerning musculoskeletal, endocrine, skin, cardiac, and digestive systems were asked more than other categories. Questions collected at the point of care provide a valuable and unique source of information on the true learning needs of practicing clinicians. The TGCQ classification allowed us to show that a majority of questions had to do with treatment, particularly drug treatment, whereas the use of the ICPC-2 classification illustrated the great variety of questions asked about the diverse conditions encountered in primary care. It is feasible to use electronically collected questions asked by primary care clinicians in clinical practice to categorize self-identified knowledge and practice needs. This could be used to inform the development of future learning activities. Copyright © 2013 The Alliance for Continuing Education in the Health Professions, the Society for Academic Continuing Medical Education, and the Council on CME, Association for Hospital Medical Education.

Discrimination of different sub-basins on Tajo River based on water influence factor

NASA Astrophysics Data System (ADS)

Bermudez, R.; Gascó, J. M.; Tarquis, A. M.; Saa-Requejo, A.

2009-04-01

Numeric taxonomy has been applied to classify Tajo basin water (Spain) till Portugal border. Several stations, a total of 52, that estimate 15 water variables have been used in this study. The different groups have been obtained applying a Euclidean distance among stations (distance classification) and a Euclidean distance between each station and the centroid estimated among them (centroid classification), varying the number of parameters and with or without variable typification. In order to compare the classification a log-log relation has been established, between number of groups created and distances, to select the best one. It has been observed that centroid classification is more appropriate following in a more logic way the natural constrictions than the minimum distance among stations. Variable typification doesn't improve the classification except when the centroid method is applied. Taking in consideration the ions and the sum of them as variables, the classification improved. Stations are grouped based on electric conductivity (CE), total anions (TA), total cations (TC) and ions ratio (Na/Ca and Mg/Ca). For a given classification and comparing the different groups created a certain variation in ions concentration and ions ratio are observed. However, the variation in each ion among groups is different depending on the case. For the last group, regardless the classification, the increase in all ions is general. Comparing the dendrograms, and groups that originated, Tajo river basin can be sub dived in five sub-basins differentiated by the main influence on water: 1. With a higher ombrogenic influence (rain fed). 2. With ombrogenic and pedogenic influence (rain and groundwater fed). 3. With pedogenic influence. 4. With lithogenic influence (geological bedrock). 5. With a higher ombrogenic and lithogenic influence added.

A Framework for Categorizing Important Project Variables

NASA Technical Reports Server (NTRS)

Parsons, Vickie S.

2003-01-01

While substantial research has led to theories concerning the variables that affect project success, no universal set of such variables has been acknowledged as the standard. The identification of a specific set of controllable variables is needed to minimize project failure. Much has been hypothesized about the need to match project controls and management processes to individual projects in order to increase the chance for success. However, an accepted taxonomy for facilitating this matching process does not exist. This paper surveyed existing literature on classification of project variables. After an analysis of those proposals, a simplified categorization is offered to encourage further research.