[Concepts of rational taxonomy].

PubMed

Pavlinov, I Ia

2011-01-01

The problems are discussed related to development of concepts of rational taxonomy and rational classifications (taxonomic systems) in biology. Rational taxonomy is based on the assumption that the key characteristic of rationality is deductive inference of certain partial judgments about reality under study from other judgments taken as more general and a priory true. Respectively, two forms of rationality are discriminated--ontological and epistemological ones. The former implies inference of classifications properties from general (essential) properties of the reality being investigated. The latter implies inference of the partial rules of judgments about classifications from more general (formal) rules. The following principal concepts of ontologically rational biological taxonomy are considered: "crystallographic" approach, inference of the orderliness of organismal diversity from general laws of Nature, inference of the above orderliness from the orderliness of ontogenetic development programs, based on the concept of natural kind and Cassirer's series theory, based on the systemic concept, based on the idea of periodic systems. Various concepts of ontologically rational taxonomy can be generalized by an idea of the causal taxonomy, according to which any biologically sound classification is founded on a contentwise model of biological diversity that includes explicit indication of general causes responsible for that diversity. It is asserted that each category of general causation and respective background model may serve as a basis for a particular ontologically rational taxonomy as a distinctive research program. Concepts of epistemologically rational taxonomy and classifications (taxonomic systems) can be interpreted in terms of application of certain epistemological criteria of substantiation of scientific status of taxonomy in general and of taxonomic systems in particular. These concepts include: consideration of taxonomy consistency from the

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.

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

“RaMassays”: Synergistic Enhancement of Plasmon-Free Raman Scattering and Mass Spectrometry for Multimodal Analysis of Small Molecules

NASA Astrophysics Data System (ADS)

Alessandri, Ivano; Vassalini, Irene; Bertuzzi, Michela; Bontempi, Nicolò; Memo, Maurizio; Gianoncelli, Alessandra

2016-10-01

SiO2/TiO2 core/shell (T-rex) beads were exploited as “all-in-one” building-block materials to create analytical assays that combine plasmon-free surface enhanced Raman scattering (SERS) and surface assisted laser desorption/ionization (SALDI) mass spectrometry (RaMassays). Such a multi-modal approach relies on the unique optical properties of T-rex beads, which are able to harvest and manage light in both UV and Vis range, making ionization and Raman scattering more efficient. RaMassays were successfully applied to the detection of small (molecular weight, M.W. <400 Da) molecules with a key relevance in biochemistry and pharmaceutical analysis. Caffeine and cocaine were utilized as molecular probes to test the combined SERS/SALDI response of RaMassays, showing excellent sensitivity and reproducibility. The differentiation between amphetamine/ephedrine and theophylline/theobromine couples demonstrated the synergistic reciprocal reinforcement of SERS and SALDI. Finally, the conversion of L-tyrosine in L-DOPA was utilized to probe RaMassays as analytical tools for characterizing reaction intermediates without introducing any spurious effects. RaMassays exhibit important advantages over plasmonic nanoparticles in terms of reproducibility, absence of interference and potential integration in multiplexed devices.

“RaMassays”: Synergistic Enhancement of Plasmon-Free Raman Scattering and Mass Spectrometry for Multimodal Analysis of Small Molecules

PubMed Central

Alessandri, Ivano; Vassalini, Irene; Bertuzzi, Michela; Bontempi, Nicolò; Memo, Maurizio; Gianoncelli, Alessandra

2016-01-01

SiO2/TiO2 core/shell (T-rex) beads were exploited as “all-in-one” building-block materials to create analytical assays that combine plasmon-free surface enhanced Raman scattering (SERS) and surface assisted laser desorption/ionization (SALDI) mass spectrometry (RaMassays). Such a multi-modal approach relies on the unique optical properties of T-rex beads, which are able to harvest and manage light in both UV and Vis range, making ionization and Raman scattering more efficient. RaMassays were successfully applied to the detection of small (molecular weight, M.W. <400 Da) molecules with a key relevance in biochemistry and pharmaceutical analysis. Caffeine and cocaine were utilized as molecular probes to test the combined SERS/SALDI response of RaMassays, showing excellent sensitivity and reproducibility. The differentiation between amphetamine/ephedrine and theophylline/theobromine couples demonstrated the synergistic reciprocal reinforcement of SERS and SALDI. Finally, the conversion of L-tyrosine in L-DOPA was utilized to probe RaMassays as analytical tools for characterizing reaction intermediates without introducing any spurious effects. RaMassays exhibit important advantages over plasmonic nanoparticles in terms of reproducibility, absence of interference and potential integration in multiplexed devices. PMID:27698368

Use of the Raman spectrometer in gemmological laboratories: Review

NASA Astrophysics Data System (ADS)

Kiefert, Lore; Karampelas, Stefanos

2011-10-01

The current paper gives an overview of the development of Raman spectrometry in gemmological laboratories. While before 1990s, no commercial gemmological laboratory possessed such an instrument, all larger international labs have acquired these instruments by now. The Raman spectrometer is routinely used for the detection of emerald fillers, HPHT treatment of diamonds, analysis of the nature of a gemstone, analysis of gemstone inclusions and treatments, and the characterisation of natural or colour enhanced pearls and corals. Future developments in gemstone research lie in the closer analysis of the features of Raman and PL spectra and in the combination of several instruments.

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.…

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.

[Discussion on diagenesis of Xilingang pluton-constrained by X-ray Fluorescence spectroscopy, plasma mass spectrometry and Raman spectroscopy].

PubMed

Tang, Yu-Kun; Chen, Guo-Neng; Zhang, Ke; Huang, Hai-Hua

2013-05-01

The results on Xilingang pluton, mainly consisting of red beds, granites containing numerous debris of red beds and granites, obtained by X-ray fluorescence spectroscopy, plasma mass spectrometry and Raman spectroscopy show: (1) Xilingang pluton from red beds, granites containing numerous debris of red beds to granites has obvious characteristics of decreasing silicon and alkali content, and rising ignition loss, dark mineral content and oxidation index; (2) Chondrite-normalized REE distribution curves and primitive mantle-normalized spider diagram for trace elements of redbed, granites containing numerous debris of red beds and granites have a good consistency, the distribution characteristics of elements are similar to Nanling transformation-type granite; (3) The value of Raman spectrogram characteristic peak of quartz crystal in Xilingang granite decreased from the center of quartz crystal, and FWHM is steady. According to the above, the authors believe that Xilingang granite formed was related to in-situ melting of red beds and underlying strata and magma consolidation. Volatile components were discharged continuously, and oxidation index decreased gradually in the melting process. In the process of diagenesis, the top of pluton tend to be an ongoing silicon and alkali increase, while TFeO and MgO continue to migrate to bottom, and crystallization environment is a relatively closed and steady system.

Teaching the New Taxonomy.

ERIC Educational Resources Information Center

Texley, Juliana

2002-01-01

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

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.

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.

Condensing Raman spectrum for single-cell phenotype analysis.

PubMed

Sun, Shiwei; Wang, Xuetao; Gao, Xin; Ren, Lihui; Su, Xiaoquan; Bu, Dongbo; Ning, Kang

2015-01-01

In recent years, high throughput and non-invasive Raman spectrometry technique has matured as an effective approach to identification of individual cells by species, even in complex, mixed populations. Raman profiling is an appealing optical microscopic method to achieve this. To fully utilize Raman proling for single-cell analysis, an extensive understanding of Raman spectra is necessary to answer questions such as which filtering methodologies are effective for pre-processing of Raman spectra, what strains can be distinguished by Raman spectra, and what features serve best as Raman-based biomarkers for single-cells, etc. In this work, we have proposed an approach called rDisc to discretize the original Raman spectrum into only a few (usually less than 20) representative peaks (Raman shifts). The approach has advantages in removing noises, and condensing the original spectrum. In particular, effective signal processing procedures were designed to eliminate noise, utilising wavelet transform denoising, baseline correction, and signal normalization. In the discretizing process, representative peaks were selected to signicantly decrease the Raman data size. More importantly, the selected peaks are chosen as suitable to serve as key biological markers to differentiate species and other cellular features. Additionally, the classication performance of discretized spectra was found to be comparable to full spectrum having more than 1000 Raman shifts. Overall, the discretized spectrum needs about 5storage space of a full spectrum and the processing speed is considerably faster. This makes rDisc clearly superior to other methods for single-cell classication.

Mineralogical Characterization of Hispano-Moresque Glazes: A µ-Raman and Scanning Electron Microscopy with X-Ray Energy Dispersive Spectrometry (SEM-EDS) Study.

PubMed

Coentro, Susana; da Silva, Rui C; Relvas, Cátia; Ferreira, Teresa; Mirão, José; Pleguezuelo, Alfonso; Trindade, Rui; Muralha, Vânia S F

2018-06-05

This work explores the combination of µ-Raman spectroscopy and scanning electron microscopy with X-ray energy dispersive spectrometry (SEM-EDS) for the study of the glazes in 15th-16th century Hispano-Moresque architectural tiles. These are high lead glazes that can be tin-opacified or transparent, and present five colors: tin-white, cobalt-blue, copper-green, iron-amber, and manganese-brown. They are generally homogenous and mineral inclusions are mostly concentrated in the glaze-ceramic interface. Through SEM-EDS, these inclusions were observed and chemically analyzed, whereas µ-Raman allowed their identification on a molecular level. K-feldspars, wollastonite and diopside were the most common compounds, as well as cassiterite agglomerates that render the glaze opaque. Malayaite was identified in green glazes, and andradite and magnesioferrite in amber glazes. Co-Ni-ferrites were identified in blue glazes, as well as Ni-Fe-olivines. Manganese-brown is the color where most compounds were identified: bustamite, jacobsite, hausmannite, braunite, and kentrolite. Through the µ-Raman analysis of different areas in large inclusions previously observed by SEM, it was possible to identify intermediate phases that illustrate the reaction process that occurs between the color-conferring compounds and the surrounding lead glaze. Furthermore, the obtained results allowed inference of the raw materials and firing temperatures used on the manufacture of these tiles.

On the Habitability of Desert Varnish: A Combined Study by Micro-Raman Spectroscopy, X-ray Diffraction, and Methylated Pyrolysis-Gas Chromatography-Mass Spectrometry.

PubMed

Malherbe, C; Hutchinson, I B; Ingley, R; Boom, A; Carr, A S; Edwards, H; Vertruyen, B; Gilbert, B; Eppe, G

2017-11-01

In 2020, the ESA ExoMars and NASA Mars 2020 missions will be launched to Mars to search for evidence of past and present life. In preparation for these missions, terrestrial analog samples of rock formations on Mars are studied in detail in order to optimize the scientific information that the analytical instrumentation will return. Desert varnishes are thin mineral coatings found on rocks in arid and semi-arid environments on Earth that are recognized as analog samples. During the formation of desert varnishes (which takes many hundreds of years), organic matter is incorporated, and microorganisms may also play an active role in the formation process. During this study, four complementary analytical techniques proposed for Mars missions (X-ray diffraction [XRD], Raman spectroscopy, elemental analysis, and pyrolysis-gas chromatography-mass spectrometry [Py-GC-MS]) were used to interrogate samples of desert varnish and describe their capacity to sustain life under extreme scenarios. For the first time, both the geochemistry and the organic compounds associated with desert varnish are described with the use of identical sets of samples. XRD and Raman spectroscopy measurements were used to nondestructively interrogate the mineralogy of the samples. In addition, the use of Raman spectroscopy instruments enabled the detection of β-carotene, a highly Raman-active biomarker. The content and the nature of the organic material in the samples were further investigated with elemental analysis and methylated Py-GC-MS, and a bacterial origin was determined to be likely. In the context of planetary exploration, we describe the habitable nature of desert varnish based on the biogeochemical composition of the samples. Possible interference of the geological substrate on the detectability of pyrolysis products is also suggested. Key Words: Desert varnish-Habitability-Raman spectroscopy-Py-GC-MS-XRD-ExoMars-Planetary science. Astrobiology 17, 1123-1137.

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

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

Bacteriophage Taxonomy: An Evolving Discipline.

PubMed

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

2018-01-01

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

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

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.

New insights into the red and green pigments in the illuminated foral charter of Setubal (1515) by combined use of μ-Raman and X-ray fluorescence spectrometry

NASA Astrophysics Data System (ADS)

Guerra, M.; Carvalho, M. L.; Le Gac, A.; Manso, M.; Mortari, C.; Longelin, S.; Pessanha, S.

2016-03-01

The richly decorated foral charter attributed by D. Manuel I of Portugal, in 1515, to the village of Setubal, was studied using Energy Dispersive X-ray Fluorescence spectrometry and Raman micro-spectroscopy. An in situ characterization of the pigments used in the production of this masterpiece showed a very different pigment palette choice when compared to other similar Manueline charters. The red and green pigments are particularly puzzling, as the widely used mercury- and copper-based pigments, vermillion and malachite, respectively, were not found in the illuminated frontispiece. Instead, the cheaper lead-based pigment minium was used in the King's flag, while a mixture of copper sulfates was found for the green color, identified by means of micro-Raman spectroscopy. This result led to a new look at the conception that only one Royal workshop existed for the elaboration of Manueline foral charters.

The Taxonomy of Intervention Intensity

ERIC Educational Resources Information Center

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

2017-01-01

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

A Taxonomy of Learning through Asynchronous Discussion

ERIC Educational Resources Information Center

Knowlton, Dave S.

2005-01-01

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

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

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

On the Habitability of Desert Varnish: A Combined Study by Micro-Raman Spectroscopy, X-ray Diffraction, and Methylated Pyrolysis-Gas Chromatography-Mass Spectrometry

NASA Astrophysics Data System (ADS)

Malherbe, C.; Hutchinson, I. B.; Ingley, R.; Boom, A.; Carr, A. S.; Edwards, H.; Vertruyen, B.; Gilbert, B.; Eppe, G.

2017-11-01

In 2020, the ESA ExoMars and NASA Mars 2020 missions will be launched to Mars to search for evidence of past and present life. In preparation for these missions, terrestrial analog samples of rock formations on Mars are studied in detail in order to optimize the scientific information that the analytical instrumentation will return. Desert varnishes are thin mineral coatings found on rocks in arid and semi-arid environments on Earth that are recognized as analog samples. During the formation of desert varnishes (which takes many hundreds of years), organic matter is incorporated, and microorganisms may also play an active role in the formation process. During this study, four complementary analytical techniques proposed for Mars missions (X-ray diffraction [XRD], Raman spectroscopy, elemental analysis, and pyrolysis-gas chromatography-mass spectrometry [Py-GC-MS]) were used to interrogate samples of desert varnish and describe their capacity to sustain life under extreme scenarios. For the first time, both the geochemistry and the organic compounds associated with desert varnish are described with the use of identical sets of samples. XRD and Raman spectroscopy measurements were used to nondestructively interrogate the mineralogy of the samples. In addition, the use of Raman spectroscopy instruments enabled the detection of β-carotene, a highly Raman-active biomarker. The content and the nature of the organic material in the samples were further investigated with elemental analysis and methylated Py-GC-MS, and a bacterial origin was determined to be likely. In the context of planetary exploration, we describe the habitable nature of desert varnish based on the biogeochemical composition of the samples. Possible interference of the geological substrate on the detectability of pyrolysis products is also suggested.

Secondary ion mass spectrometry and Raman spectroscopy for tissue engineering applications

PubMed Central

Ilin, Yelena; Kraft, Mary L.

2014-01-01

Identifying the matrix properties that permit directing stem cell fate is critical for expanding desired cell lineages ex vivo for disease treatment. Such efforts require knowledge of matrix surface chemistry and the cell responses they elicit. Recent progress in analyzing biomaterial composition and identifying cell phenotype with two label-free chemical imaging techniques, TOF-SIMS and Raman spectroscopy are presented. TOF-SIMS is becoming indispensable for the surface characterization of biomaterial scaffolds. Developments in TOF-SIMS data analysis enable correlating surface chemistry with biological response. Advances in the interpretation of Raman spectra permit identifying the fate decisions of individual, living cells with location specificity. Here we highlight this progress and discuss further improvements that would facilitate efforts to develop artificial scaffolds for tissue regeneration. PMID:25462628

Morphological and chemical changes in dentin after using endodontic agents: Fourier transform Raman spectroscopy, energy-dispersive x-ray fluorescence spectrometry, and scanning electron microscopy study

NASA Astrophysics Data System (ADS)

Pascon, Fernanda Miori; Kantovitz, Kamila Rosamilia; Soares, Luís Eduardo Silva; Santo, Ana Maria do Espírito; Martin, Airton Abraha~o.; Puppin-Rontani, Regina Maria

2012-07-01

We examine the morphological and chemical changes in the pulp chamber dentin after using endodontic agents by scanning electron microscopy (SEM), Fourier transform Raman spectroscopy (FT-Raman), and micro energy-dispersive x-ray fluorescence spectrometry (μEDXRF). Thirty teeth were sectioned exposing the pulp chamber and divided by six groups (n=5): NT-no treatment; CHX-2% chlorhexidine; CHXE-2% chlorhexidine+17% EDTA E-17% EDTA; SH5-5.25% NaOCl; SH5E-5.25% NaOCl+17% EDTA. The inorganic and organic content was analyzed by FT-Raman. μEDXRF examined calcium (Ca) and phosphorus (P) content as well as Ca/P ratio. Impressions of specimens were evaluated by SEM. Data were submitted to Kruskal-Wallis and Dunn tests (p<0.05). Differences were observed among groups for the 960 cm-1 peak. Ca and P content differences were significant (SH5>NT=SH5E>CHX>E>CHXE). CHXE and E presented the highest Ca/P ratio values compared to the other groups (p<0.05). The SEM images in the EDTA-treated groups had the highest number of open tubules. Erosion in the tubules was observed in CHX and SH5E groups. Endodontic agents change the inorganic and organic content of pulp chamber dentin. NaOCl used alone, or in association with EDTA, was the most effective agent considering chemical and morphological approaches.

Comprehensive Social Skills Taxonomy: Development and Application.

PubMed

Kauffman, Nancy A; Kinnealey, Moya

2015-01-01

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

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.

A psychologically-based taxonomy of misdirection

PubMed Central

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

2014-01-01

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

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.

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

PubMed

Reis, Harry T

2018-03-01

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

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.

A Taxonomy of Community Living Skills.

ERIC Educational Resources Information Center

Dever, Richard B.

1989-01-01

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

Tumor taxonomy for the developmental lineage classification of neoplasms

PubMed Central

Berman, Jules J

2004-01-01

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

Ecogenomics and Taxonomy of Cyanobacteria Phylum

PubMed Central

Walter, Juline M.; Coutinho, Felipe H.; Dutilh, Bas E.; Swings, Jean; Thompson, Fabiano L.; Thompson, Cristiane C.

2017-01-01

Cyanobacteria are major contributors to global biogeochemical cycles. The genetic diversity among Cyanobacteria enables them to thrive across many habitats, although only a few studies have analyzed the association of phylogenomic clades to specific environmental niches. In this study, we adopted an ecogenomics strategy with the aim to delineate ecological niche preferences of Cyanobacteria and integrate them to the genomic taxonomy of these bacteria. First, an appropriate phylogenomic framework was established using a set of genomic taxonomy signatures (including a tree based on conserved gene sequences, genome-to-genome distance, and average amino acid identity) to analyse ninety-nine publicly available cyanobacterial genomes. Next, the relative abundances of these genomes were determined throughout diverse global marine and freshwater ecosystems, using metagenomic data sets. The whole-genome-based taxonomy of the ninety-nine genomes allowed us to identify 57 (of which 28 are new genera) and 87 (of which 32 are new species) different cyanobacterial genera and species, respectively. The ecogenomic analysis allowed the distinction of three major ecological groups of Cyanobacteria (named as i. Low Temperature; ii. Low Temperature Copiotroph; and iii. High Temperature Oligotroph) that were coherently linked to the genomic taxonomy. This work establishes a new taxonomic framework for Cyanobacteria in the light of genomic taxonomy and ecogenomic approaches. PMID:29184540

Ecogenomics and Taxonomy of Cyanobacteria Phylum.

PubMed

Walter, Juline M; Coutinho, Felipe H; Dutilh, Bas E; Swings, Jean; Thompson, Fabiano L; Thompson, Cristiane C

2017-01-01

Cyanobacteria are major contributors to global biogeochemical cycles. The genetic diversity among Cyanobacteria enables them to thrive across many habitats, although only a few studies have analyzed the association of phylogenomic clades to specific environmental niches. In this study, we adopted an ecogenomics strategy with the aim to delineate ecological niche preferences of Cyanobacteria and integrate them to the genomic taxonomy of these bacteria. First, an appropriate phylogenomic framework was established using a set of genomic taxonomy signatures (including a tree based on conserved gene sequences, genome-to-genome distance, and average amino acid identity) to analyse ninety-nine publicly available cyanobacterial genomes. Next, the relative abundances of these genomes were determined throughout diverse global marine and freshwater ecosystems, using metagenomic data sets. The whole-genome-based taxonomy of the ninety-nine genomes allowed us to identify 57 (of which 28 are new genera) and 87 (of which 32 are new species) different cyanobacterial genera and species, respectively. The ecogenomic analysis allowed the distinction of three major ecological groups of Cyanobacteria (named as i. Low Temperature; ii. Low Temperature Copiotroph; and iii. High Temperature Oligotroph) that were coherently linked to the genomic taxonomy. This work establishes a new taxonomic framework for Cyanobacteria in the light of genomic taxonomy and ecogenomic approaches.

New look inside human breast ducts with Raman imaging. Raman candidates as diagnostic markers for breast cancer prognosis: Mammaglobin, palmitic acid and sphingomyelin.

PubMed

Abramczyk, Halina; Brozek-Pluska, Beata

2016-02-25

Looking inside the human body fascinated mankind for thousands of years. Current diagnostic and therapy methods are often limited by inadequate sensitivity, specificity and spatial resolution. Raman imaging may bring revolution in monitoring of disease and treatment. The main advantage of Raman imaging is that it gives spatial information about various chemical constituents in defined cellular organelles in contrast to conventional methods (liquid chromatography/mass spectrometry, NMR, HPLC) that rely on bulk or fractionated analyses of extracted components. We demonstrated how Raman imaging can drive the progress on breast cancer just unimaginable a few years ago. We looked inside human breast ducts answering fundamental questions about location and distribution of various biochemical components inside the lumen, epithelial cells of the duct and the stroma around the duct during cancer development. We have identified Raman candidates as diagnostic markers for breast cancer prognosis: carotenoids, mammaglobin, palmitic acid and sphingomyelin as key molecular targets in ductal breast cancer in situ, and propose the molecular mechanisms linking oncogenes with lipid programming. Copyright © 2016 Elsevier B.V. All rights reserved.

The Cartesian Heritage of Bloom's Taxonomy

ERIC Educational Resources Information Center

Bertucio, Brett

2017-01-01

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

Differentiating the growth phases of single bacteria using Raman spectroscopy

NASA Astrophysics Data System (ADS)

Strola, S. A.; Marcoux, P. R.; Schultz, E.; Perenon, R.; Simon, A.-C.; Espagnon, I.; Allier, C. P.; Dinten, J.-M.

2014-03-01

In this paper we present a longitudinal study of bacteria metabolism performed with a novel Raman spectrometer system. Longitudinal study is possible with our Raman setup since the overall procedure to localize a single bacterium and collect a Raman spectrum lasts only 1 minute. Localization and detection of single bacteria are performed by means of lensfree imaging, whereas Raman signal (from 600 to 3200 cm-1) is collected into a prototype spectrometer that allows high light throughput (HTVS technology, Tornado Spectral System). Accomplishing time-lapse Raman spectrometry during growth of bacteria, we observed variation in the net intensities for some band groups, e.g. amides and proteins. The obtained results on two different bacteria species, i.e. Escherichia coli and Bacillus subtilis clearly indicate that growth affects the Raman chemical signature. We performed a first analysis to check spectral differences and similarities. It allows distinguishing between lag, exponential and stationary growth phases. And the assignment of interest bands to vibration modes of covalent bonds enables the monitoring of metabolic changes in bacteria caused by growth and aging. Following the spectra analysis, a SVM (support vector machine) classification of the different growth phases is presented. In sum this longitudinal study by means of a compact and low-cost Raman setup is a proof of principle for routine analysis of bacteria, in a real-time and non-destructive way. Real-time Raman studies on metabolism and viability of bacteria pave the way for future antibiotic susceptibility testing.

Backyard Taxonomy.

ERIC Educational Resources Information Center

Gotsch, Margaret; Harris, Shannon

1990-01-01

Described is a backyard activity that can be used to introduce children to the divisions of the plant and animal kingdoms in their local environment. Preparation, procedures and followup are discussed. Background information on taxonomy and two activity cards are provided. (CW)

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

Solution and solid trinitrotoluene (TNT) photochemistry: persistence of TNT-like ultraviolet (UV) resonance Raman bands.

PubMed

Gares, Katie L; Bykov, Sergei V; Godugu, Bhaskar; Asher, Sanford A

2014-01-01

We examined the 229 nm deep-ultraviolet resonance Raman (DUVRR) spectra of solution and solid-state trinitrotoluene (TNT) and its solution and solid-state photochemistry. Although TNT photodegrades with a solution quantum yield of ϕ ∼ 0.015, the initial photoproducts show DUVRR spectra extraordinarily similar to pure TNT, due to the similar photoproduct enhancement of the -NO2 stretching vibrations. This results in TNT-like DUVRR spectra even after complete TNT photolysis. These ultraviolet resonance Raman spectral bands enable DUVRR of trace as well as DUVRR standoff TNT detection. We determined the structure of various initial TNT photoproducts by using liquid chromatography-mass spectrometry and tandem mass spectrometry. Similar TNT DUVRR spectra and photoproducts are observed in the solution and solid states.

A Rain Taxonomy for Degraded Visual Environment Mitigation

NASA Technical Reports Server (NTRS)

Gatlin, P. N.; Petersen, W. A.

2018-01-01

This Technical Memorandum (TM) provides a description of a rainfall taxonomy that defines the detailed characteristics of naturally occurring rainfall. The taxonomy is based on raindrop size measurements collected around the globe and encompasses several different climate types. Included in this TM is a description of these rainfall observations, an explanation of methods used to process those data, and resultant metrics comprising the rain taxonomy database. Each of the categories in the rain taxonomy are characterized by a unique set of raindrop sizes that can be used in simulations of electromagnetic wave propagation through a rain medium.

Combined use of direct analysis in real-time/Orbitrap mass spectrometry and micro-Raman spectroscopy for the comprehensive characterization of real explosive samples.

PubMed

Bridoux, Maxime C; Schwarzenberg, Adrián; Schramm, Sébastien; Cole, Richard B

2016-08-01

Direct Analysis in Real Time (DART™) high-resolution Orbitrap™ mass spectrometry (HRMS) in combination with Raman microscopy was used for the detailed molecular level characterization of explosives including not only the charge but also the complex matrix of binders, plasticizers, polymers, and other possible organic additives. A total of 15 defused military weapons including grenades, mines, rockets, submunitions, and mortars were examined. Swabs and wipes were used to collect trace (residual) amounts of explosives and their organic constituents from the defused military weapons and micrometer-size explosive particles were transferred using a vacuum suction-impact collection device (vacuum impactor) from wipe and swap samples to an impaction plate made of carbon. The particles deposited on the carbon plate were then characterized using micro-Raman spectroscopy followed by DART-HRMS providing fingerprint signatures of orthogonal nature. The optical microscope of the micro-Raman spectrometer was first used to localize and characterize the explosive charge on the impaction plate which was then targeted for identification by DART-HRMS analysis in both the negative and positive modes. Raman spectra of the explosives TNT, RDX and PETN were acquired from micrometer size particles and characterized by the presence of their characteristic Raman bands obtained directly at the surface of the impaction plate nondestructively without further sample preparation. Negative mode DART-HRMS confirmed the types of charges contained in the weapons (mainly TNT, RDX, HMX, and PETN; either as individual components or as mixtures). These energetic compounds were mainly detected as deprotonated species [M-H](-), or as adduct [M + (35)Cl](-), [M + (37)Cl](-), or [M + NO3](-) anions. Chloride adducts were promoted in the heated DART reagent gas by adding chloroform vapors to the helium stream using an "in-house" delivery method. When the polarity was switched to positive mode

SCIRehab Project Series: The Psychology Taxonomy

PubMed Central

Wilson, Catherine; Huston, Toby; Koval, Jill; Gordon, Samuel A; Schwebel, Andrea; Gassaway, Julie

2009-01-01

Context: The integration of psychologists as members of the rehabilitation team has occurred in conjunction with the evolution and adoption of interdisciplinary teams as the standard of care in spinal cord injury (SCI) rehabilitation. Although the value of psychological services during rehabilitation is endorsed widely, specific interventions and their association with patient outcomes have not been examined adequately. Objective: To address this shortcoming, psychologists from 6 SCI centers collaborated to develop a psychology intervention taxonomy and documentation framework. Methods: Utilizing an interactive process, the lead psychologists from 6 centers compiled an inclusive list of patient characteristics assessed and interventions delivered in routine psychological practice at the participating rehabilitation facilities. These were systematically grouped, defined, and compared. Results: The resulting taxonomy became the basis of a documentation framework utilized by psychologists for the study. The psychology taxonomy includes 4 major clinical categories (assessment, psychotherapeutic interventions, psychoeducational interventions, and consultation) with 5 to 10 specific activities in each category. Conclusions: Examination of psychological interventions and their potential association with positive outcomes for persons who sustain SCI requires the development of a taxonomy. Results of these efforts illustrate similarities and differences in psychological practice among SCI centers and offer the opportunity to blend research and clinical practice in an innovative approach to evidence-based practice improvement. The established taxonomy provides a basic framework for future studies on the effect of psychological interventions. PMID:19810633

Application of a Taxonomy to Characterize the Public Health Workforce.

PubMed

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

2015-01-01

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

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);…

Evaluating a medical error taxonomy.

PubMed

Brixey, Juliana; Johnson, Todd R; Zhang, Jiajie

2002-01-01

Healthcare has been slow in using human factors principles to reduce medical errors. The Center for Devices and Radiological Health (CDRH) recognizes that a lack of attention to human factors during product development may lead to errors that have the potential for patient injury, or even death. In response to the need for reducing medication errors, the National Coordinating Council for Medication Errors Reporting and Prevention (NCC MERP) released the NCC MERP taxonomy that provides a standard language for reporting medication errors. This project maps the NCC MERP taxonomy of medication error to MedWatch medical errors involving infusion pumps. Of particular interest are human factors associated with medical device errors. The NCC MERP taxonomy of medication errors is limited in mapping information from MEDWATCH because of the focus on the medical device and the format of reporting.

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.;

Diagnosing clean margins through Raman spectroscopy in human and animal mammary tumour surgery: a short review

PubMed Central

Birtoiu, I. A.; Rizea, C.; Togoe, D.; Munteanu, R. M.; Micsa, C.; Rusu, M. I.; Tautan, M.; Braic, L.; Scoicaru, L. O.; Parau, A.; Becherescu-Barbu, N. D.; Udrea, M. V.; Tonetto, A.; Notonier, R.

2016-01-01

Breast cancer frequency in human and other mammal female populations has worryingly increased lately. The acute necessity for taxonomy of the aetiological factors along with seeking for new diagnostic tools and therapy procedures aimed at reducing mortality have yielded in an intense research effort worldwide. Surgery is a regular method to counteract extensive development of breast cancer and prevent metastases provided that negative surgical margins are achieved. This highly technical challenge requires fast, extremely sensitive and selective discrimination between malignant and benign tissues even down to molecular level. The particular advantages of Raman spectroscopy, such as high chemical specificity, and the ability to measure raw samples and optical responses in the visible or near-infrared spectral range, have recently recommended it as a means with elevated potential in precise diagnostic in oncology surgery. This review spans mainly the latter 10 years of exceptional efforts of scientists implementing Raman spectroscopy as a nearly real-time diagnostic tool for clean margins assessment in mastectomy and lumpectomy. Although greatly contributing to medical discoveries for the wealth of humanity, animals as patients have benefitted less from advances in surgery diagnostic using Raman spectroscopy. This work also dedicates a few lines to applications of surface enhanced Raman spectroscopy in veterinary oncological surgery. PMID:27920899

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

Analytical procedure for characterization of medieval wall-paintings by X-ray fluorescence spectrometry, laser ablation inductively coupled plasma mass spectrometry and Raman spectroscopy

NASA Astrophysics Data System (ADS)

Syta, Olga; Rozum, Karol; Choińska, Marta; Zielińska, Dobrochna; Żukowska, Grażyna Zofia; Kijowska, Agnieszka; Wagner, Barbara

2014-11-01

Analytical procedure for the comprehensive chemical characterization of samples from medieval Nubian wall-paintings by means of portable X-ray fluorescence (pXRF), laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS) and Raman spectroscopy (RS) was proposed in this work. The procedure was used for elemental and molecular investigations of samples from archeological excavations in Nubia (modern southern Egypt and northern Sudan). Numerous remains of churches with painted decorations dated back to the 7th-14th century were excavated in the region of medieval kingdoms of Nubia but many aspects of this art and its technology are still unknown. Samples from the selected archeological sites (Faras, Old Dongola and Banganarti) were analyzed in the form of transfers (n = 26), small fragments collected during the excavations (n = 35) and cross sections (n = 15). XRF was used to collect data about elemental composition, LA-ICPMS allowed mapping of selected elements, while RS was used to get the molecular information about the samples. The preliminary results indicated the usefulness of the proposed analytical procedure for distinguishing the substances, from both the surface and sub-surface domains of the wall-paintings. The possibility to identify raw materials from the wall-paintings will be used in the further systematic, archeometric studies devoted to the detailed comparison of various historic Nubian centers.

Spatial organization of Pseudomonas aeruginosa biofilms probed by combined matrix-assisted laser desorption ionization mass spectrometry and confocal Raman microscopy.

PubMed

Masyuko, Rachel N; Lanni, Eric J; Driscoll, Callan M; Shrout, Joshua D; Sweedler, Jonathan V; Bohn, Paul W

2014-11-21

Bacteria growing as surface attached biofilms differ significantly from planktonic cells in several important traits that are reflected in the spatiotemporal organization of the cells and the extracellular polymeric substances they secrete. The structural and chemical features that define these biofilms are explored here using a combination of matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) and confocal Raman microspectroscopies (CRM) to characterize and compare the composition and distribution of biomolecules found in biofilms and planktonic cells of the bacterium Pseudomonas aeruginosa. Three-day old P. aeruginosa biofilms show dramatic differences in molecular composition compared to planktonic cultures. CRM reveals that wild-type planktonic cell Raman spectra are characterized by bands linked to cellular constituents and are dominated by contributions from DNA- and RNA-related bands. In contrast, biofilm spectra are dominated by bands characteristic of glycolipids - rhamnolipids - polysaccharides and by secreted proteins. LDI MS was applied in turn to identify the rhamnolipids present in the biofilm. Experiments were also conducted using an acyl homoserine lactone quorum sensing-deficient mutant (ΔlasIΔrhlI), which is incapable of producing rhamnolipids. CRM and LDI MS analyses revealed that while molecular composition of the planktonic quorum sensing-deficient cells is similar to that of the wild-type planktonic cells, several compositional differences are observed in the mutant after biofilm growth, including complete absence of detectable rhamnolipids. CRM vibrational spectra of the mutant cells are very similar for planktonic and biofilm growth conditions, indicating that biofilm formation is greatly hindered in the absence of functioning quorum sensing machinery.

Taxonomies of Educational Technology Uses: Dewey, Chip and Me

ERIC Educational Resources Information Center

Levin, James A.

2014-01-01

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

Spumaretroviruses: Updated taxonomy and nomenclature.

PubMed

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

2018-03-01

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

Nondestructive identification for red ink entries of seals by Raman and Fourier transform infrared spectrometry.

PubMed

Wang, Xiang-Feng; Yu, Jing; Zhang, Ai-Lan; Zhou, Dai-Wei; Xie, Meng-Xia

2012-11-01

Determination of the red ink entries of seals on documents can provide valuable evidences for solving related crimes, distinguishing the truth of artworks, and so establishment of nondestructive approaches would play a key role in forensic analysis and related aspects. Raman and FT-IR spectroscopy have been applied for analyzing 105 kinds of red ink entries on documents. The dye components of the ink entries were identified by FT-Raman and confocal Raman microspectroscopy, and then the ink entries were classified into four groups based on these dye components. The ink entries were further discriminated by their FT-IR spectra according to adsorption peaks of the main components, the relative intensities of the characteristic bands and the profiles of the spectra. The results showed that 70 ink entries out of 105 have been individually identified and the remaining 35 ink entries can be divided into 13 subclasses. Combination of Raman and FT-IR spectroscopic methods can provide a powerful nondestructive discriminating tool for identification of the red ink entries of seals on papers. These approaches would have potential application in archeology, art and forensic science. Copyright © 2012 Elsevier B.V. All rights reserved.

DIFFERENTIATION OF AEROMONAS ISOLATES OBTAINED FROM DRINKING WATER DISTRIBUTION SYSTEM USING MATRIX-ASSISTED LASER DESCRIPTION/IONIZATION-MASS SPECTROMETRY (MALDI-MS)

EPA Science Inventory

The genus Aeromonas is one of several medically significant genera that have gained prominence due to their evolving taxonomy and controversial role in human diseases. In this study, matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) was used to analyze the...

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/ ).

An Android Communication App Forensic Taxonomy.

PubMed

Azfar, Abdullah; Choo, Kim-Kwang Raymond; Liu, Lin

2016-09-01

Due to the popularity of Android devices and applications (apps), Android forensics is one of the most studied topics within mobile forensics. Communication apps, such as instant messaging and Voice over IP (VoIP), are one popular app category used by mobile device users, including criminals. Therefore, a taxonomy outlining artifacts of forensic interest involving the use of Android communication apps will facilitate the timely collection and analysis of evidentiary materials from such apps. In this paper, 30 popular Android communication apps were examined, where a logical extraction of the Android phone images was collected using XRY, a widely used mobile forensic tool. Various information of forensic interest, such as contact lists and chronology of messages, was recovered. Based on the findings, a two-dimensional taxonomy of the forensic artifacts of the communication apps is proposed, with the app categories in one dimension and the classes of artifacts in the other dimension. Finally, the artifacts identified in the study of the 30 communication apps are summarized using the taxonomy. It is expected that the proposed taxonomy and the forensic findings in this paper will assist forensic investigations involving Android communication apps. © 2016 American Academy of Forensic Sciences.

Taxonomy for Assessing Evaluation Competencies in Extension

ERIC Educational Resources Information Center

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

2012-01-01

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

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.

An Empirical Taxonomy of Hospital Governing Board Roles

PubMed Central

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

2008-01-01

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

ICTV Virus Taxonomy Profile: Nyamiviridae.

PubMed

Dietzgen, Ralf G; Ghedin, Elodie; Jiāng, Dàohóng; Kuhn, Jens H; Song, Timothy; Vasilakis, Nikos; Wang, David; Ictv Report Consortium

2017-12-01

The Nyamiviridae is a family of viruses with unsegmented, negative-sense RNA genomes of 11.3-12.2 kb that produce enveloped, spherical virions. Viruses of the genus Nyavirus are tick-borne and some also infect birds. Other nyamiviruses infecting parasitoid wasps and plant parasitic nematodes have been classified into the genera Peropuvirus and Socyvirus, respectively. This is a summary of the current International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of Nyamiviridae, which is available at www.ictv.global/report/nyamiviridae.

A taxonomy of behaviour change methods: an Intervention Mapping approach

PubMed Central

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

2016-01-01

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

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

PubMed

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

2016-09-01

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

Bloom's taxonomy of cognitive learning objectives.

PubMed

Adams, Nancy E

2015-07-01

Information professionals who train or instruct others can use Bloom's taxonomy to write learning objectives that describe the skills and abilities that they desire their learners to master and demonstrate. Bloom's taxonomy differentiates between cognitive skill levels and calls attention to learning objectives that require higher levels of cognitive skills and, therefore, lead to deeper learning and transfer of knowledge and skills to a greater variety of tasks and contexts.

Taxonomy of the order Mononegavirales: update 2018.

PubMed

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

2018-04-11

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

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

ERIC Educational Resources Information Center

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

2016-01-01

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

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

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

NONE

1994-12-31

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

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

Rapid characterisation of Klebsiella oxytoca isolates from contaminated liquid hand soap using mass spectrometry, FTIR and Raman spectroscopy.

PubMed

Dieckmann, Ralf; Hammerl, Jens Andre; Hahmann, Hartmut; Wicke, Amal; Kleta, Sylvia; Dabrowski, Piotr Wojciech; Nitsche, Andreas; Stämmler, Maren; Al Dahouk, Sascha; Lasch, Peter

2016-06-23

Microbiological monitoring of consumer products and the efficiency of early warning systems and outbreak investigations depend on the rapid identification and strain characterisation of pathogens posing risks to the health and safety of consumers. This study evaluates the potential of three rapid analytical techniques for identification and subtyping of bacterial isolates obtained from a liquid hand soap product, which has been recalled and reported through the EU RAPEX system due to its severe bacterial contamination. Ten isolates recovered from two bottles of the product were identified as Klebsiella oxytoca and subtyped using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI TOF MS), near-infrared Fourier transform (NIR FT) Raman spectroscopy and Fourier transform infrared (FTIR) spectroscopy. Comparison of the classification results obtained by these phenotype-based techniques with outcomes of the DNA-based methods pulsed-field gel electrophoresis (PFGE), multi-locus sequence typing (MLST) and single nucleotide polymorphism (SNP) analysis of whole-genome sequencing (WGS) data revealed a high level of concordance. In conclusion, a set of analytical techniques might be useful for rapid, reliable and cost-effective microbial typing to ensure safe consumer products and allow source tracking.

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.

Forensic Taxonomy of Android Social Apps.

PubMed

Azfar, Abdullah; Choo, Kim-Kwang Raymond; Liu, Lin

2017-03-01

An Android social app taxonomy incorporating artifacts that are of forensic interest will enable users and forensic investigators to identify the personally identifiable information (PII) stored by the apps. In this study, 30 popular Android social apps were examined. Artifacts of forensic interest (e.g., contacts lists, chronology of messages, and timestamp of an added contact) were recovered. In addition, images were located, and Facebook token strings used to tie account identities and gain access to information entered into Facebook by a user were identified. Based on the findings, a two-dimensional taxonomy of the forensic artifacts of the social apps is proposed. A comparative summary of existing forensic taxonomies of different categories of Android apps, designed to facilitate timely collection and analysis of evidentiary materials from Android devices, is presented. © 2016 American Academy of Forensic Sciences.

In situ Measurement of Pore-Water pH in Anoxic Sediments Using Laser Raman Spectrometry

NASA Astrophysics Data System (ADS)

Peltzer, E. T.; Luna, M.; Walz, P. M.; Zhang, X.; Brewer, P. G.

2010-12-01

Accurate measurement of the geochemical properties of sediment pore waters is of fundamental importance in ocean geochemistry and microbiology. Recent work has shown that the properties of pore waters can be measured rapidly in situ with a novel Raman based insertion probe (Zhang et al., 2010), and that data obtained from anoxic sediments on in situ dissolved methane concentrations are very different (~30x) than from recovered cores due the large scale degassing that occurs during core recovery (Zhang et al., submitted). Degassing of methane must carry with it via Henry’s Law partioning significant quantities of H2S, which is clearly detectable by smell during sample processing, and thus in situ measurement of H2S is also highly desirable. In practice, dissolved H2S is partitioned between the HS- and H2S species as a function of pH with pKa ~7 for the acid dissociation reaction. Since both species are Raman active full determination of the sulfide system is possible if the relative Raman cross sections are known. The diagenetic equations for these reactions are commonly summarized as: 2CH2O + SO4= ↔ 2HCO3- + H2S CH4 + SO4= ↔ HCO3- + HS- + H2O Three of the major components of these equations, CH4, SO4=, and H2S/HS-, are all observable directly by Raman spectroscopy; but the detection of HCO3- presents a challenge due to its low Raman cross section and thus poor sensitivity. We show that pore water pH, which is a good estimator of HCO3- if total CO2 or alkalinity are known, can be measured by observing the H2S / HS- ratio via the equation: pH = pKa + log([HS-]/[H2S]) thereby fully constraining these equations within a single measurement protocol. The Raman peak for HS- is at 2573 cm-1 and for H2S is at 2592 cm-1; thus the peaks are well separated and may easily be deconvoluted from the observed spectrum. We have determined the relative Raman cross sections by a series of laboratory measurements over a range of pH and by using the definition that when pH = p

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

PubMed Central

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

2016-01-01

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

A taxonomy of medical uncertainties in clinical genome sequencing.

PubMed

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

2017-08-01

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

A Taxonomy of Medical Uncertainties in Clinical Genome Sequencing

PubMed Central

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

2017-01-01

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

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

NASA Technical Reports Server (NTRS)

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

1997-01-01

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

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

NASA Technical Reports Server (NTRS)

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

1997-01-01

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

Nanofabrication of densely packed metal-polymer arrays for surface-enhanced Raman spectrometry.

PubMed

De Jesús, M A; Giesfeldt, K S; Oran, J M; Abu-Hatab, N A; Lavrik, N V; Sepaniak, M J

2005-12-01

A key element to improve the analytical capabilities of surface-enhanced Raman spectroscopy (SERS) resides in the performance characteristics of the SERS-active substrate. Variables such as shape, size, and homogeneous distribution of the metal nanoparticles throughout the substrate surface are important in the design of more analytically sensitive and reliable substrates. Electron-beam lithography (EBL) has emerged as a powerful tool for the systematic fabrication of substrates with periodic nanoscale features. EBL also allows the rational design of nanoscale features that are optimized to the frequency of the Raman laser source. In this work, the efficiency of EBL fabricated substrates are studied by measuring the relative SERS signals of Rhodamine 6G and 1,10-phenanthro-line adsorbed on a series of cubic, elliptical, and hexagonal nanopatterned pillars of ma-N 2403 directly coated by physical vapor deposition with 25 nm films of Ag or Au. The raw analyte SERS signals, and signals normalized to metal nanoparticle surface area or numbers of loci, are used to study the effects of nanoparticle morphology on the performance of a rapidly created, diverse collection of substrates. For the excitation wavelength used, the nanoparticle size, geometry, and orientation of the particle primary axis relative to the excitation polarization vector, and particularly the density of nanoparticles, are shown to strongly influence substrate performance. A correlation between the inverse of the magnitude of the laser backscatter passed by the spectrometer and SERS activities of the various substrate patterns is also noted and provides a simple means to evaluate possible efficient coupling of the excitation radiation to localized surface plasmons for Raman enhancement.

Defining viral species: making taxonomy useful.

PubMed

Peterson, A Townsend

2014-07-23

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

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

Methodology of mycobacteria tuberculosis bacteria detection by Raman spectroscopy

NASA Astrophysics Data System (ADS)

Zyubin, A.; Lavrova, A.; Manicheva, O.; Dogonadze, M.; Tsibulnikova, A.; Samusev, I.

2018-01-01

We have developed a methodology for the study of deactivated strains of Mycobacterium tuberculosis. Strains of the Beijing species obtained from pulmonary patient secrete (XDR strain) and reference strain (H37Rv) were investigated by Raman spectrometry with He-Ne (632,8 nm) laser excitation source. As a result of the research, the optimal experimental parameters have been obtained to get spectra of mycolic acids, which are part of the cell wall of mycobacteria.

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

Determination of chemical changes in heat-treated wood using ATR-FTIR and FT Raman spectrometry

NASA Astrophysics Data System (ADS)

Özgenç, Özlem; Durmaz, Sefa; Boyaci, Ismail Hakki; Eksi-Kocak, Haslet

2017-01-01

In this study, attenuated total reflectance-Fourier transform infrared (ATR-FTIR) and Fourier-transform Raman (FT-Raman) spectroscopy techniques were used to determine changes in the chemical structure of heat-treated woods. For this purpose, scots pine (Pinus sylvestris L.), oriental beech (Fagus orientalis L.), and oriental spruce (Picea orientalis L.) wood species were heat-treated at different temperatures. The effect of chemical changes on the FT-Raman and ATR-FTIR bands or ratios of heat-treated wood was related with the OH association of cellulose, functional groups, and the aromatic system of lignin. The effects of heat treatment on the carbohydrate and lignin peaks varied depending on the wood species. The spectral changes that occurred after heat treatment reflected the progress of the condensation reaction of lignin. Degradation of hemicelluloses led to a decrease in free hydroxyl groups. High temperature caused crystalline cellulose to increase due to the degradation of amorphous cellulose.

Determination of chemical changes in heat-treated wood using ATR-FTIR and FT Raman spectrometry.

PubMed

Özgenç, Özlem; Durmaz, Sefa; Boyaci, Ismail Hakki; Eksi-Kocak, Haslet

2017-01-15

In this study, attenuated total reflectance-Fourier transform infrared (ATR-FTIR) and Fourier-transform Raman (FT-Raman) spectroscopy techniques were used to determine changes in the chemical structure of heat-treated woods. For this purpose, scots pine (Pinus sylvestris L.), oriental beech (Fagus orientalis L.), and oriental spruce (Picea orientalis L.) wood species were heat-treated at different temperatures. The effect of chemical changes on the FT-Raman and ATR-FTIR bands or ratios of heat-treated wood was related with the OH association of cellulose, functional groups, and the aromatic system of lignin. The effects of heat treatment on the carbohydrate and lignin peaks varied depending on the wood species. The spectral changes that occurred after heat treatment reflected the progress of the condensation reaction of lignin. Degradation of hemicelluloses led to a decrease in free hydroxyl groups. High temperature caused crystalline cellulose to increase due to the degradation of amorphous cellulose. Copyright © 2016 Elsevier B.V. All rights reserved.

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

PubMed

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

2016-02-01

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

Structure and Composition of Air-Plane Soots and Surrogates Analyzed by Raman Spectroscopy and Laser/Ions Desorption Mass Spectrometry

NASA Astrophysics Data System (ADS)

Ortega, Ismael; Chazallon, Bertrand; Carpentier, Yvain; Irimiea, Cornelia; Focsa, Cristian; Ouf, François-Xavier; Salm, François; Delhaye, David; Gaffié, Daniel; Yon, Jérôme

2015-04-01

Aviation alters the composition of the atmosphere globally and can thus drive climate change and ozone depletion [1]. An aircraft exhaust plume contains species emitted by the engines, species formed in the plume from the emitted species and atmospheric species that become entrained into the plume. The majority of emitted species (gases and soot particles) are produced by the combustion of kerosene with ambient air in the combustion chamber of the engine. Emissions of soot particles by air-planes produce persistent contrails in the upper troposphere in ice-supersaturated air masses that contribute to cloudiness and impact the radiative properties of the atmosphere. These aerosol-cloud interactions represent one of the largest sources of uncertainty in global climate models [2]. Though the formation of atmospheric ice particles has been studied since many years [3], there are still numerous opened questions on nucleation properties of soot particles [4], as the ice nucleation experiments showed a large spread in results depending on the nucleation mode chosen and origin of the soot produced. Most likely one of the reasons behind these discrepancies resides in the different physico-chemical properties (composition, structure) of soot particles produced in different conditions, e.g. with respect to fuel or combustion techniques. In this work, we use Raman microscopy (266, 514 and 785 nm excitation) and ablation techniques (SIMS, Secondary Ions Mass Spectrometry, and Laser Desorption Mass Spectrometry) to characterize soot particles produced from air-plane at different engine regimes simulating a landing and taking-off (LTO) cycle. First, the spectral parameters of the first-order Raman band of various soot samples, collected from three different sources in the frame of the MERMOSE project (http://mermose.onera.fr/): PowerJet SaM-146 turbofan (four engine regimes), CAST generator (propane fuel, four different global equivalence ratios), and Kerosene laboratory flame

A value-based taxonomy of improvement approaches in healthcare.

PubMed

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

2017-06-19

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

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

PubMed

Sheth, Bhavisha P; Thaker, Vrinda S

2017-07-01

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

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.

ICTV Virus Taxonomy Profile: Rhabdoviridae.

PubMed

Walker, Peter J; Blasdell, Kim R; Calisher, Charles H; Dietzgen, Ralf G; Kondo, Hideki; Kurath, Gael; Longdon, Ben; Stone, David M; Tesh, Robert B; Tordo, Noël; Vasilakis, Nikos; Whitfield, Anna E; Nbsp Ictv Report Consortium

2018-04-01

The family Rhabdoviridae comprises viruses with negative-sense (-) single-stranded RNA genomes of 10.8-16.1 kb. Virions are typically enveloped with bullet-shaped or bacilliform morphology but can also be non-enveloped filaments. Rhabdoviruses infect plants and animals including mammals, birds, reptiles and fish, as well as arthropods which serve as single hosts or act as biological vectors for transmission to animals or plants. Rhabdoviruses include important pathogens of humans, livestock, fish and agricultural crops. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of Rhabdoviridae, which is available at www.ictv.global/report/rhabdoviridae.

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.

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

Sub-Micrometer-Scale Mapping of Magnetite Crystals and Sulfur Globules in Magnetotactic Bacteria Using Confocal Raman Micro-Spectrometry

PubMed Central

Eder, Stephan H. K.; Gigler, Alexander M.; Hanzlik, Marianne; Winklhofer, Michael

2014-01-01

The ferrimagnetic mineral magnetite is biomineralized by magnetotactic microorganisms and a diverse range of animals. Here we demonstrate that confocal Raman microscopy can be used to visualize chains of magnetite crystals in magnetotactic bacteria, even though magnetite is a poor Raman scatterer and in bacteria occurs in typical grain sizes of only 35–120 nm, well below the diffraction-limited optical resolution. When using long integration times together with low laser power (<0.25 mW) to prevent laser induced damage of magnetite, we can identify and map magnetite by its characteristic Raman spectrum (303, 535, 665 ) against a large autofluorescence background in our natural magnetotactic bacteria samples. While greigite (cubic ; Raman lines of 253 and 351 ) is often found in the Deltaproteobacteria class, it is not present in our samples. In intracellular sulfur globules of Candidatus Magnetobacterium bavaricum (Nitrospirae), we identified the sole presence of cyclo-octasulfur (: 151, 219, 467 ), using green (532 nm), red (638 nm) and near-infrared excitation (785 nm). The Raman-spectra of phosphorous-rich intracellular accumulations point to orthophosphate in magnetic vibrios and to polyphosphate in magnetic cocci. Under green excitation, the cell envelopes are dominated by the resonant Raman lines of the heme cofactor of the b or c-type cytochrome, which can be used as a strong marker for label-free live-cell imaging of bacterial cytoplasmic membranes, as well as an indicator for the redox state. PMID:25233081

Exploring and Upgrading the Educational Business-Game Taxonomy

ERIC Educational Resources Information Center

Jerman Blažic, Andrej; Džonova Jerman Blažic, Borka

2015-01-01

This article explores existing attempts to design a comprehensive and complex taxonomy framework for an educational business game intended to categorize and evaluate various properties. The identified missing elements in the current proposed taxonomies were used as a starting point for the design of a new category that addresses the game's…

Understanding the Advising Learning Process Using Learning Taxonomies

ERIC Educational Resources Information Center

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

2014-01-01

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

A Raman spectroscopic study of thermally treated glushinskite--the natural magnesium oxalate dihydrate.

PubMed

Frost, Ray L; Adebajo, Moses; Weier, Matt L

2004-02-01

Raman spectroscopy has been used to study the thermal transformations of natural magnesium oxalate dihydrate known in mineralogy as glushinskite. The data obtained by Raman spectroscopy was supplemented with that of infrared emission spectroscopy. The vibrational spectroscopic data was complimented with high resolution thermogravimetric analysis combined with evolved gas mass spectrometry. TG-MS identified two mass loss steps at 146 and 397 degrees C. In the first mass loss step water is evolved only, in the second step carbon dioxide is evolved. The combination of Raman microscopy and a thermal stage clearly identifies the changes in the molecular structure with thermal treatment. Glushinskite is the dihydrate phase in the temperature range up to the pre-dehydration temperature of 146 degrees C. Above 397 degrees C, magnesium oxide is formed. Infrared emission spectroscopy shows that this mineral decomposes at around 400 degrees C. Changes in the position and intensity of the CO and CC stretching vibrations in the Raman spectra indicate the temperature range at which these phase changes occur.

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...

Quantitative fiber-optic Raman spectroscopy for tissue Raman measurements

NASA Astrophysics Data System (ADS)

Duraipandian, Shiyamala; Bergholt, Mads; Zheng, Wei; Huang, Zhiwei

2014-03-01

Molecular profiling of tissue using near-infrared (NIR) Raman spectroscopy has shown great promise for in vivo detection and prognostication of cancer. The Raman spectra measured from the tissue generally contain fundamental information about the absolute biomolecular concentrations in tissue and its changes associated with disease transformation. However, producing analogues tissue Raman spectra present a great technical challenge. In this preliminary study, we propose a method to ensure the reproducible tissue Raman measurements and validated with the in vivo Raman spectra (n=150) of inner lip acquired using different laser powers (i.e., 30 and 60 mW). A rapid Raman spectroscopy system coupled with a ball-lens fiber-optic Raman probe was utilized for tissue Raman measurements. The investigational results showed that the variations between the spectra measured with different laser powers are almost negligible, facilitating the quantitative analysis of tissue Raman measurements in vivo.

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

PubMed

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

2018-06-29

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

ICTV Virus Taxonomy Profile: Ophioviridae

PubMed Central

Bó, Elena Dal; da Graça, John V.; Gago-Zachert, Selma; Hammond, John; Moreno, Pedro; Natsuaki, Tomohide; Pallás, Vicente; Navarro, Jose A.; Reyes, Carina A.; Luna, Gabriel Robles; Sasaya, Takahide; Tzanetakis, Ioannis E.; Vaira, Anna María; Verbeek, Martin

2017-01-01

The Ophioviridae is a family of filamentous plant viruses, with single-stranded negative, and possibly ambisense, RNA genomes of 11.3–12.5 kb divided into 3–4 segments, each encapsidated separately. Virions are naked filamentous nucleocapsids, forming kinked circles of at least two different contour lengths. The sole genus, Ophiovirus, includes seven species. Four ophioviruses are soil-transmitted and their natural hosts include trees, shrubs, vegetables and bulbous or corm-forming ornamentals, both monocots and dicots. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Ophioviridae, which is available at http://www.ictv.global/report/ophioviridae. PMID:28635587

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.

ICTV Virus Taxonomy Profile: Pneumoviridae.

PubMed

Rima, Bert; Collins, Peter; Easton, Andrew; Fouchier, Ron; Kurath, Gael; Lamb, Robert A; Lee, Benhur; Maisner, Andrea; Rota, Paul; Wang, Linfa; Ictv Report Consortium

2017-12-01

The family Pneumoviridae comprises large enveloped negative-sense RNA viruses. This taxon was formerly a subfamily within the Paramyxoviridae, but was reclassified in 2016 as a family with two genera, Orthopneumovirus and Metapneumovirus. Pneumoviruses infect a range of mammalian species, while some members of the Metapneumovirus genus may also infect birds. Some viruses are specific and pathogenic for humans, such as human respiratory syncytial virus and human metapneumovirus. There are no known vectors for pneumoviruses and transmission is thought to be primarily by aerosol droplets and contact. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Pneumoviridae, which is available at www.ictv.global/report/pneumoviridae.

ICTV Virus Taxonomy Profile: Hepeviridae.

PubMed

Purdy, Michael A; Harrison, Tim J; Jameel, S; Meng, X-J; Okamoto, H; Van der Poel, W H M; Smith, Donald B; Ictv Report Consortium

2017-11-01

The family Hepeviridae includes enterically transmitted small non-enveloped positive-sense RNA viruses. It includes the genera Piscihepevirus, whose members infect fish, and Orthohepevirus, whose members infect mammals and birds. Members of the genus Orthohepevirus include hepatitis E virus, which is responsible for self-limiting acute hepatitis in humans and several mammalian species; the infection may become chronic in immunocompromised individuals. Extrahepatic manifestations of Guillain-Barré syndrome, neuralgic amyotrophy, glomerulonephritis and pancreatitis have been described in humans. Avian hepatitis E virus causes hepatitis-splenomegaly syndrome in chickens. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Hepeviridae, which is available at www.ictv.global/report/hepeviridae.

ICTV Virus Taxonomy Profile: Chrysoviridae.

PubMed

Ghabrial, Said A; Castón, José R; Coutts, Robert H A; Hillman, Bradley I; Jiang, Daohong; Kim, Dae-Hyun; Moriyama, Hiromitsu; Ictv Report Consortium

2018-01-01

The Chrysoviridae is a family of small, isometric, non-enveloped viruses (40 nm in diameter) with segmented dsRNA genomes (typically four segments). The genome segments are individually encapsidated and together comprise 11.5-12.8 kbp. The single genus Chrysovirus includes nine species. Chrysoviruses lack an extracellular phase to their life cycle; they are transmitted via intracellular routes within an individual during hyphal growth, in asexual or sexual spores, or between individuals via hyphal anastomosis. There are no known natural vectors for chrysoviruses. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Chrysoviridae, which is available at www.ictv.global/report/chrysoviridae.

ICTV Virus Taxonomy Profile: Partitiviridae.

PubMed

Vainio, Eeva J; Chiba, Sotaro; Ghabrial, Said A; Maiss, Edgar; Roossinck, Marilyn; Sabanadzovic, Sead; Suzuki, Nobuhiro; Xie, Jiatao; Nibert, Max; Ictv Report Consortium

2018-01-01

The Partitiviridae is a family of small, isometric, non-enveloped viruses with bisegmented double-stranded (ds) RNA genomes of 3-4.8 kbp. The two genome segments are individually encapsidated. The family has five genera, with characteristic hosts for members of each genus: either plants or fungi for genera Alphapartitivirus and Betapartitivirus, fungi for genus Gammapartitivirus, plants for genus Deltapartitivirus and protozoa for genus Cryspovirus. Partitiviruses are transmitted intracellularly via seeds (plants), oocysts (protozoa) or hyphal anastomosis, cell division and sporogenesis (fungi); there are no known natural vectors. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Partitiviridae, which is available at www.ictv.global/report/partitiviridae.

Taxonomy of the order Mononegavirales: update 2016.

PubMed

Afonso, Claudio L; Amarasinghe, Gaya K; Bányai, Krisztián; Bào, Yīmíng; Basler, Christopher F; Bavari, Sina; Bejerman, Nicolás; Blasdell, Kim R; Briand, François-Xavier; Briese, Thomas; Bukreyev, Alexander; Calisher, Charles H; Chandran, Kartik; Chéng, Jiāsēn; Clawson, Anna N; Collins, Peter L; Dietzgen, Ralf G; Dolnik, Olga; Domier, Leslie L; Dürrwald, Ralf; Dye, John M; Easton, Andrew J; Ebihara, Hideki; Farkas, Szilvia L; Freitas-Astúa, Juliana; Formenty, Pierre; Fouchier, Ron A M; Fù, Yànpíng; Ghedin, Elodie; Goodin, Michael M; Hewson, Roger; Horie, Masayuki; Hyndman, Timothy H; Jiāng, Dàohóng; Kitajima, Elliot W; Kobinger, Gary P; Kondo, Hideki; Kurath, Gael; Lamb, Robert A; Lenardon, Sergio; Leroy, Eric M; Li, Ci-Xiu; Lin, Xian-Dan; Liú, Lìjiāng; Longdon, Ben; Marton, Szilvia; Maisner, Andrea; Mühlberger, Elke; Netesov, Sergey V; Nowotny, Norbert; Patterson, Jean L; Payne, Susan L; Paweska, Janusz T; Randall, Rick E; Rima, Bertus K; Rota, Paul; Rubbenstroth, Dennis; Schwemmle, Martin; Shi, Mang; Smither, Sophie J; Stenglein, Mark D; Stone, David M; Takada, Ayato; Terregino, Calogero; Tesh, Robert B; Tian, Jun-Hua; Tomonaga, Keizo; Tordo, Noël; Towner, Jonathan S; Vasilakis, Nikos; Verbeek, Martin; Volchkov, Viktor E; Wahl-Jensen, Victoria; Walsh, John A; Walker, Peter J; Wang, David; Wang, Lin-Fa; Wetzel, Thierry; Whitfield, Anna E; Xiè, Ji Tāo; Yuen, Kwok-Yung; Zhang, Yong-Zhen; Kuhn, Jens H

2016-08-01

In 2016, the order Mononegavirales was emended through the addition of two new families (Mymonaviridae and Sunviridae), the elevation of the paramyxoviral subfamily Pneumovirinae to family status (Pneumoviridae), the addition of five free-floating genera (Anphevirus, Arlivirus, Chengtivirus, Crustavirus, and Wastrivirus), and several other changes at the genus and species levels. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).

Taxonomy of the order Mononegavirales: update 2016

USGS Publications Warehouse

Afonso, C.L.; Kurath, Gael; 82 Additional Authors,

2016-01-01

In 2016, the order Mononegavirales was emended through the addition of two new families (Mymonaviridae and Sunviridae), the elevation of the paramyxoviral subfamily Pneumovirinae to family status (Pneumoviridae), the addition of five free-floating genera (Anphevirus, Arlivirus, Chengtivirus, Crustavirus, and Wastrivirus), and several other changes at the genus and species levels. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).

Taxonomy of the order Mononegavirales: update 2016

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

Afonso, Claudio L.; Amarasinghe, Gaya K.; Bányai, Krisztián

2016-05-23

In 2016, the order Mononegavirales was emended through the addition of two new families (Mymonaviridae and Sunviridae), the elevation of the paramyxoviral subfamily Pneumovirinae to family status (Pneumoviridae), the addition of five free-floating genera (Anphevirus, Arlivirus, Chengtivirus, Crustavirus, and Wastrivirus), and several other changes at the genus and species levels. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).

TAXONOMY OF THE ORDER MONONEGAVIRALES: UPDATE 2016

PubMed Central

Afonso, Claudio L.; Amarasinghe, Gaya K.; Bányai, Krisztián; Bào, Yīmíng; Basler, Christopher F.; Bavari, Sina; Bejerman, Nicolás; Blasdell, Kim R.; Briand, François-Xavier; Briese, Thomas; Bukreyev, Alexander; Calisher, Charles H.; Chandran, Kartik; Chéng, Jiāsēn; Clawson, Anna N.; Collins, Peter L.; Dietzgen, Ralf G.; Dolnik, Olga; Domier, Leslie L.; Dürrwald, Ralf; Dye, John M.; Easton, Andrew J.; Ebihara, Hideki; Farkas, Szilvia L.; Freitas-Astúa, Juliana; Formenty, Pierre; Fouchier, Ron A. M.; Fù, Yànpíng; Ghedin, Elodie; Goodin, Michael M.; Hewson, Roger; Horie, Masayuki; Hyndman, Timothy H.; Jiāng, Dàohóng; Kitajima, Elliot W.; Kobinger, Gary P.; Kondo, Hideki; Kurath, Gael; Lamb, Robert A.; Lenardon, Sergio; Leroy, Eric M.; Li, Ci-Xiu; Lin, Xian-Dan; Liú, Lìjiāng; Longdon, Ben; Marton, Szilvia; Maisner, Andrea; Mühlberger, Elke; Netesov, Sergey V.; Nowotny, Norbert; Patterson, Jean L.; Payne, Susan L.; Paweska, Janusz T.; Randall, Rick E.; Rima, Bertus K.; Rota, Paul; Rubbenstroth, Dennis; Schwemmle, Martin; Shi, Mang; Smither, Sophie J.; Stenglein, Mark D.; Stone, David M.; Takada, Ayato; Terregino, Calogero; Tesh, Robert B.; Tian, Jun-Hua; Tomonaga, Keizo; Tordo, Noël; Towner, Jonathan S.; Vasilakis, Nikos; Verbeek, Martin; Volchkov, Viktor E.; Wahl-Jensen, Victoria; Walsh, John A.; Walker, Peter J.; Wang, David; Wang, Lin-Fa; Wetzel, Thierry; Whitfield, Anna E.; Xiè, Jiǎtāo; Yuen, Kwok-Yung; Zhang, Yong-Zhen; Kuhn, Jens H.

2016-01-01

In 2016, the order Mononegavirales was emended through the addition of two new families (Mymonaviridae and Sunviridae), the elevation of the paramyxoviral subfamily Pneumovirinae to family status (Pneumoviridae), the addition of five free-floating genera (Anphevirus, Arlivirus, Chengtivirus, Crustavirus, and Wastrivirus), and several other changes at the genus and species levels. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV). PMID:27216929

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

ERIC Educational Resources Information Center

Snyder, Lester M., Jr.

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

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.

Fourier-Transform Raman Spectroscopy Of Biological Assemblies

NASA Astrophysics Data System (ADS)

Levin, Ira W.; Lewis, E. Neil

1989-12-01

Although the successful coupling of Raman scattered near-infrared radiation to a Michelson interferometer has recently created an outburst of intense interest in Fourier-transform (FT) Raman spectrometry," extended applications of the technique to macromolecular assemblies of biochemical and biophysical relevance have not progressed as rapidly as studies directed primarily at more conventional chemical characterizations. Since biological materials sampled with visible laser excitation sources typically emit a dominant fluorescence signal originating either from the intrinsic fluorescence of the molecular scatterer or from unrelenting contaminants, the use of near-infrared Nd:YAG laser excitation offers a convenient approach for avoiding this frequently overwhelming effect. In addition, the FT-Raman instrumentation provides a means of eliminating the deleterious resonance and decomposition effects often observed with the more accessible green and blue laser emissions. However, in choosing the incident near-infrared wavelength at, for example, 1064nm, the Raman scattered intensity decreases by factors of eighteen to forty from the Raman emissions induced by the shorter, visible excitations. Depending upon the experiment, this disadvantage is offset by the throughput and multiplex advantages afforded by the interferometric design. Thus, for most chemical systems, near-infrared FT-Raman spectroscopy, clearly provides a means for obtaining vibrational Raman spectra from samples intractable to the use of visible laser sources. In particular, for neat liquids, dilute solutions or polycrystalline materials, the ability to achieve high quality, reproducible spectra is, with moderate experience and perhaps relatively high laser powers, as straightforward as the conventional methods used to obtain Raman spectra with visible excitation and dispersive monochromators. In using near-infrared FT techniques to determine the Raman spectra of biological samples, one encounters new

Sub-micrometer-scale mapping of magnetite crystals and sulfur globules in magnetotactic bacteria using confocal Raman micro-spectrometry.

PubMed

Eder, Stephan H K; Gigler, Alexander M; Hanzlik, Marianne; Winklhofer, Michael

2014-01-01

The ferrimagnetic mineral magnetite Fe3O4 is biomineralized by magnetotactic microorganisms and a diverse range of animals. Here we demonstrate that confocal Raman microscopy can be used to visualize chains of magnetite crystals in magnetotactic bacteria, even though magnetite is a poor Raman scatterer and in bacteria occurs in typical grain sizes of only 35-120 nm, well below the diffraction-limited optical resolution. When using long integration times together with low laser power (<0.25 mW) to prevent laser induced damage of magnetite, we can identify and map magnetite by its characteristic Raman spectrum (303, 535, 665 cm(-1)) against a large autofluorescence background in our natural magnetotactic bacteria samples. While greigite (cubic Fe3S4; Raman lines of 253 and 351 cm(-1)) is often found in the Deltaproteobacteria class, it is not present in our samples. In intracellular sulfur globules of Candidatus Magnetobacterium bavaricum (Nitrospirae), we identified the sole presence of cyclo-octasulfur (S8: 151, 219, 467 cm(-1)), using green (532 nm), red (638 nm) and near-infrared excitation (785 nm). The Raman-spectra of phosphorous-rich intracellular accumulations point to orthophosphate in magnetic vibrios and to polyphosphate in magnetic cocci. Under green excitation, the cell envelopes are dominated by the resonant Raman lines of the heme cofactor of the b or c-type cytochrome, which can be used as a strong marker for label-free live-cell imaging of bacterial cytoplasmic membranes, as well as an indicator for the redox state.

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.

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.

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.

Recent taxonomy changes and their impact on biocontrol agents

USDA-ARS?s Scientific Manuscript database

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

An Analytical Overview of Spirituality in NANDA-I Taxonomies.

PubMed

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

2017-03-01

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

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.

Future of phytonematode taxonomy

USDA-ARS?s Scientific Manuscript database

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

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

Numerical taxonomy on data: Experimental results

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

Cohen, J.; Farach, M.

1997-12-01

The numerical taxonomy problems associated with most of the optimization criteria described above are NP - hard [3, 5, 1, 4]. In, the first positive result for numerical taxonomy was presented. They showed that if e is the distance to the closest tree metric under the L{sub {infinity}} norm. i.e., e = min{sub T} [L{sub {infinity}} (T-D)], then it is possible to construct a tree T such that L{sub {infinity}} (T-D) {le} 3e, that is, they gave a 3-approximation algorithm for this problem. We will refer to this algorithm as the Single Pivot (SP) heuristic.

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

PubMed

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

2014-02-01

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

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

ERIC Educational Resources Information Center

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

2009-01-01

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

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

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

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

2014-12-23

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

A Taxonomy of Functions of Dental X-Ray Technologists.

ERIC Educational Resources Information Center

Doty, Charles R.; And Others

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

A taxonomy update for the family Polyomaviridae.

PubMed

Calvignac-Spencer, Sébastien; Feltkamp, Mariet C W; Daugherty, Matthew D; Moens, Ugo; Ramqvist, Torbjörn; Johne, Reimar; Ehlers, Bernhard

2016-06-01

Many distinct polyomaviruses infecting a variety of vertebrate hosts have recently been discovered, and their complete genome sequence could often be determined. To accommodate this fast-growing diversity, the International Committee on Taxonomy of Viruses (ICTV) Polyomaviridae Study Group designed a host- and sequence-based rationale for an updated taxonomy of the family Polyomaviridae. Applying this resulted in numerous recommendations of taxonomical revisions, which were accepted by the Executive Committee of the ICTV in December 2015. New criteria for definition and creation of polyomavirus species were established that were based on the observed distance between large T antigen coding sequences. Four genera (Alpha-, Beta, Gamma- and Deltapolyomavirus) were delineated that together include 73 species. Species naming was made as systematic as possible - most species names now consist of the binomial name of the host species followed by polyomavirus and a number reflecting the order of discovery. It is hoped that this important update of the family taxonomy will serve as a stable basis for future taxonomical developments.

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…

An exercise in rational taxonomy.

PubMed

Ho, M W

1990-11-07

The quest for a rational taxonomy of living forms began in the 17th century. Since the general acceptance of Darwin's theory of descent with modification, however, students of morphology became preoccupied with a systematics based on the genealogy of groups; and the rise of molecular phylogenies in recent years results in a further decline in the science of morphology. Reconstructing phylogenies by itself brings us no closer to the goal of rational taxonomy, which is to uncover the natural order inherent in the forms of living things. It is proposed that the rational taxonomy of forms should be derived from a study of development, much as von Baer had envisaged. To illustrate the method, a set of segmentation abnormalities in Drosophila larvae (previously exposed to either vapour) is considered, which can be individually classified as distinct disturbances in the process responsible for establishing normal segmental pattern. The process consists of a hierarchy of four successive bifurcations dividing the embryo's body first into two parts, then four, eight, and finally 16 subdivisions or segments. This gives rise to a taxonomic map of all possible transformations which contains the "phylogeny" of the actual forms and provides a natural system for classifying them. Attempts to recover the "true" phylogeny by various numerical methods are summarized and their implications for the validity of the basic assumptions of contemporary systematics discussed.

Molecular taxonomy and phylogeny

USDA-ARS?s Scientific Manuscript database

The cyst nematodes comprise a group of sedentary endoparasitic nematodes that impact a wide range of crops in both tropical and temperate regions of the world. This chapter updates the taxonomy and phylogeny of this group and describes the nuclear protein coding, ribosomal, and mitochondrial sequenc...

Let's rise up to unite taxonomy and technology.

PubMed

Bik, Holly M

2017-08-01

What do you think of when you think of taxonomy? An 18th century gentlemen in breeches? Or perhaps botany drawings hung on the walls of a boutique hotel? Such old-fashioned conceptions to the contrary, taxonomy is alive today although constantly struggling for survival and recognition. The scientific community is losing valuable resources as taxonomy experts age and retire, and funding for morphological studies and species descriptions remains stagnant. At the same time, organismal knowledge (morphology, ecology, physiology) has never been more important: genomic studies are becoming more taxon focused, the scientific community is recognizing the limitations of traditional "model" organisms, and taxonomic expertise is desperately needed to fight against global biodiversity declines resulting from human impacts. There has never been a better time for a taxonomic renaissance.

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

Determination of glucose and ethanol after enzymatic hydrolysis and fermentation of biomass using Raman spectroscopy.

PubMed

Shih, Chien-Ju; Smith, Emily A

2009-10-27

Raman spectroscopy has been used for the quantitative determination of the conversion efficiency at each step in the production of ethanol from biomass. The method requires little sample preparation; therefore, it is suitable for screening large numbers of biomass samples and reaction conditions in a complex sample matrix. Dilute acid or ammonia-pretreated corn stover was used as a model biomass for these studies. Ammonia pretreatment was suitable for subsequent measurements with Raman spectroscopy, but dilute acid-pretreated corn stover generated a large background signal that surpassed the Raman signal. The background signal is attributed to lignin, which remains in the plant tissue after dilute acid pretreatment. A commercial enzyme mixture was used for the enzymatic hydrolysis of corn stover, and glucose levels were measured with a dispersive 785 nm Raman spectrometer. The glucose detection limit in hydrolysis liquor by Raman spectroscopy was 8 g L(-1). The mean hydrolysis efficiency for three replicate measurements obtained with Raman spectroscopy (86+/-4%) was compared to the result obtained using an enzymatic reaction with UV-vis spectrophotometry detection (78+/-8%). The results indicate good accuracy, as determined using a Student's t-test, and better precision for the Raman spectroscopy measurement relative to the enzymatic detection assay. The detection of glucose in hydrolysis broth by Raman spectroscopy showed no spectral interference, provided the sample was filtered to remove insoluble cellulose prior to analysis. The hydrolysate was further subjected to fermentation to yield ethanol. The detection limit for ethanol in fermentation broth by Raman spectroscopy was found to be 6 g L(-1). Comparison of the fermentation efficiencies measured by Raman spectroscopy (80+/-10%) and gas chromatography-mass spectrometry (87+/-9%) were statistically the same. The work demonstrates the utility of Raman spectroscopy for screening the entire conversion process to

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

PubMed

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

2017-07-01

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

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

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

Taxonomy of the order Mononegavirales: update 2017.

PubMed

Amarasinghe, Gaya K; Bào, Yīmíng; Basler, Christopher F; Bavari, Sina; Beer, Martin; Bejerman, Nicolás; Blasdell, Kim R; Bochnowski, Alisa; Briese, Thomas; Bukreyev, Alexander; Calisher, Charles H; Chandran, Kartik; Collins, Peter L; Dietzgen, Ralf G; Dolnik, Olga; Dürrwald, Ralf; Dye, John M; Easton, Andrew J; Ebihara, Hideki; Fang, Qi; Formenty, Pierre; Fouchier, Ron A M; Ghedin, Elodie; Harding, Robert M; Hewson, Roger; Higgins, Colleen M; Hong, Jian; Horie, Masayuki; James, Anthony P; Jiāng, Dàohóng; Kobinger, Gary P; Kondo, Hideki; Kurath, Gael; Lamb, Robert A; Lee, Benhur; Leroy, Eric M; Li, Ming; Maisner, Andrea; Mühlberger, Elke; Netesov, Sergey V; Nowotny, Norbert; Patterson, Jean L; Payne, Susan L; Paweska, Janusz T; Pearson, Michael N; Randall, Rick E; Revill, Peter A; Rima, Bertus K; Rota, Paul; Rubbenstroth, Dennis; Schwemmle, Martin; Smither, Sophie J; Song, Qisheng; Stone, David M; Takada, Ayato; Terregino, Calogero; Tesh, Robert B; Tomonaga, Keizo; Tordo, Noël; Towner, Jonathan S; Vasilakis, Nikos; Volchkov, Viktor E; Wahl-Jensen, Victoria; Walker, Peter J; Wang, Beibei; Wang, David; Wang, Fei; Wang, Lin-Fa; Werren, John H; Whitfield, Anna E; Yan, Zhichao; Ye, Gongyin; Kuhn, Jens H

2017-08-01

In 2017, the order Mononegavirales was expanded by the inclusion of a total of 69 novel species. Five new rhabdovirus genera and one new nyamivirus genus were established to harbor 41 of these species, whereas the remaining new species were assigned to already established genera. Furthermore, non-Latinized binomial species names replaced all paramyxovirus and pneumovirus species names, thereby accomplishing application of binomial species names throughout the entire order. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).

Type material in the NCBI Taxonomy Database

PubMed Central

Federhen, Scott

2015-01-01

Type material is the taxonomic device that ties formal names to the physical specimens that serve as exemplars for the species. For the prokaryotes these are strains submitted to the culture collections; for the eukaryotes they are specimens submitted to museums or herbaria. The NCBI Taxonomy Database (http://www.ncbi.nlm.nih.gov/taxonomy) now includes annotation of type material that we use to flag sequences from type in GenBank and in Genomes. This has important implications for many NCBI resources, some of which are outlined below. PMID:25398905

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).

Asteroid taxonomy

NASA Technical Reports Server (NTRS)

Tholen, David J.; Barucci, M. Antonietta

1989-01-01

The spectral reflectivity of asteroid surfaces over the wavelength range of 0.3 to 1.1 micron can be used to classify these objects into several broad groups with similar spectral characteristics. The three most recently developed taxonomies group the asteroids into 9, 11, or 14 different clases, depending on the technique used to perform the analysis. The distribution of the taxonomic classes shows that darker and redder objects become more dominant at larger heliocentric distances, while the rare asteroid types are found more frequently among the small objects of the planet-crossing population.

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.

Raman spectroscopy

USDA-ARS?s Scientific Manuscript database

Raman spectroscopy has gained increased use and importance in recent years for accurate and precise detection of physical and chemical properties of food materials, due to the greater specificity and sensitivity of Raman techniques over other analytical techniques. This book chapter presents Raman s...

A philosophical taxonomy of ethically significant moral distress.

PubMed

Thomas, Tessy A; McCullough, Laurence B

2015-02-01

Moral distress is one of the core topics of clinical ethics. Although there is a large and growing empirical literature on the psychological aspects of moral distress, scholars, and empirical investigators of moral distress have recently called for greater conceptual clarity. To meet this recognized need, we provide a philosophical taxonomy of the categories of what we call ethically significant moral distress: the judgment that one is not able, to differing degrees, to act on one's moral knowledge about what one ought to do. We begin by unpacking the philosophical components of Andrew Jameton's original formulation from his landmark 1984 work and identify two key respects in which that formulation remains unclear: the origins of moral knowledge and impediments to acting on that moral knowledge. We then selectively review subsequent literature that shows that there is more than one concept of moral distress and that explores the origin of the values implicated in moral distress and impediments to acting on those values. This review sets the stage for identifying the elements of a philosophical taxonomy of ethically significant moral distress. The taxonomy uses these elements to create six categories of ethically significant moral distress: challenges to, threats to, and violations of professional integrity; and challenges to, threats to, and violations of individual integrity. We close with suggestions about how the proposed philosophical taxonomy of ethically significant moral distress sheds light on the concepts of moral residue and crescendo effect of moral distress and how the proposed taxonomy might usefully guide prevention of and future qualitative and quantitative empirical research on ethically significant moral distress. © The Author 2014. Published by Oxford University Press, on behalf of the Journal of Medicine and Philosophy Inc. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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.

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

ERIC Educational Resources Information Center

Kyllonen, Patrick C.; Shute, Valerie J.

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

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

PubMed

Cook, Sarah; Parrott, Dominic

2009-01-01

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

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

PubMed

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

2017-08-01

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

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

PubMed

Gibbs, Adrian J

2013-08-09

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

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

NASA Astrophysics Data System (ADS)

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

2016-06-01

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

Instruments and Taxonomy of Workplace Bullying in Health Care Organizations.

PubMed

Park, Eun-Jun; Lee, Mikyoung; Park, Myungsook

2017-12-01

This study was aimed to evaluate the methodological issues and comprehensiveness of workplace bullying instruments and to suggest a taxonomy of psychological abuse. Nineteen instruments applied in health care organizations and 469 questionnaire items mainly regarding psychological abuse were collected through a literature review. Three researchers classified the questionnaire items according to a "taxonomy of psychological abuse in the workplace." Many instruments of workplace bullying were developed in the 2000s using a reflective measurement model, but their psychometric property was not sufficient and the measurement model is questioned. Based on the questionnaire items, the "taxonomy of psychological abuse in the workplace" was modified by adding two new subcategories (unachievable work and unfair treatment) and clarifying some operational definitions. According to the modified taxonomy of 11 (sub)categories, the reviewed instruments assessed 6.5 (sub)categories on average. No instrument measured all (sub)categories. Category 4.2 (disrespect, humiliation, and rejection of the person) was measured in all instruments, followed by Categories 5 (professional discredit and denigration) and 1.2 (social isolation) behaviors. The current instruments are not comprehensive enough. It is suggested that the modified taxonomy is verified and guide more reliable and inclusive instruments in the future. Furthermore, a formative measurement model, which defines a bullying as an inventory of different types of behaviors, should be used. Copyright © 2017. Published by Elsevier B.V.

Plant Taxonomy as a Field Study

ERIC Educational Resources Information Center

Dalby, D. H.

1970-01-01

Suggests methods of teaching plant identification and taxonomic theory using keys, statistical analyses, and biometrics. Population variation, genotype- environment interaction and experimental taxonomy are used in laboratory and field. (AL)

Let’s rise up to unite taxonomy and technology

PubMed Central

2017-01-01

What do you think of when you think of taxonomy? An 18th century gentlemen in breeches? Or perhaps botany drawings hung on the walls of a boutique hotel? Such old-fashioned conceptions to the contrary, taxonomy is alive today although constantly struggling for survival and recognition. The scientific community is losing valuable resources as taxonomy experts age and retire, and funding for morphological studies and species descriptions remains stagnant. At the same time, organismal knowledge (morphology, ecology, physiology) has never been more important: genomic studies are becoming more taxon focused, the scientific community is recognizing the limitations of traditional “model” organisms, and taxonomic expertise is desperately needed to fight against global biodiversity declines resulting from human impacts. There has never been a better time for a taxonomic renaissance. PMID:28820884

Manifest Variable Granger Causality Models for Developmental Research: A Taxonomy

ERIC Educational Resources Information Center

von Eye, Alexander; Wiedermann, Wolfgang

2015-01-01

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

FT-Raman Spectroscopy: A Catalyst for the Raman Explosion?

ERIC Educational Resources Information Center

Chase, Bruce

2007-01-01

The limitations of Fourier transform (FT) Raman spectroscopy, which is used to detect and analyze the scattered radiation, are discussed. FT-Raman has served to revitalize a field that was lagging and the presence of Raman instrumentation as a routine analytical tool is established for the foreseeable future.

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)

Scanning angle Raman spectroscopy: Investigation of Raman scatter enhancement techniques for chemical analysis

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

Meyer, Matthew W.

2013-01-01

This thesis outlines advancements in Raman scatter enhancement techniques by applying evanescent fields, standing-waves (waveguides) and surface enhancements to increase the generated mean square electric field, which is directly related to the intensity of Raman scattering. These techniques are accomplished by employing scanning angle Raman spectroscopy and surface enhanced Raman spectroscopy. A 1064 nm multichannel Raman spectrometer is discussed for chemical analysis of lignin. Extending dispersive multichannel Raman spectroscopy to 1064 nm reduces the fluorescence interference that can mask the weaker Raman scattering. Overall, these techniques help address the major obstacles in Raman spectroscopy for chemical analysis, which include themore » inherently weak Raman cross section and susceptibility to fluorescence interference.« less

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

ERIC Educational Resources Information Center

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

2017-01-01

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

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.

Reforming the taxonomy in disorders of consciousness.

PubMed

Bayne, Tim; Hohwy, Jakob; Owen, Adrian M

2017-12-01

This article examines the serious shortcomings that characterize the current taxonomy of postcomatose disorders of consciousness (DoC), and it provides guidelines for how an improved DoC taxonomy might be developed. In particular, it is argued that behavioral criteria for the application of DoC categories should be supplemented with brain-based criteria (eg, information derived from electroencephalography and functional magnetic resonance imaging), and that the categorical framework that currently characterizes DoC should be replaced by a multidimensional framework that better captures the performance of patients across a range of cognitive and behavioural tasks. Ann Neurol 2017;82:866-872. © 2017 American Neurological Association.

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.

Integrative taxonomy of the fly orchid group: insights from chemical ecology

NASA Astrophysics Data System (ADS)

Joffard, Nina; Buatois, Bruno; Schatz, Bertrand

2016-10-01

Several authors have recently stressed the need to develop an integrative approach in taxonomy, but studies applying such an approach to Mediterranean orchids are scarce. In sexually deceptive orchids from the taxonomically difficult genus Ophrys, pollination is specific and performed by male insects attracted to the flowers by sex pheromone-mimicking floral scents. Floral compounds are therefore of primary importance for reproductive isolation and species delimitations in this genus. In the fly orchid group, molecular, morphological, and ecological characters have been extensively studied, but a comprehensive survey of floral scents is still lacking. In the present study, the blends of floral compounds of its three members, Ophrys insectifera, Ophrys aymoninii, and Ophrys subinsectifera, were extracted and analyzed by gas chromatography-mass spectrometry. A total of 107 compounds were found, with a majority of saturated and unsaturated hydrocarbons. Significant differentiation, both qualitative and quantitative, was found among the three taxa. This result, pooled with those from the literature, forms a comprehensive and congruent dataset that allows us to elucidate the taxonomic rank of the three members of the fly orchid group.

Climbing Bloom's taxonomy pyramid: Lessons from a graduate histology course.

PubMed

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

2017-09-01

Bloom's taxonomy was adopted to create a subject-specific scoring tool for histology multiple-choice questions (MCQs). This Bloom's Taxonomy Histology Tool (BTHT) was used to analyze teacher- and student-generated quiz and examination questions from a graduate level histology course. Multiple-choice questions using histological images were generally assigned a higher BTHT level than simple text questions. The type of microscopy technique (light or electron microscopy) used for these image-based questions did not result in any significant differences in their Bloom's taxonomy scores. The BTHT levels for teacher-generated MCQs correlated positively with higher discrimination indices and inversely with the percent of students answering these questions correctly (difficulty index), suggesting that higher-level Bloom's taxonomy questions differentiate well between higher- and lower-performing students. When examining BTHT scores for MCQs that were written by students in a Multiple-Choice Item Development Assignment (MCIDA) there was no significant correlation between these scores and the students' ability to answer teacher-generated MCQs. This suggests that the ability to answer histology MCQs relies on a different skill set than the aptitude to construct higher-level Bloom's taxonomy questions. However, students significantly improved their average BTHT scores from the midterm to the final MCIDA task, which indicates that practice, experience and feedback increased their MCQ writing proficiency. Anat Sci Educ 10: 456-464. © 2017 American Association of Anatomists. © 2017 American Association of Anatomists.

Characterization of Air Plane Soot Surrogates using Raman spectroscopy and laser ablation techniques

NASA Astrophysics Data System (ADS)

Chazallon, Bertrand; Ortega, Ismael Kenneth; Ikhenazene, Raouf; Pirim, Claire; Carpentier, Yvain; Irimiea, Cornelia; Focsa, Cristian; Ouf, François-Xavier

2016-04-01

Aviation alters the composition of the atmosphere globally and can thus drive climate change and ozone depletion [1]. Aircraft exhaust plumes contain species (gases and soot particles) produced by the combustion of kerosene with ambient air in the combustion chamber of the engine. Soot particles emitted by air-planes produce persistent contrails in the upper troposphere in ice-supersaturated air masses that contribute to cloudiness and impact the radiative properties of the atmosphere. These aerosol-cloud interactions represent one of the largest sources of uncertainty in global climate models [2]. Though the formation of atmospheric ice particles has been studied for many years [3], there are still numerous opened questions on nucleation properties of soot particles [4], as the ice nucleation experiments showed a large spread in results depending on the nucleation mode chosen and origin of the soot produced. The reasons behind these discrepancies reside in the different physico-chemical properties (composition, structure) of soot particles produced in different conditions, e.g., with respect to fuel or combustion techniques. In this work, we use Raman microscopy (514 and 785 nm excitation wavelengths) and ablation techniques (Secondary Ions Mass Spectrometry, and Laser Desorption Mass Spectrometry) to characterize soot particle surrogates produced from a CAST generator (propane fuel, four different global equivalence ratios). They are produced as analogues of air-plane soot collected at different engine regimes (PowerJet SaM-146 turbofan) simulating a landing and take-off (LTO) cycle (MERMOSE project (http://mermose.onera.fr/)) [6]. The spectral parameters of the first-order Raman bands of these soot samples are analyzed using a de-convolution approach described by Sadezky et al. (2005) [5]. A systematic Raman analysis is carried out to select a number of parameters (laser wavelength, irradiance at sample, exposure time) that will alter the sample and the

EPA's Information Architecture and Web Taxonomy

EPA Pesticide Factsheets

EPA's Information Architecture creates a topical organization of our website, instead of an ownership-based organization. The EPA Web Taxonomy allows audiences easy access to relevant information from EPA programs, by using a common vocabulary.

NASA Taxonomies for Searching Problem Reports and FMEAs

NASA Technical Reports Server (NTRS)

Malin, Jane T.; Throop, David R.

2006-01-01

Many types of hazard and risk analyses are used during the life cycle of complex systems, including Failure Modes and Effects Analysis (FMEA), Hazard Analysis, Fault Tree and Event Tree Analysis, Probabilistic Risk Assessment, Reliability Analysis and analysis of Problem Reporting and Corrective Action (PRACA) databases. The success of these methods depends on the availability of input data and the analysts knowledge. Standard nomenclature can increase the reusability of hazard, risk and problem data. When nomenclature in the source texts is not standard, taxonomies with mapping words (sets of rough synonyms) can be combined with semantic search to identify items and tag them with metadata based on a rich standard nomenclature. Semantic search uses word meanings in the context of parsed phrases to find matches. The NASA taxonomies provide the word meanings. Spacecraft taxonomies and ontologies (generalization hierarchies with attributes and relationships, based on terms meanings) are being developed for types of subsystems, functions, entities, hazards and failures. The ontologies are broad and general, covering hardware, software and human systems. Semantic search of Space Station texts was used to validate and extend the taxonomies. The taxonomies have also been used to extract system connectivity (interaction) models and functions from requirements text. Now the Reconciler semantic search tool and the taxonomies are being applied to improve search in the Space Shuttle PRACA database, to discover recurring patterns of failure. Usual methods of string search and keyword search fall short because the entries are terse and have numerous shortcuts (irregular abbreviations, nonstandard acronyms, cryptic codes) and modifier words cannot be used in sentence context to refine the search. The limited and fixed FMEA categories associated with the entries do not make the fine distinctions needed in the search. The approach assigns PRACA report titles to problem classes in

Kerogen maturation and incipient graphitization of hydrocarbon source rocks in the Arkoma Basin, Oklahoma and Arkansas: A combined petrographic and Raman spectrometric study

USGS Publications Warehouse

Spotl, C.; Houseknecht, D.W.; Jaques, R.C.

1998-01-01

Dispersed kerogen of the Woodford-Chattanooga and Atoka Formations from the subsurface of the Arkoma Basin show a wide range of thermal maturities (0.38 to 6.1% R(o)) indicating thermal conditions ranging from diagenesis to incipient rock metamorphism. Raman spectral analysis reveals systematic changes of both the first- and second-order spectrum with increasing thermal maturity. These changes include a pronounced increase in the D/O peak height ratio accompanied by a narrowing of the D peak, a gradual decrease in the D/O peak width ratio, and a shift of both peaks toward higher wave numbers. Second-order Raman peaks, though less intensive, also show systematic peak shifting as a function of R(o). These empirical results underscore the high potential of Raman spectrometry as a fast and reliable geothermometer of mature to supermature hydrocarbon source rocks, and as an indicator of thermal maturity levels within the anchizone.Dispersed kerogen of the Woodford-Chattanooga and Atoka Formations from the subsurface of the Arkoma Basin show a wide range of thermal maturities (0.38 to 6.1% Ro) indicating thermal conditions ranging from diagenesis to incipient rock metamorphism. Raman spectral analysis reveals systematic changes of both the first- and second-order spectrum with increasing thermal maturity. These changes include a pronounced increase in the D/O peak height ratio accompanied by a narrowing of the D peak, a gradual decrease in the D/O peak width ratio, and a shift of both peaks toward higher wave numbers. Second-order Raman peaks, though less intensive, also show systematic peak shifting as a function of Ro. These empirical results underscore the high potential of Raman spectrometry as a fast and reliable geothermometer of mature to supermature hydrocarbon source rocks, and as an indicator of thermal maturity levels within the anchizone.

Software Vulnerability Taxonomy Consolidation

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

Polepeddi, Sriram S.

2004-12-07

In today's environment, computers and networks are increasing exposed to a number of software vulnerabilities. Information about these vulnerabilities is collected and disseminated via various large publicly available databases such as BugTraq, OSVDB and ICAT. Each of these databases, individually, do not cover all aspects of a vulnerability and lack a standard format among them, making it difficult for end-users to easily compare various vulnerabilities. A central database of vulnerabilities has not been available until today for a number of reasons, such as the non-uniform methods by which current vulnerability database providers receive information, disagreement over which features of amore » particular vulnerability are important and how best to present them, and the non-utility of the information presented in many databases. The goal of this software vulnerability taxonomy consolidation project is to address the need for a universally accepted vulnerability taxonomy that classifies vulnerabilities in an unambiguous manner. A consolidated vulnerability database (CVDB) was implemented that coalesces and organizes vulnerability data from disparate data sources. Based on the work done in this paper, there is strong evidence that a consolidated taxonomy encompassing and organizing all relevant data can be achieved. However, three primary obstacles remain: lack of referencing a common ''primary key'', un-structured and free-form descriptions of necessary vulnerability data, and lack of data on all aspects of a vulnerability. This work has only considered data that can be unambiguously extracted from various data sources by straightforward parsers. It is felt that even with the use of more advanced, information mining tools, which can wade through the sea of unstructured vulnerability data, this current integration methodology would still provide repeatable, unambiguous, and exhaustive results. Though the goal of coalescing all available data, which would be of use

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.

[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.

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

ERIC Educational Resources Information Center

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

2015-01-01

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

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

PubMed Central

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

2011-01-01

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

Expanding the taxonomy of the diagnostic criteria for temporomandibular disorders.

PubMed

Peck, C C; Goulet, J-P; Lobbezoo, F; Schiffman, E L; Alstergren, P; Anderson, G C; de Leeuw, R; Jensen, R; Michelotti, A; Ohrbach, R; Petersson, A; List, T

2014-01-01

There is a need to expand the current temporomandibular disorders' (TMDs) classification to include less common but clinically important disorders. The immediate aim was to develop a consensus-based classification system and associated diagnostic criteria that have clinical and research utility for less common TMDs. The long-term aim was to establish a foundation, vis-à-vis this classification system, that will stimulate data collection, validity testing and further criteria refinement. A working group [members of the International RDC/TMD Consortium Network of the International Association for Dental Research (IADR), members of the Orofacial Pain Special Interest Group (SIG) of the International Association for the Study of Pain (IASP), and members from other professional societies] reviewed disorders for inclusion based on clinical significance, the availability of plausible diagnostic criteria and the ability to operationalise and study the criteria. The disorders were derived from the literature when possible and based on expert opinion as necessary. The expanded TMDs taxonomy was presented for feedback at international meetings. Of 56 disorders considered, 37 were included in the expanded taxonomy and were placed into the following four categories: temporomandibular joint disorders, masticatory muscle disorders, headache disorders and disorders affecting associated structures. Those excluded were extremely uncommon, lacking operationalised diagnostic criteria, not clearly related to TMDs, or not sufficiently distinct from disorders already included within the taxonomy. The expanded TMDs taxonomy offers an integrated approach to clinical diagnosis and provides a framework for further research to operationalise and test the proposed taxonomy and diagnostic criteria. © 2014 John Wiley & Sons Ltd.

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).

Investigation of detection limits for solutes in water measured by laser raman spectrometry

USGS Publications Warehouse

Goldberg, M.C.

1977-01-01

The influence of experimental parameters on detection sensitivity was determined for laser Raman analysis of dissolved solutes in water. Individual solutions of nitrate, sulfate, carbonate, bicarbonate, monohydrogen phosphate, dihydrogen phosphate, acetate ion, and acetic acid were measured. An equation is derived which expresses the signal-to-noise ratio in terms of solute concentration, measurement time, spectral slit width, laser power fluctuations, and solvent background intensity. Laser beam intensity fluctuations at the sample and solvent background intensity are the most important limiting factors.

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

ERIC Educational Resources Information Center

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

2012-01-01

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

Biosignatures observed by Raman mapping in silicified materials

NASA Astrophysics Data System (ADS)

Foucher, F.; Westall, F.; Knoll, A.

2012-04-01

converts to quartz but, in this case where the rocks are very poorly metamorphosed, conversion seems to have been inhibited by the kerogen matrix within which the opal precipitated. Both anatase and pyrite may be formed abiogenically but their intimate association with the remnants of microorganisms suggests a link between the diagenesis of the dead organisms and the precipitation of these minerals. Interestingly, the Raman maps of the Draken microfossils also document differences in the D/G peak ratios within a particular microfossil structure. Thus, we demonstrate that mapping using micro-Raman spectrometry is a rapid method of investigation of potential biosignatures and an excellent complement to other methods of biosignature detection. Reference: [1] Knoll, A. H., Swett, K., and Mark, J., 1991, Journal of Paleontology 65, 531-569.

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...

Learning a Taxonomy of Predefined and Discovered Activity Patterns

PubMed Central

Krishnan, Narayanan; Cook, Diane J.; Wemlinger, Zachary

2013-01-01

Many intelligent systems that focus on the needs of a human require information about the activities that are being performed by the human. At the core of this capability is activity recognition. Activity recognition techniques have become robust but rarely scale to handle more than a few activities. They also rarely learn from more than one smart home data set because of inherent differences between labeling techniques. In this paper we investigate a data-driven approach to creating an activity taxonomy from sensor data found in disparate smart home datasets. We investigate how the resulting taxonomy can help analyze the relationship between classes of activities. We also analyze how the taxonomy can be used to scale activity recognition to a large number of activity classes and training datasets. We describe our approach and evaluate it on 34 smart home datasets. The results of the evaluation indicate that the hierarchical modeling can reduce training time while maintaining accuracy of the learned model. PMID:25302084

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.

Defect formation in MeV H+ implanted GaN and 4H-SiC investigated by cross-sectional Raman spectroscopy

NASA Astrophysics Data System (ADS)

Huang, Kai; Jia, Qi; You, Tiangui; Zhang, Shibin; Lin, Jiajie; Zhang, Runchun; Zhou, Min; Yu, Wenjie; Zhang, Bo; Ou, Xin; Wang, Xi

2017-09-01

Cross-sectional Raman spectroscopy is used to characterize the defect formation and the defect recovery in MeV H+ implanted bulk GaN and 4H-SiC in the high energy MeV ion-cut process. The Raman intensity decreases but the forbidden modes are activated at the damage region, and the intensity decrease is proportional to the damage level. The Raman spectrum is quite sensitive to detect the damage recovery after annealing. The main peak intensity increases and the forbidden mode disappears in both annealed GaN and 4H-SiC samples. The Raman spectra of GaN samples annealed at different temperatures suggest that higher annealing temperature is more efficient for damage recovery. While, the Raman spectra of SiC indicate that higher implantation temperature results in heavier lattice damage and other polytype clusters might be generated by high annealing temperature in the annealed SiC samples. The cross-sectional Raman spectroscopy is a straightforward method to characterize lattice damage and damage recovery in high energy ion-cut process. It can serve as a fast supplementary measurement technique to Rutherford backscattering spectrometry (RBS), nuclear reaction analysis (NRA) and transmission electron microscope (TEM) for the defect characterizations.

Abstraction of complex concepts with a refined partial-area taxonomy of SNOMED

PubMed Central

Wang, Yue; Halper, Michael; Wei, Duo; Perl, Yehoshua; Geller, James

2012-01-01

An algorithmically-derived abstraction network, called the partial-area taxonomy, for a SNOMED hierarchy has led to the identification of concepts considered complex. The designation “complex” is arrived at automatically on the basis of structural analyses of overlap among the constituent concept groups of the partial-area taxonomy. Such complex concepts, called overlapping concepts, constitute a tangled portion of a hierarchy and can be obstacles to users trying to gain an understanding of the hierarchy’s content. A new methodology for partitioning the entire collection of overlapping concepts into singly-rooted groups, that are more manageable to work with and comprehend, is presented. Different kinds of overlapping concepts with varying degrees of complexity are identified. This leads to an abstract model of the overlapping concepts called the disjoint partial-area taxonomy, which serves as a vehicle for enhanced, high-level display. The methodology is demonstrated with an application to SNOMED’s Specimen hierarchy. Overall, the resulting disjoint partial-area taxonomy offers a refined view of the hierarchy’s structural organization and conceptual content that can aid users, such as maintenance personnel, working with SNOMED. The utility of the disjoint partial-area taxonomy as the basis for a SNOMED auditing regimen is presented in a companion paper. PMID:21878396

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.

Application of Raman spectroscopy for direct analysis of Carlina acanthifolia subsp. utzka root essential oil.

PubMed

Strzemski, Maciej; Wójciak-Kosior, Magdalena; Sowa, Ireneusz; Agacka-Mołdoch, Monika; Drączkowski, Piotr; Matosiuk, Dariusz; Kurach, Łukasz; Kocjan, Ryszard; Dresler, Sławomir

2017-11-01

Carlina genus plants e.g. Carlina acanthifolia subsp. utzka have been still used in folk medicine of many European countries and its biological activity is mostly associated with root essential oils. In the present paper, Raman spectroscopy (RS) was applied for the first time for evaluation of essential oil distribution in root of C. acnthifolia subsp. utzka and identification of root structures containing the essential oil. Furthermore, RS technique was applied to assess chemical stability of oil during drying of plant material or distillation process. Gas chromatography-mass spectrometry was used for qualitative and quantitative analysis of the essential oil. The identity of compounds was confirmed using Raman, ATR-IR and NMR spectroscopy. Carlina oxide was found to be the main component of the oil (98.96% ± 0.15). The spectroscopic study showed the high stability of essential oil and Raman distribution analysis indicated that the oil reservoirs were localized mostly in the structures of outer layer of the root while the inner part showed nearly no signal assigned to the oil. Raman spectroscopy technique enabled rapid, non-destructive direct analysis of plant material with minimal sample preparation and allowed straightforward, unambiguous identification of the essential oil in the sample. Copyright © 2017. Published by Elsevier B.V.

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.

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

PubMed

Rodwell, John; Gulyas, Andre

2013-04-08

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

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

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.

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

PubMed

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

2012-03-01

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

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

PubMed

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

2010-09-01

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

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

PubMed Central

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

2012-01-01

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

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.

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.

Transmission Raman Measurements Using a Spatial Heterodyne Raman Spectrometer (SHRS).

PubMed

Strange, K Alicia; Paul, Kelly C; Angel, S Michael

2017-02-01

A spatial heterodyne Raman spectrometer (SHRS) was used to measure transmission Raman spectra of highly scattering compounds. Transmission Raman spectral intensities of ibuprofen were only 2.4 times lower in intensity than backscatter Raman spectra. The throughput was about eight times higher than an f/1.8 dispersive spectrometer, and the width of the area viewed was found to be seven to nine times higher, using 50.8 mm and 250 mm focal length collection lenses. However, the signal-to-noise (S/N) ratio was two times lower for the SHRS than the f/1.8 dispersive spectrometer, apparently due to high levels of stray light.

Quantitative analysis of essential oils of Thymus daenensis using laser-induced fluorescence and Raman spectroscopy.

PubMed

Khoshroo, H; Khadem, H; Bahreini, M; Tavassoli, S H; Hadian, J

2015-11-10

Laser-induced fluorescence and Raman spectroscopy are used for the investigation of different genotypes of Thymus daenensis native to the Ilam province of Iran. Different genotypes of T. daenensis essential oils, labeled T1 through T7, possess slight differences with regard to the composition of the thymol. The gas chromatography-mass spectrometry (GC-MS) method is performed to determine the concentration of each constituent as a reference method. The Raman spectra of different concentrations of pure thymol dissolved in hexane as standard samples are obtained via a laboratory prototype Raman spectroscopy setup for the calculation of the calibration curve. The regression coefficient and limit of detection are calculated. The possibility of the differentiation of different genotypes of T. daenensis is also examined by laser-induced fluorescence spectroscopy, although we do not know the exact amounts of their components. All the fluorescence spectral information is used jointly by cluster analysis to differentiate between 7 genotypes. Our results demonstrate the acceptable precision of Raman spectroscopy with GC-MS and corroborate the capacity of Raman spectroscopy in applications in the quantitative analysis field. Furthermore, the cluster analysis results show that laser-induced fluorescence spectroscopy is an acceptable technique for the rapid classification of different genotypes of T. daenensis without having any previous information of their exact amount of constituents. So, the ability to rapidly and nondestructively differentiate between genotypes makes it possible to efficiently select high-quality herbs from many samples.

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

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

ERIC Educational Resources Information Center

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

2017-01-01

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

A new taxonomy for stakeholder engagement in patient-centered outcomes research.

PubMed

Concannon, Thomas W; Meissner, Paul; Grunbaum, Jo Anne; McElwee, Newell; Guise, Jeanne-Marie; Santa, John; Conway, Patrick H; Daudelin, Denise; Morrato, Elaine H; Leslie, Laurel K

2012-08-01

Despite widespread agreement that stakeholder engagement is needed in patient-centered outcomes research (PCOR), no taxonomy exists to guide researchers and policy makers on how to address this need. We followed an iterative process, including several stages of stakeholder review, to address three questions: (1) Who are the stakeholders in PCOR? (2) What roles and responsibilities can stakeholders have in PCOR? (3) How can researchers start engaging stakeholders? We introduce a flexible taxonomy called the 7Ps of Stakeholder Engagement and Six Stages of Research for identifying stakeholders and developing engagement strategies across the full spectrum of research activities. The path toward engagement will not be uniform across every research program, but this taxonomy offers a common starting point and a flexible approach.

The Bootstrap, the Jackknife, and the Randomization Test: A Sampling Taxonomy.

PubMed

Rodgers, J L

1999-10-01

A simple sampling taxonomy is defined that shows the differences between and relationships among the bootstrap, the jackknife, and the randomization test. Each method has as its goal the creation of an empirical sampling distribution that can be used to test statistical hypotheses, estimate standard errors, and/or create confidence intervals. Distinctions between the methods can be made based on the sampling approach (with replacement versus without replacement) and the sample size (replacing the whole original sample versus replacing a subset of the original sample). The taxonomy is useful for teaching the goals and purposes of resampling schemes. An extension of the taxonomy implies other possible resampling approaches that have not previously been considered. Univariate and multivariate examples are presented.

Quantitative measurement of carbon isotopic composition in CO2 gas reservoir by Micro-Laser Raman spectroscopy

NASA Astrophysics Data System (ADS)

Li, Jiajia; Li, Rongxi; Zhao, Bangsheng; Guo, Hui; Zhang, Shuan; Cheng, Jinghua; Wu, Xiaoli

2018-04-01

The use of Micro-Laser Raman spectroscopy technology for quantitatively determining gas carbon isotope composition is presented. In this study, 12CO2 and 13CO2 were mixed with N2 at various molar fraction ratios to obtain Raman quantification factors (F12CO2 and F13CO2), which provide a theoretical basis for calculating the δ13C value. And the corresponding values were 0.523 (0 < C12CO2/CN2 < 2) and 1.11998 (0 < C13CO2/CN2 < 1.5) respectively. It has shown that the representative Raman peak area can be used for the determination of δ13C values within the relative errors range of 0.076% to 1.154% in 13CO2/12CO2 binary mixtures when F12CO2/F13CO2 is 0.466972625. In addition, measurement of δ13C values by Micro-Laser Raman analysis were carried out on natural CO2 gas from Shengli Oil-field at room temperature under different pressures. The δ13C values obtained by Micro-Laser Raman spectroscopy technology and Isotope Ratio Mass Spectrometry (IRMS) technology are in good agreement with each other, and the relative errors range of δ13C values is 1.232%-6.964%. This research provides a fundamental analysis tool for determining gas carbon isotope composition (δ13C values) quantitatively by using Micro-Laser Raman spectroscopy. Experiment of results demonstrates that this method has the potential for obtaining δ13C values in natural CO2 gas reservoirs.

Genomic taxonomy of vibrios

PubMed Central

Thompson, Cristiane C; Vicente, Ana Carolina P; Souza, Rangel C; Vasconcelos, Ana Tereza R; Vesth, Tammi; Alves, Nelson; Ussery, David W; Iida, Tetsuya; Thompson, Fabiano L

2009-01-01

Background Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera) from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA), supertrees, Average Amino Acid Identity (AAI), genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios. Results We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.). A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, ≤ 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree. Conclusion The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in the birth of the online

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

PubMed

Holmqvist, Kajsa Lidström; Holmefur, Marie

2018-05-03

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

A knowledge network for a dynamic taxonomy of psychiatric disease.

PubMed

Krishnan, Ranga R

2015-03-01

Current taxonomic approaches in medicine and psychiatry are limited in validity and utility. They do serve simple communication purposes for medical coding, teaching, and reimbursement, but they are not suited for the modern era with its rapid explosion of knowledge from the "omics" revolution. The National Academy of Sciences published a report entitled Toward Precision Medicine: Building a Knowledge Network for Biomedical Research and a New Taxonomy of Disease. The authors advocate a new taxonomy that would integrate molecular data, clinical data, and health outcomes in a dynamic, iterative fashion, bringing together research, public health, and health-care delivery with the interlinked goals of advancing our understanding of disease pathogenesis and thereby improving health. As the need for an information hub and a knowledge network with a dynamic taxonomy based on integration of clinical and research data is vital, and timely, this proposal merits consideration.

Molecular Taxonomy of Phytopathogenic Fungi: A Case Study in Peronospora

PubMed Central

Göker, Markus; García-Blázquez, Gema; Voglmayr, Hermann; Tellería, M. Teresa; Martín, María P.

2009-01-01

Background Inappropriate taxon definitions may have severe consequences in many areas. For instance, biologically sensible species delimitation of plant pathogens is crucial for measures such as plant protection or biological control and for comparative studies involving model organisms. However, delimiting species is challenging in the case of organisms for which often only molecular data are available, such as prokaryotes, fungi, and many unicellular eukaryotes. Even in the case of organisms with well-established morphological characteristics, molecular taxonomy is often necessary to emend current taxonomic concepts and to analyze DNA sequences directly sampled from the environment. Typically, for this purpose clustering approaches to delineate molecular operational taxonomic units have been applied using arbitrary choices regarding the distance threshold values, and the clustering algorithms. Methodology Here, we report on a clustering optimization method to establish a molecular taxonomy of Peronospora based on ITS nrDNA sequences. Peronospora is the largest genus within the downy mildews, which are obligate parasites of higher plants, and includes various economically important pathogens. The method determines the distance function and clustering setting that result in an optimal agreement with selected reference data. Optimization was based on both taxonomy-based and host-based reference information, yielding the same outcome. Resampling and permutation methods indicate that the method is robust regarding taxon sampling and errors in the reference data. Tests with newly obtained ITS sequences demonstrate the use of the re-classified dataset in molecular identification of downy mildews. Conclusions A corrected taxonomy is provided for all Peronospora ITS sequences contained in public databases. Clustering optimization appears to be broadly applicable in automated, sequence-based taxonomy. The method connects traditional and modern taxonomic disciplines by

Molecular taxonomy of phytopathogenic fungi: a case study in Peronospora.

PubMed

Göker, Markus; García-Blázquez, Gema; Voglmayr, Hermann; Tellería, M Teresa; Martín, María P

2009-07-29

Inappropriate taxon definitions may have severe consequences in many areas. For instance, biologically sensible species delimitation of plant pathogens is crucial for measures such as plant protection or biological control and for comparative studies involving model organisms. However, delimiting species is challenging in the case of organisms for which often only molecular data are available, such as prokaryotes, fungi, and many unicellular eukaryotes. Even in the case of organisms with well-established morphological characteristics, molecular taxonomy is often necessary to emend current taxonomic concepts and to analyze DNA sequences directly sampled from the environment. Typically, for this purpose clustering approaches to delineate molecular operational taxonomic units have been applied using arbitrary choices regarding the distance threshold values, and the clustering algorithms. Here, we report on a clustering optimization method to establish a molecular taxonomy of Peronospora based on ITS nrDNA sequences. Peronospora is the largest genus within the downy mildews, which are obligate parasites of higher plants, and includes various economically important pathogens. The method determines the distance function and clustering setting that result in an optimal agreement with selected reference data. Optimization was based on both taxonomy-based and host-based reference information, yielding the same outcome. Resampling and permutation methods indicate that the method is robust regarding taxon sampling and errors in the reference data. Tests with newly obtained ITS sequences demonstrate the use of the re-classified dataset in molecular identification of downy mildews. A corrected taxonomy is provided for all Peronospora ITS sequences contained in public databases. Clustering optimization appears to be broadly applicable in automated, sequence-based taxonomy. The method connects traditional and modern taxonomic disciplines by specifically addressing the issue of

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

PubMed

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

2013-06-01

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

Towards 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.

Raman spectroscopy and Raman imaging for early detection of cancer

NASA Astrophysics Data System (ADS)

Joshi, Narahari V.; Ortega, Angel; Estrela, Jose Maria

2004-06-01

Raman spectroscopy is a powerful technique as it provides fundamental information about vibrational modes of a system. Eigenvalues of these modes are very sensitive to the strength of the chemical bonds and perturbations caused by the environment, particularly charge distribution and alterations in the dipole strength of the system. All these parameters are profoundly modified during the tumor formation process nad hence Raman technique could be a unique and also a direct approach for evaluating tumor genesis at early stages. for this pupose the present investigation was carried out. We used cultured wild type and c-ras transformed NIH 3T3 fibroblast. The samples were treated with methyl alcohol solution ina conventional manner and then Raman spectra nad images were obtained by a specially developed confocal Raman microscope. The present results reveal differences between both cell types in the spectral details as well as in the morphology. Raman images are able to detect the exact site where cancer-related changes have taken place. These results clearly indicate the superiority of the present technique over conventional methods such as images obtained by X-rays or Nuclear Magnetic Resonance (NMR). Moreover, unlike other approaches, Raman images detect alterations at the submicron level rather than in the centimeter or millimeter range. Being an optical method it can be applied in vivo as a non-invasive technique potentially useful to early detection of cancer (particularly easy accessible cancers such as those of the skin and the digestive tract). The obtained resulsts suggest the great potential of Raman imaging in premature clinical diagnostic approaches.

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

Developing Integrated Taxonomies for a Tiered Information Architecture

NASA Technical Reports Server (NTRS)

Dutra, Jayne E.

2006-01-01

This viewgraph presentation reviews the concept of developing taxonomies for an information architecture. In order to assist people in accessing information required to access information and retrieval, including cross repository searching, a system of nested taxonomies is being developed. Another facet of this developmental project is collecting and documenting attributes about people, to allow for several uses: access management, i.e., who are you and what can you see?; targeted content delivery i.e., what content helps you get your work done?; w ork force planning i.e., what skill sets do you have that we can appl y to work?; and IT Services i.e., How can we provision you with the proper IT services?

Surface-enhanced Raman scattering of amorphous silica gel adsorbed on gold substrates for optical fiber sensors

NASA Astrophysics Data System (ADS)

Degioanni, S.; Jurdyc, A. M.; Cheap, A.; Champagnon, B.; Bessueille, F.; Coulm, J.; Bois, L.; Vouagner, D.

2015-10-01

Two kinds of gold substrates are used to produce surface-enhanced Raman scattering (SERS) of amorphous silica obtained via the sol-gel route using tetraethoxysilane Si(OC2H5)4 (TEOS) solution. The first substrate consists of a gold nanometric film elaborated on a glass slide by sputter deposition, controlling the desired gold thickness and sputtering current intensity. The second substrate consists of an array of micrometer-sized gold inverted pyramidal pits able to confine surface plasmon (SP) enhancing electric field, which results in a distribution of electromagnetic energy inside the cavities. These substrates are optically characterized to observe SPR with, respectively, extinction and reflectance spectrometries. Once coated with thin layers of amorphous silica (SiO2) gel, these samples show Raman amplification of amorphous SiO2 bands. This enhancement can occur in SERS sensors using amorphous SiO2 gel as shells, spacers, protective coatings, or waveguides, and represents particularly a potential interest in the field of Raman distributed sensors, which use the amorphous SiO2 core of optical fibers as a transducer to make temperature measurements.

Scientific Teaching: Defining a Taxonomy of Observable Practices

PubMed Central

Couch, Brian A.; Brown, Tanya L.; Schelpat, Tyler J.; Graham, Mark J.; Knight, Jennifer K.

2015-01-01

Over the past several decades, numerous reports have been published advocating for changes to undergraduate science education. These national calls inspired the formation of the National Academies Summer Institutes on Undergraduate Education in Biology (SI), a group of regional workshops to help faculty members learn and implement interactive teaching methods. The SI curriculum promotes a pedagogical framework called Scientific Teaching (ST), which aims to bring the vitality of modern research into the classroom by engaging students in the scientific discovery process and using student data to inform the ongoing development of teaching methods. With the spread of ST, the need emerges to systematically define its components in order to establish a common description for education researchers and practitioners. We describe the development of a taxonomy detailing ST’s core elements and provide data from classroom observations and faculty surveys in support of its applicability within undergraduate science courses. The final taxonomy consists of 15 pedagogical goals and 37 supporting practices, specifying observable behaviors, artifacts, and features associated with ST. This taxonomy will support future educational efforts by providing a framework for researchers studying the processes and outcomes of ST-based course transformations as well as a concise guide for faculty members developing classes. PMID:25713097

A taxonomy of dignity: a grounded theory study.

PubMed

Jacobson, Nora

2009-02-24

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

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.

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.

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

Assessing Quality of Data Standards: Framework and Illustration Using XBRL GAAP Taxonomy

NASA Astrophysics Data System (ADS)

Zhu, Hongwei; Wu, Harris

The primary purpose of data standards or metadata schemas is to improve the interoperability of data created by multiple standard users. Given the high cost of developing data standards, it is desirable to assess the quality of data standards. We develop a set of metrics and a framework for assessing data standard quality. The metrics include completeness and relevancy. Standard quality can also be indirectly measured by assessing interoperability of data instances. We evaluate the framework using data from the financial sector: the XBRL (eXtensible Business Reporting Language) GAAP (Generally Accepted Accounting Principles) taxonomy and US Securities and Exchange Commission (SEC) filings produced using the taxonomy by approximately 500 companies. The results show that the framework is useful and effective. Our analysis also reveals quality issues of the GAAP taxonomy and provides useful feedback to taxonomy users. The SEC has mandated that all publicly listed companies must submit their filings using XBRL. Our findings are timely and have practical implications that will ultimately help improve the quality of financial data.

Reduction of Raman scattering and fluorescence from anvils in high pressure Raman scattering

NASA Astrophysics Data System (ADS)

Dierker, S. B.; Aronson, M. C.

2018-05-01

We describe a new design and use of a high pressure anvil cell that significantly reduces the Raman scattering and fluorescence from the anvils in high pressure Raman scattering experiments. The approach is particularly useful in Raman scattering studies of opaque, weakly scattering samples. The effectiveness of the technique is illustrated with measurements of two-magnon Raman scattering in La2CuO4.

A Taxonomy of CEDA Debate Critics.

ERIC Educational Resources Information Center

Dudczak, Craig A.; Day, Donald L.

To develop a taxonomy of Cross Examination Debate Association (CEDA) critics, a study associated professed judging philosophy and responses to survey questions with ballot behavior and elaborated judging profiles. Subjects were debate critics who judged rounds at CEDA tournaments in the Northeast during the Spring 1989 season. In all, 13 critics…

Visualizing a Taxonomy for Virtual Worlds

ERIC Educational Resources Information Center

Downey, Steve

2012-01-01

Since the mid-1990s, however, the popularity, diversity, and application of virtual worlds have spread rapidly. As a result, existing taxonomies and topologies increasingly are becoming less effective at being able to classify and organize the growing diversification of content available in today's virtual worlds. This article presents the…

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…

Raman Spectroscopy.

ERIC Educational Resources Information Center

Gerrard, Donald L.

1984-01-01

Reviews literature on Raman spectroscopy from late 1981 to late 1983. Topic areas include: instrumentation and sampling; liquids and solutions; gases and matrix isolation; biological molecules; polymers; high-temperature and high-pressure studies; Raman microscopy; thin films and surfaces; resonance-enhanced and surface-enhanced spectroscopy; and…

Penicillium strains isolated from Slovak grape berries taxonomy assessment by secondary metabolite profile.

PubMed

Santini, Antonello; Mikušová, Petra; Sulyok, Michael; Krska, Rudolf; Labuda, Roman; Srobárová, Antónia

2014-11-01

The secondary metabolite profiles of microfungi of the genus Penicillium isolated from samples of grape berries collected in two different phases during two vegetative seasons in Slovakia is described to assess the taxonomy. Three Slovak vine regions have been selected for this study, based on their climatic differences and national economic importance. Cultures of microfungi isolated from berries were incubated on different selective media for macro and micromorphology identification. The species Penicillium brevicompactum, Penicillium crustosum, Penicillium chrysogenum, Penicillium expansum, Penicillium palitans and Penicillium polonicum were identified according to growth and morphology. The related strains were found to produce a broad spectrum of fungal metabolites, including roquefortine C, chaetoglobosin A, penitrem A, cyclopeptin, cyclopenin, viridicatin, methylviridicatin, verrucofortine, secalonic acid D, cyclopiazonic acid, fumigaclavine and mycophenolic acid. Chemotaxonomy was performed using high-performance liquid chromatography (HPLC) and mass spectrometry (MS). Dried grape berries were also analyzed allowing to assess the presence of patulin, roquefortine C and penicillic acid; this last one has been identified in dried berries but not in vitro.

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

NASA Technical Reports Server (NTRS)

Wallace, Robert

1986-01-01

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

Taxonomy of the family Arenaviridae and the order Bunyavirales: update 2018.

PubMed

Maes, Piet; Alkhovsky, Sergey V; Bào, Yīmíng; Beer, Martin; Birkhead, Monica; Briese, Thomas; Buchmeier, Michael J; Calisher, Charles H; Charrel, Rémi N; Choi, Il Ryong; Clegg, Christopher S; de la Torre, Juan Carlos; Delwart, Eric; DeRisi, Joseph L; Di Bello, Patrick L; Di Serio, Francesco; Digiaro, Michele; Dolja, Valerian V; Drosten, Christian; Druciarek, Tobiasz Z; Du, Jiang; Ebihara, Hideki; Elbeaino, Toufic; Gergerich, Rose C; Gillis, Amethyst N; Gonzalez, Jean-Paul J; Haenni, Anne-Lise; Hepojoki, Jussi; Hetzel, Udo; Hồ, Thiện; Hóng, Ní; Jain, Rakesh K; Jansen van Vuren, Petrus; Jin, Qi; Jonson, Miranda Gilda; Junglen, Sandra; Keller, Karen E; Kemp, Alan; Kipar, Anja; Kondov, Nikola O; Koonin, Eugene V; Kormelink, Richard; Korzyukov, Yegor; Krupovic, Mart; Lambert, Amy J; Laney, Alma G; LeBreton, Matthew; Lukashevich, Igor S; Marklewitz, Marco; Markotter, Wanda; Martelli, Giovanni P; Martin, Robert R; Mielke-Ehret, Nicole; Mühlbach, Hans-Peter; Navarro, Beatriz; Ng, Terry Fei Fan; Nunes, Márcio Roberto Teixeira; Palacios, Gustavo; Pawęska, Janusz T; Peters, Clarence J; Plyusnin, Alexander; Radoshitzky, Sheli R; Romanowski, Víctor; Salmenperä, Pertteli; Salvato, Maria S; Sanfaçon, Hélène; Sasaya, Takahide; Schmaljohn, Connie; Schneider, Bradley S; Shirako, Yukio; Siddell, Stuart; Sironen, Tarja A; Stenglein, Mark D; Storm, Nadia; Sudini, Harikishan; Tesh, Robert B; Tzanetakis, Ioannis E; Uppala, Mangala; Vapalahti, Olli; Vasilakis, Nikos; Walker, Peter J; Wáng, Guópíng; Wáng, Lìpíng; Wáng, Yànxiăng; Wèi, Tàiyún; Wiley, Michael R; Wolf, Yuri I; Wolfe, Nathan D; Wú, Zhìqiáng; Xú, Wénxìng; Yang, Li; Yāng, Zuòkūn; Yeh, Shyi-Dong; Zhāng, Yǒng-Zhèn; Zhèng, Yàzhōu; Zhou, Xueping; Zhū, Chénxī; Zirkel, Florian; Kuhn, Jens H

2018-04-21

In 2018, the family Arenaviridae was expanded by inclusion of 1 new genus and 5 novel species. At the same time, the recently established order Bunyavirales was expanded by 3 species. This article presents the updated taxonomy of the family Arenaviridae and the order Bunyavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV) and summarizes additional taxonomic proposals that may affect the order in the near future.

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.

Identification of Aeromonas isolates by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

PubMed

Lamy, Brigitte; Kodjo, Angeli; Laurent, Frédéric

2011-09-01

We evaluated the accuracy of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for identifying aeromonads with an extraction procedure. Genus-level accuracy was 100%. Compared to rpoB gene sequencing, species-level accuracy was 90.6% (29/32) for type and reference strains and 91.4% for a collection of 139 clinical and environmental isolates, making this system one of the most accurate and rapid methods for phenotypic identification. The reliability of this technique was very promising, although some improvements in database composition, taxonomy, and discriminatory power are needed. Copyright © 2011 Elsevier Inc. All rights reserved.

[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.

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.

Surface-enhanced Raman spectroscopy of urine by an ingenious near-infrared Raman spectrometer

NASA Astrophysics Data System (ADS)

Feng, Shangyuan; Chen, Weiwei; Li, Yongzeng; Chen, Guannan; Huang, Zufang; Liao, Xiaohua; Xie, Zhiming; Chen, Rong

2007-11-01

This paper demonstrates the potential of an elaborately devised near-infrared Raman system in analysis of urine. The broad band in the long-wavelength region of the electronic absorption spectra of the sol with added adsorbent at certain concentrations has been explained in terms of the aggregation of the colloidal silver particles. We have reported the surface-enhanced Raman (SERS) spectra of urine, and studied the silver solution enhanced effects on the urine Raman scattering. The Raman bands of human's urine was assigned to certain molecule vibrations. We have found that different donators have dissimilar SERS of urine in different physiological condition. Comparatively few studies have explored the ability of Raman spectroscopy for the analysis of urine acid. In the present report, we investigated the ability of surface enhanced Raman spectroscopy to measure uric acid in the human urine. The results suggested that the present Raman system holds considerable promise for practical use. Practical applications such as the quantitative medical examination of urine metabolites may also be feasible in the near future.

MicroRaman Spectroscopy and Raman Imaging of Basal Cell Carcinoma

NASA Astrophysics Data System (ADS)

Short, M. A.; Zeng, H.; Lui, H.

2005-03-01

We have measured the Raman spectra of normal and cancerous skin tissues using a confocal microRaman spectrograph with a sub-micron spatial resolution. We found that the Raman spectrum of a cell nucleolus is different from the spectra measured outside the nucleolus and considerably different from those measured outside the nucleus. In addition, we found significant spectroscopic differences between normal and cancer-bearing sites in the dermis region. In order to utilize these differences for non-invasive skin cancer diagnosis, we have developed a Raman imaging system that clearly demonstrates the structure, location and distribution of cells in unstained skin biopsy samples. Our method is expected to be useful for the detection and characterization of skin cancer based on the known distinct cellular differences between normal and malignant skin.

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.

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

ERIC Educational Resources Information Center

Leeder, Chris; Markey, Karen; Yakel, Elizabeth

2012-01-01

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

Quantitative measurement of carbon isotopic composition in CO2 gas reservoir by Micro-Laser Raman spectroscopy.

PubMed

Li, Jiajia; Li, Rongxi; Zhao, Bangsheng; Guo, Hui; Zhang, Shuan; Cheng, Jinghua; Wu, Xiaoli

2018-04-15

The use of Micro-Laser Raman spectroscopy technology for quantitatively determining gas carbon isotope composition is presented. In this study, 12 CO 2 and 13 CO 2 were mixed with N 2 at various molar fraction ratios to obtain Raman quantification factors (F 12CO2 and F 13CO2 ), which provide a theoretical basis for calculating the δ 13 C value. And the corresponding values were 0.523 (0Raman peak area can be used for the determination of δ 13 C values within the relative errors range of 0.076% to 1.154% in 13 CO 2 / 12 CO 2 binary mixtures when F 12CO2 /F 13CO2 is 0.466972625. In addition, measurement of δ 13 C values by Micro-Laser Raman analysis were carried out on natural CO 2 gas from Shengli Oil-field at room temperature under different pressures. The δ 13 C values obtained by Micro-Laser Raman spectroscopy technology and Isotope Ratio Mass Spectrometry (IRMS) technology are in good agreement with each other, and the relative errors range of δ 13 C values is 1.232%-6.964%. This research provides a fundamental analysis tool for determining gas carbon isotope composition (δ 13 C values) quantitatively by using Micro-Laser Raman spectroscopy. Experiment of results demonstrates that this method has the potential for obtaining δ 13 C values in natural CO 2 gas reservoirs. Copyright © 2018. Published by Elsevier B.V.

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.

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

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/

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

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.

Taxonomies of Cyber Adversaries and Attacks: A Survey of Incidents and Approaches

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

Meyers, C A; Powers, S S; Faissol, D M

In this paper we construct taxonomies of cyber adversaries and methods of attack, drawing from a survey of the literature in the area of cyber crime. We begin by addressing the scope of cyber crime, noting its prevalence and effects on the US economy. We then survey the literature on cyber adversaries, presenting a taxonomy of the different types of adversaries and their corresponding methods, motivations, maliciousness, and skill levels. Subsequently we survey the literature on cyber attacks, giving a taxonomy of the different classes of attacks, subtypes, and threat descriptions. The goal of this paper is to inform futuremore » studies of cyber security on the shape and characteristics of the risk space and its associated adversaries.« less

A Taxonomy of Operational Risks

DTIC Science & Technology

2005-09-01

the operational organization. Con - tractual constraints or requirements can impose risk if the mission delivers products or services under contract...Carnegie Mellon Software Engineering Institute A Taxonomy of Operational Risks CMU/SEI-2005-TN-036 Brian P. Gallagher Pamela J. Case DIST...Operational Risks CMU/SEI-2005-TN-036 Brian P. Gallagher Pamela J. Case Rita C. Creel Susan Kushner Ray C. Williams September2005 Acquisition Support Program

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 Diagnostic Taxonomy of Adult Career Problems.

ERIC Educational Resources Information Center

Campbell, Robert E.; Cellini, James V.

1981-01-01

Developed a taxonomy for the differential diagnosis of adult career development problems. Problem categories identified were: (1) problems in career decision making; (2) problems in implementing career plans; (3) problems in organizational/institutional performance; and (4) problems in organizational/institutional adaption. (Author)

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

ERIC Educational Resources Information Center

Kantor, Paul B.; Saracevic, Tefko

1995-01-01

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

A revised taxonomy of assistance animals

PubMed Central

Parenti, Lindsay; Foreman, Anne; Meade, B. Jean; Wirth, Oliver

2015-01-01

The use of animals in various assistive, therapeutic, and emotional support roles has contributed to the uncoordinated expansion of labels used to distinguish these animals. To address the inconsistent vocabulary and confusion, this article proposes a concise taxonomy for classifying assistance animals. Several factors were identified to differentiate categories, including (1) whether the animal performs work or tasks related to an individual’s disability; (2) the typical level of skill required by the animal performing the work or task; (3) whether the animal is used by public service, military, or healthcare professionals; (4) whether training certifications or standards are available; and (5) the existence of legal public access protections for the animal and handler. Acknowledging that some category labels have already been widely accepted or codified, six functional categories were identified: (1) service animal; (2) public service animal; (3) therapy animal; (4) visitation animal; (5) sporting, recreational, or agricultural animal; and (6) support animal. This taxonomy provides a clear vocabulary for use by consumers, professionals working in the field, researchers, policy makers, and regulatory agencies. PMID:24203538

A revised taxonomy of assistance animals.

PubMed

Parenti, Lindsay; Foreman, Anne; Meade, B Jean; Wirth, Oliver

2013-01-01

The use of animals in various assistive, therapeutic, and emotional support roles has contributed to the uncoordinated expansion of labels used to distinguish these animals. To address the inconsistent vocabulary and confusion, this article proposes a concise taxonomy for classifying assistance animals. Several factors were identified to differentiate categories, including (1) whether the animal performs work or tasks related to an individual's disability; (2) the typical level of skill required by the animal performing the work or task; (3) whether the animal is used by public service, military, or healthcare professionals; (4) whether training certifications or standards are available; and (5) the existence of legal public access protections for the animal and handler. Acknowledging that some category labels have already been widely accepted or codified, six functional categories were identified: (1) service animal; (2) public service animal; (3) therapy animal; (4) visitation animal; (5) sporting, recreational, or agricultural animal; and (6) support animal. This taxonomy provides a clear vocabulary for use by consumers, professionals working in the field, researchers, policy makers, and regulatory agencies.

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

The HCBS Taxonomy: A New Language for Classifying Home- and Community-Based Services

PubMed Central

Peebles, Victoria; Bohl, Alex

2014-01-01

Introduction As states make home- and community-based services (HCBS) more accessible, researchers have become more interested in understanding service use and spending. Because state Medicaid programs differ in the types of services they offer and in how they report these services, analyzing HCBS at the national level is challenging. Objective Describe the HCBS taxonomy and present findings on HCBS waiver expenditures and users. Data This brief analyzed fee-for-service claims from 28 approved states in 2010 Medicaid Analytic eXtract (MAX) files. We summed all expenditures and counted the unique number of users across each HCBS taxonomy service and category. Methods The taxonomy was developed jointly by Truven Health (at that time Thomson Reuters) and Mathematica Policy Research, with stakeholder input, and reviewed using procedure codes. Today, the taxonomy is organized by 18 categories and over 60 specific services. Findings For calendar year 2010, 28 states spent almost $23.6 billion on HCBS, with 80 percent of expenditures categorized as round-the-clock, home-based, and day services. Other services, such as case management, or equipment, modifications, and technology were widely used, but are not particularly costly and do not account for a large proportion of expenditures in every state. Conclusions By providing a common language, the taxonomy presents detailed information on services and makes it easier to assess and identify state-level variation for HCBS. PMID:25343057

A new concept of efficient therapeutic drug monitoring using the high-resolution continuum source absorption spectrometry and the surface enhanced Raman spectroscopy

NASA Astrophysics Data System (ADS)

Xing, Yanlong; Fuss, Harald; Lademann, Jürgen; Huang, Mao Dong; Becker-Ross, Helmut; Florek, Stefan; Patzelt, Alexa; Meinke, Martina C.; Jung, Sora; Esser, Norbert

2018-04-01

In this study, a new therapeutic drug monitoring approach has been tested based on the combination of CaF molecular absorption using high-resolution continuum source absorption spectrometry (HR-CSAS) and surface enhanced Raman spectroscopy (SERS). HR-CSAS with mini graphite tube was successfully tested for clinical therapeutic drug monitoring of the fluorine-containing drug capecitabine in sweat samples of cancer patients: It showed advantageous features of high selectivity (no interference from Cl), high sensitivity (characteristic mass of 0.1 ng at CaF 583.069 nm), low sample consumption (down to 30 nL) and fast measurement (no sample pretreatment and less than 1 min of responding time) in tracing the fluorine signal out of capecitabine. However, this technique has the disadvantage of the total loss of the drug's structure information after burning the sample at very high temperature. Therefore, a new concept of combining HR-CSAS with a non-destructive spectroscopic method (SERS) was proposed for the sensitive sensing and specific identification of capecitabine. We tested and succeed in obtaining the molecular characteristics of the metabolite of capecitabine (named 5-fluorouracil) by the non-destructive SERS technique. With the results shown in this work, it is demonstrated that the combined spectroscopic technique of HR-CSAS and SERS will be very useful in efficient therapeutic drug monitoring in the future.

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

PubMed

White, W T; Last, P R

2012-04-01

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

A taxonomy of dignity: a grounded theory study

PubMed Central

2009-01-01

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

A taxonomy for mechanical ventilation: 10 fundamental maxims.

PubMed

Chatburn, Robert L; El-Khatib, Mohamad; Mireles-Cabodevila, Eduardo

2014-11-01

The American Association for Respiratory Care has declared a benchmark for competency in mechanical ventilation that includes the ability to "apply to practice all ventilation modes currently available on all invasive and noninvasive mechanical ventilators." This level of competency presupposes the ability to identify, classify, compare, and contrast all modes of ventilation. Unfortunately, current educational paradigms do not supply the tools to achieve such goals. To fill this gap, we expand and refine a previously described taxonomy for classifying modes of ventilation and explain how it can be understood in terms of 10 fundamental constructs of ventilator technology: (1) defining a breath, (2) defining an assisted breath, (3) specifying the means of assisting breaths based on control variables specified by the equation of motion, (4) classifying breaths in terms of how inspiration is started and stopped, (5) identifying ventilator-initiated versus patient-initiated start and stop events, (6) defining spontaneous and mandatory breaths, (7) defining breath sequences (8), combining control variables and breath sequences into ventilatory patterns, (9) describing targeting schemes, and (10) constructing a formal taxonomy for modes of ventilation composed of control variable, breath sequence, and targeting schemes. Having established the theoretical basis of the taxonomy, we demonstrate a step-by-step procedure to classify any mode on any mechanical ventilator. Copyright © 2014 by Daedalus Enterprises.

Overview of the taxonomy of zooxanthellate Scleractinia.

PubMed

Veron, John

2013-11-01

Coral taxonomy has entered a historical phase where nomenclatorial uncertainty is rapidly increasing. The fundamental cause is mandatory adherence to historical monographs that lack essential information of all sorts, and also to type specimens, if they exist at all, that are commonly unrecognizable fragments or are uncharacteristic of the species they are believed to represent. Historical problems, including incorrect subsequent type species designations, also create uncertainty for many well-established genera. The advent of in situ studies in the 1970s revealed these issues; now molecular technology is again changing the taxonomic landscape. The competing methodologies involved must be seen in context if they are to avoid becoming an additional basis for continuing nomenclatorial instability. To prevent this happening, the International Commission on Zoological Nomenclature (ICZN) will need to focus on rules that consolidate well-established nomenclature and allow for the designation of new type specimens that are unambiguous, and which include both skeletal material and soft tissue for molecular study. Taxonomic and biogeographic findings have now become linked, with molecular methodologies providing the capacity to re-visit past taxonomic decisions, and to extend both taxonomy and biogeography into the realm of evolutionary theory. It is proposed that most species will ultimately be seen as operational taxonomic units that are human rather than natural constructs, which in consequence will always have fuzzy morphological, genetic, and distribution boundaries. The pathway ahead calls for the integration of morphological and molecular taxonomies, and for website delivery of information that crosses current discipline boundaries.

An Empirical Study on Raman Peak Fitting and Its Application to Raman Quantitative Research.

PubMed

Yuan, Xueyin; Mayanovic, Robert A

2017-10-01

Fitting experimentally measured Raman bands with theoretical model profiles is the basic operation for numerical determination of Raman peak parameters. In order to investigate the effects of peak modeling using various algorithms on peak fitting results, the representative Raman bands of mineral crystals, glass, fluids as well as the emission lines from a fluorescent lamp, some of which were measured under ambient light whereas others under elevated pressure and temperature conditions, were fitted using Gaussian, Lorentzian, Gaussian-Lorentzian, Voigtian, Pearson type IV, and beta profiles. From the fitting results of the Raman bands investigated in this study, the fitted peak position, intensity, area and full width at half-maximum (FWHM) values of the measured Raman bands can vary significantly depending upon which peak profile function is used in the fitting, and the most appropriate fitting profile should be selected depending upon the nature of the Raman bands. Specifically, the symmetric Raman bands of mineral crystals and non-aqueous fluids are best fit using Gaussian-Lorentzian or Voigtian profiles, whereas the asymmetric Raman bands are best fit using Pearson type IV profiles. The asymmetric O-H stretching vibrations of H 2 O and the Raman bands of soda-lime glass are best fit using several Gaussian profiles, whereas the emission lines from a florescent light are best fit using beta profiles. Multiple peaks that are not clearly separated can be fit simultaneously, provided the residuals in the fitting of one peak will not affect the fitting of the remaining peaks to a significant degree. Once the resolution of the Raman spectrometer has been properly accounted for, our findings show that the precision in peak position and intensity can be improved significantly by fitting the measured Raman peaks with appropriate profiles. Nevertheless, significant errors in peak position and intensity were still observed in the results from fitting of weak and wide Raman

Expanding the Taxonomy of the Diagnostic Criteria for Temporomandibular Disorders (DC/TMD)

PubMed Central

Peck, Christopher C.; Goulet, Jean-Paul; Lobbezoo, Frank; Schiffman, Eric L.; Alstergren, Per; Anderson, Gary C.; de Leeuw, Reny; Jensen, Rigmor; Michelotti, Ambra; Ohrbach, Richard; Petersson, Arne; List, Thomas

2014-01-01

Background There is a need to expand the current temporomandibular disorder (TMD) classification to include less common, but clinically important disorders. The immediate aim was to develop a consensus-based classification system and associated diagnostic criteria that have clinical and research utility for less common TMDs. The long-term aim was to establish a foundation, vis-à-vis this classification system, that will stimulate data collection, validity testing, and further criteria refinement. Methods A working group [members of the International RDC/TMD Consortium Network of the International Association for Dental Research (IADR), members of the Orofacial Pain Special Interest Group (SIG) of the International Association for the Study of Pain (IASP), and members from other professional societies] reviewed disorders for inclusion based on clinical significance, the availability of plausible diagnostic criteria, and the ability to operationalize and study the criteria. The disorders were derived from the literature when possible and based on expert opinion as necessary. The expanded TMD taxonomy was presented for feedback at international meetings. Results Of 56 disorders considered, 37 were included in the expanded taxonomy and were placed into the following four categories: temporomandibular joint disorders, masticatory muscle disorders, headache disorders, and disorders affecting associated structures. Those excluded were extremely uncommon, lacking operationalized diagnostic criteria, not clearly related to TMDs, or not sufficiently distinct from disorders already included within the taxonomy. Conclusions The expanded TMD taxonomy offers an integrated approach to clinical diagnosis and provides a framework for further research to operationalize and test the proposed taxonomy and diagnostic criteria. PMID:24443898

The lipid phenotype of breast cancer cells characterized by Raman microspectroscopy: towards a stratification of malignancy.

PubMed

Nieva, Claudia; Marro, Monica; Santana-Codina, Naiara; Rao, Satish; Petrov, Dmitri; Sierra, Angels

2012-01-01

Although molecular classification brings interesting insights into breast cancer taxonomy, its implementation in daily clinical care is questionable because of its expense and the information supplied in a single sample allocation is not sufficiently reliable. New approaches, based on a panel of small molecules derived from the global or targeted analysis of metabolic profiles of cells, have found a correlation between activation of de novo lipogenesis and poorer prognosis and shorter disease-free survival for many tumors. We hypothesized that the lipid content of breast cancer cells might be a useful indirect measure of a variety of functions coupled to breast cancer progression. Raman microspectroscopy was used to characterize metabolism of breast cancer cells with different degrees of malignancy. Raman spectra from MDA-MB-435, MDA-MB-468, MDA-MB-231, SKBR3, MCF7 and MCF10A cells were acquired with an InVia Raman microscope (Renishaw) with a backscattered configuration. We used Principal Component Analysis and Partial Least Squares Discriminant Analyses to assess the different profiling of the lipid composition of breast cancer cells. Characteristic bands related to lipid content were found at 3014, 2935, 2890 and 2845 cm(-1), and related to lipid and protein content at 2940 cm(-1). A classificatory model was generated which segregated metastatic cells and non-metastatic cells without basal-like phenotype with a sensitivity of 90% and a specificity of 82.1%. Moreover, expression of SREBP-1c and ABCA1 genes validated the assignation of the lipid phenotype of breast cancer cells. Indeed, changes in fatty acid unsaturation were related with the epithelial-to-mesenchymal transition phenotype. Raman microspectroscopy is a promising technique for characterizing and classifying the malignant phenotype of breast cancer cells on the basis of their lipid profiling. The algorithm for the discrimination of metastatic ability is a first step towards stratifying breast cancer

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

Utility of Classical α-Taxonomy for Biodiversity of Aquatic Nematodes

PubMed Central

Decraemer, Wilfrida; Backeljau, Thierry

2015-01-01

“Classical α-taxonomy” has different interpretations. Therefore, within the framework of an integrated taxonomic approach it is not relevant to divide taxonomy in different components, each being allocated a different weight of importance. Preferably, taxonomy should be seen in a holistic way, including the act of delimiting and describing taxa, based on different features and available methods, and taxonomy can not be interpreted without looking at evolutionary relationships. The concept of diversity itself is quite diverse as is the measure of diversity. Taxonomic descriptions of free-living aquatic nematodes are very valuable as they provide basic phenotypic information that is necessary for the functional ecological, behavioral, and evolutionary interpretation of data gathered from molecular analyses and of the organism as a whole. In general, molecular taxonomic analyses have the advantage of being much faster and of being able to deal with a larger number of specimens but also possess the important advantage of dealing with a huge amount of features compared to the morphology-based approach. However, just as morphological studies, molecular analyses deal only with partial of an organism. PMID:25861112

VecScreen_plus_taxonomy: imposing a tax(onomy) increase on vector contamination screening.

PubMed

Schäffer, Alejandro A; Nawrocki, Eric P; Choi, Yoon; Kitts, Paul A; Karsch-Mizrachi, Ilene; McVeigh, Richard

2018-03-01

Nucleic acid sequences in public databases should not contain vector contamination, but many sequences in GenBank do (or did) contain vectors. The National Center for Biotechnology Information uses the program VecScreen to screen submitted sequences for contamination. Additional tools are needed to distinguish true-positive (contamination) from false-positive (not contamination) VecScreen matches. A principal reason for false-positive VecScreen matches is that the sequence and the matching vector subsequence originate from closely related or identical organisms (for example, both originate in Escherichia coli). We collected information on the taxonomy of sources of vector segments in the UniVec database used by VecScreen. We used that information in two overlapping software pipelines for retrospective analysis of contamination in GenBank and for prospective analysis of contamination in new sequence submissions. Using the retrospective pipeline, we identified and corrected over 8000 contaminated sequences in the nonredundant nucleotide database. The prospective analysis pipeline has been in production use since April 2017 to evaluate some new GenBank submissions. Data on the sources of UniVec entries were included in release 10.0 (ftp://ftp.ncbi.nih.gov/pub/UniVec/). The main software is freely available at https://github.com/aaschaffer/vecscreen_plus_taxonomy. aschaffe@helix.nih.gov. Supplementary data are available at Bioinformatics online. Published by Oxford University Press 2017. This work is written by US Government employees and are in the public domain in the US.

Puppets, robots, critics, and actors within a taxonomy of attention for developmental disorders

PubMed Central

DENNIS, MAUREEN; SINOPOLI, KATIA J.; FLETCHER, JACK M.; SCHACHAR, RUSSELL

2008-01-01

This review proposes a new taxonomy of automatic and controlled attention. The taxonomy distinguishes among the role of the attendee (puppet and robot, critic and actor), the attention process (stimulus orienting vs. response control), and the attention operation (activation vs. inhibition vs. adjustment), and identifies cognitive phenotypes by which attention is overtly expressed. We apply the taxonomy to four childhood attention disorders: attention deficit hyperactivity disorder, spina bifida meningomyelocele, traumatic brain injury, and acute lymphoblastic leukemia. Variations in attention are related to specific brain regions that support normal attention processes when intact, and produce disordered attention when impaired. The taxonomy explains group differences in behavioral inattention, hyperactivity, and impulsiveness, as well as medication response. We also discuss issues relevant to theories of the cognitive and neural architecture of attention: functional dissociations within and between automatic and controlled attention; the relative importance of type of brain damage and developmental timing to attention profile; cognitive-energetic models of attention and white matter damage; temporal processing deficits, attention deficits and cerebellar damage; and the issue of cognitive phenotypes as candidate endophenotypes. PMID:18764966

A Hierarchical Causal Taxonomy of Psychopathology across the Life Span

PubMed Central

Lahey, Benjamin B.; Krueger, Robert F.; Rathouz, Paul J.; Waldman, Irwin D.; Zald, David H.

2016-01-01

We propose a taxonomy of psychopathology based on patterns of shared causal influences identified in a review of multivariate behavior genetic studies that distinguish genetic and environmental influences that are either common to multiple dimensions of psychopathology or unique to each dimension. At the phenotypic level, first-order dimensions are defined by correlations among symptoms; correlations among first-order dimensions similarly define higher-order domains (e.g., internalizing or externalizing psychopathology). We hypothesize that the robust phenotypic correlations among first-order dimensions reflect a hierarchy of increasingly specific etiologic influences. Some nonspecific etiologic factors increase risk for all first-order dimensions of psychopathology to varying degrees through a general factor of psychopathology. Other nonspecific etiologic factors increase risk only for all first-order dimensions within a more specific higher-order domain. Furthermore, each first-order dimension has its own unique causal influences. Genetic and environmental influences common to family members tend to be nonspecific, whereas environmental influences unique to each individual are more dimension-specific. We posit that these causal influences on psychopathology are moderated by sex and developmental processes. This causal taxonomy also provides a novel framework for understanding the heterogeneity of each first-order dimension: Different persons exhibiting similar symptoms may be influenced by different combinations of etiologic influences from each of the three levels of the etiologic hierarchy. Furthermore, we relate the proposed causal taxonomy to transdimensional psychobiological processes, which also impact the heterogeneity of each psychopathology dimension. This causal taxonomy implies the need for changes in strategies for studying the etiology, psychobiology, prevention, and treatment of psychopathology. PMID:28004947

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.

Raman crystallography of RNA.

PubMed

Gong, Bo; Chen, Jui-Hui; Yajima, Rieko; Chen, Yuanyuan; Chase, Elaine; Chadalavada, Durga M; Golden, Barbara L; Carey, Paul R; Bevilacqua, Philip C

2009-10-01

Raman crystallography is the application of Raman spectroscopy to single crystals. This technique has been applied to a variety of protein molecules where it has provided unique information about biopolymer folding, substrate binding, and catalysis. Here, we describe the application of Raman crystallography to functional RNA molecules. RNA represents unique opportunities and challenges for Raman crystallography. One issue that confounds studies of RNA is its tendency to adopt multiple non-functional folds. Raman crystallography has the advantage that it isolates a single state of the RNA within the crystal and can evaluate its fold, metal ion binding properties (ligand identity, stoichiometry, and affinity), proton binding properties (identity, stoichiometry, and affinity), and catalytic potential. In particular, base-specific stretches can be identified and then associated with the binding of metal ions and protons. Because measurements are carried out in the hanging drop at ambient, rather than cryo, conditions and because RNA crystals tend to be approximately 70% solvent, RNA dynamics and conformational changes become experimentally accessible. This review focuses on experimental setup and procedures, acquisition and interpretation of Raman data, and determination of physicochemical properties of the RNA. Raman crystallographic and solution biochemical experiments on the HDV RNA enzyme are summarized and found to be in excellent agreement. Remarkably, characterization of the crystalline state has proven to help rather than hinder functional characterization of functional RNA, most likely because the tendency of RNA to fold heterogeneously is limited in a crystalline environment. Future applications of Raman crystallography to RNA are briefly discussed.

Toward a comprehensive taxonomy of human motives

PubMed Central

Talevich, Jennifer R.; Walsh, David A.; Iyer, Ravi; Chopra, Gurveen

2017-01-01

A major success in personality has been the development of a consensual structure of traits. However, much less progress has been made on the structure of an equally important aspect of human psychology: motives. We present an empirically and theoretically structured hierarchical taxonomy of 161 motives gleaned from a literature review from McDougall to the present and based on the cluster analysis of similarity judgments among these 161 motives, a broader sampling of motives than previous work. At the broadest level were: Meaning, Communion, and Agency. These divided into nine clusters: Morality & Virtue, Religion & Spirituality, Self-Actualization, Avoidance, Social Relating, Family, Health, Mastery & Competence, and Financial & Occupational Success. Each divided into more concrete clusters to form 5 levels. We discuss contributions to research on motives, especially recent work on goal systems, and the aiding of communication and systematization of research. Finally, we compare the taxonomy to other motive organizations. PMID:28231252

Ten-minute analysis of drugs and metabolites in saliva by surface-enhanced Raman spectroscopy

NASA Astrophysics Data System (ADS)

Shende, Chetan; Inscore, Frank; Maksymiuk, Paul; Farquharson, Stuart

2005-11-01

Rapid analysis of drugs in emergency room overdose patients is critical to selecting appropriate medical care. Saliva analysis has long been considered an attractive alternative to blood plasma analysis for this application. However, current clinical laboratory analysis methods involve extensive sample extraction followed by gas chromatography and mass spectrometry, and typically require as much as one hour to perform. In an effort to overcome this limitation we have been investigating metal-doped sol-gels to both separate drugs and their metabolites from saliva and generate surface-enhanced Raman spectra. We have incorporated the sol-gel in a disposable lab-on-a-chip format, and generally no more than a drop of sample is required. The detailed molecular vibrational information allows chemical identification, while the increase in Raman scattering by six orders of magnitude or more allows detection of microg/mL concentrations. Measurements of cocaine, its metabolite benzoylecgonine, and several barbiturates are presented.

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.

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.

Laser ablation surface-enhanced Raman microspectroscopy.

PubMed

Londero, Pablo S; Lombardi, John R; Leona, Marco

2013-06-04

Improved identification of trace organic compounds in complex matrixes is critical for a variety of fields such as material science, heritage science, and forensics. Surface-enhanced Raman scattering (SERS) is a vibrational spectroscopy technique that can attain single-molecule sensitivity and has been shown to complement mass spectrometry, but lacks widespread application without a robust method that utilizes the effect. We demonstrate a new, highly sensitive, and widely applicable approach to SERS analysis based on laser ablation in the presence of a tailored plasmonic substrate. We analyze several challenging compounds, including non-water-soluble pigments and dyed leather from an ancient Egyptian chariot, achieving sensitivity as high as 120 amol for a 1:1 signal-to-noise ratio and 5 μm spatial resolution. This represents orders of magnitude improvement in spatial resolution and sensitivity compared to those of other SERS approaches intended for widespread application, greatly increasing the applicability of SERS.

Structural Interventions in HIV Prevention: A Taxonomy and Descriptive Systematic Review

PubMed Central

Sipe, Theresa Ann; Barham, Terrika L.; Johnson, Wayne; Joseph, Heather; Tungol-Ashmon, Maria Luisa; O’Leary, Ann

2018-01-01

One of the four national HIV prevention goals is to incorporate combinations of effective, evidence-based approaches to prevent HIV infection. In fields of public health, techniques that alter environment and affect choice options are effective. Structural approaches may be effective in preventing HIV infection. Existing frameworks for structural interventions were lacking in breadth and/or depth. We conducted a systematic review and searched CDC’s HIV/AIDS Prevention Research Synthesis Project’s database for relevant interventions during 1988–2013. We used an iterative process to develop the taxonomy. We identified 213 structural interventions: Access (65%), Policy/Procedure (32%), Mass Media (29%), Physical Structure (27%), Capacity Building (24%), Community Mobilization (9%), and Social Determinants of Health (8%). Forty percent targeted high-risk populations (e.g., people who inject drugs [12%]). This paper describes a comprehensive, well-defined taxonomy of structural interventions with 7 categories and 20 subcategories. The taxonomy accommodated all interventions identified. PMID:29159594

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

Near-field Raman spectroscopy

NASA Astrophysics Data System (ADS)

Ayars, Eric James

2000-10-01

The purpose of this research is to investigate differences observed between Raman spectra when seen through a Near-field Scanning Optical Microscope (NSOM) and spectra of the same materials in conventional Raman or micro-Raman configurations. One source of differences in the observed spectra is a strong z polarized component in the near-field radiation; observations of the magnitude of this effect are compared with theoretical predictions for the field intensity near an NSOM tip. Large electric field gradients near the sharp NSOM probe may be another source of differences. This Gradient-Field Raman (GFR) effect was observed, and there is good evidence that it plays a significant role in Surface-Enhanced Raman Spectroscopy (SERS). The NSOM data seen, however, are not sufficient to prove conclusively that the spectral variations seen are due to the field gradients.

Eliciting the Functional Taxonomy from protein annotations and taxa

PubMed Central

Falda, Marco; Lavezzo, Enrico; Fontana, Paolo; Bianco, Luca; Berselli, Michele; Formentin, Elide; Toppo, Stefano

2016-01-01

The advances of omics technologies have triggered the production of an enormous volume of data coming from thousands of species. Meanwhile, joint international efforts like the Gene Ontology (GO) consortium have worked to provide functional information for a vast amount of proteins. With these data available, we have developed FunTaxIS, a tool that is the first attempt to infer functional taxonomy (i.e. how functions are distributed over taxa) combining functional and taxonomic information. FunTaxIS is able to define a taxon specific functional space by exploiting annotation frequencies in order to establish if a function can or cannot be used to annotate a certain species. The tool generates constraints between GO terms and taxa and then propagates these relations over the taxonomic tree and the GO graph. Since these constraints nearly cover the whole taxonomy, it is possible to obtain the mapping of a function over the taxonomy. FunTaxIS can be used to make functional comparative analyses among taxa, to detect improper associations between taxa and functions, and to discover how functional knowledge is either distributed or missing. A benchmark test set based on six different model species has been devised to get useful insights on the generated taxonomic rules. PMID:27534507

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

Integrative taxonomy: Where we are now, with a focus on the resolution of three tropical fruit fly species complexes

USDA-ARS?s Scientific Manuscript database

Accurate species delimitation underpins good taxonomy. Formalisation of integrative taxonomy in the last decade has provided a framework for using multidisciplinary data to increase rigor in species delimitation hypotheses. We address the state of integrative taxonomy by using an international proje...

[Quality of psychological strain in police work--development of a taxonomy of sources of stress].

PubMed

Reinecke, Stefan; Runde, Bernd; Bastians, Frauke; Weiss, Udo; Heuft, Gereon; Bär, Olaf

2007-01-01

Police officers frequently face traumatic stressors of different origins and thus bear an increased risk of developing a post-traumatic stress disorder. The most mentally burdening situations range from shootings, death of fellow officers, dealing with dead bodies in general, the effects of shift work, time pressure or discontent with management due to mobbing. Part of the present study examines the quality of stress in police work with the goal of developing a taxonomy of the origins of stress. A stratified sample of 109 police officers participated in the study. They were interviewed about stressful situations in their work life. In the interviews participants generated incidents describing stressful or straining situations. These incidents were used to develop a taxonomy of stressful situations in everyday police work. A further 22 interviews with officers of the federal police were carried out to examine the transferability of the developed taxonomy to other occupational groups. The taxonomy distinguishes between five sources of strain. Strain can arise from (1.) the task itself, (2.) the organization and structure of work, (3.) the temporal conditions and (4.) the social conditions. The fifth category describes the source of strain based on other conditions. The results also show that the taxonomy is transferable to other occupational groups. This taxonomy leads to the systematisation of the differences among the stress phenomena which occur in police work. The results can help in the development of practical prevention, counselling and therapeutic programs.

A Taxonomy for Mannerisms of Blind Children.

ERIC Educational Resources Information Center

Eichel, Valerie J.

1979-01-01

The investigation involving 24 blind children (2-11 years old) set out to develop and validate a coding procedure which employed a set of 34 descriptors with their corresponding definitions. The use of the taxonomy enabled a detailed, systematic study of manneristic behavior in blind children. (Author/SBH)

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.

Raman spectral, elemental, crystallinity, and oxygen-isotope variations in conodont apatite during diagenesis

NASA Astrophysics Data System (ADS)

Zhang, Lei; Cao, Ling; Zhao, Laishi; Algeo, Thomas J.; Chen, Zhong-Qiang; Li, Zhihong; Lv, Zhengyi; Wang, Xiangdong

2017-08-01

Conodont apatite has long been used in paleoenvironmental studies, often with minimal evaluation of the influence of diagenesis on measured elemental and isotopic signals. In this study, we evaluate diagenetic influences on conodonts using an integrated set of analytical techniques. A total of 92 points in 19 coniform conodonts from Ordovician marine units of South China were analyzed by micro-laser Raman spectroscopy (M-LRS), laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS), high-resolution X-ray microdiffraction (HXRD), and secondary ion mass spectrometry (SIMS). Each conodont element was analyzed along its full length, including the albid crown, hyaline crown, and basal body, in either a whole specimen (i.e., reflecting the composition of its outer layer) or a split specimen (i.e., reflecting the composition of its interior). In the conodonts of this study, the outer surfaces consist of hydroxyfluorapatite and the interiors of strontian hydroxyfluorapatite. Ionic substitutions resulted in characteristic Raman spectral shifts in the position (SS1) and width (SS2) of the ν1-PO43- stretching band. Although multiple elements were enriched (Sr2+, Mg2+) and depleted (Fe3+, Mn2+, Ca2+) during diagenesis, geochemical modeling constraints and known Raman spectral patterns suggest that Sr uptake was the dominant influence on diagenetic redshifts of SS1. All study specimens show lower SS2 values than modern bioapatite and synthetic apatite, suggesting that band width decreases with time in ancient bioapatite, possibly through an annealing process that produces larger, more uniform crystal domains. Most specimens consist mainly of amorphous or poorly crystalline apatite, which is inferred to represent the original microstructure of conodonts. In a subset of specimens, some tissues (especially albid crown) exhibit an increased degree of crystallinity developed through aggrading neomorphism. However, no systematic relationship was observed between

Modes of Discourse in Educational Administration: A Taxonomy.

ERIC Educational Resources Information Center

Vice, James W.

1983-01-01

Uses examples from higher education to present a taxonomy of discourse, classifying verbal interchanges into three minor modes (rote pronouncement, passing time, and gossip), a transitional mode (true conversation), and three major modes (rhetoric, dialectic, and deliberation). (JAC)

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

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

On Dramatic Instruction: Towards a Taxonomy of Methods.

ERIC Educational Resources Information Center

Courtney, Richard

1987-01-01

Examines the many possible methods used by instructors who work with dramatic action: in educational drama, drama therapy, social drama, and theater. Discusses an emergent taxonomy whereby instructors choose either spontaneous/formal, overt/covert/, or intrinsic/extrinsic methods. (JC)

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

PubMed

Ytow, Nozomi

2016-01-01

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

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

PubMed

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

2010-08-01

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

In situ Raman spectroscopic investigation of chromium surfaces under hydrothermal conditions

NASA Astrophysics Data System (ADS)

Maslar, J. E.; Hurst, W. S.; Bowers, W. J.; Hendricks, J. H.; Aquino, M. I.; Levin, I.

2001-08-01

Three chromium coupons were exposed to air-saturated water at pressures of ca. 25 MPa and temperatures up to 545°C in an optically accessible flow cell. In situ Raman spectra were collected at different temperatures as the coupons were heated and then cooled. Coupons were also characterized ex situ with Raman spectroscopy, scanning electron microscopy, energy-dispersive X-ray spectrometry, and X-ray diffraction. Coupons heated to either 374 or 505°C exhibited the same corrosion product, tentatively identified as α-CrOOH that originated as corrosion product released from the optical cell and/or flow system. A coupon heated to 545°C exhibited a variety of Cr III, mixed chromium valence Cr III/Cr VI, and/or Cr VI species during heating. During cooling, the same corrosion product was observed at all temperatures on this coupon and was tentatively identified as Cr 2O 3 with Cr VI incorporated into the Cr 2O 3 Cr III-oxygen network. The difference in observed corrosion processes among the three coupons was attributed to a difference in water purity to which they were exposed.

Rapid Quantitative Determination of Squalene in Shark Liver Oils by Raman and IR Spectroscopy.

PubMed

Hall, David W; Marshall, Susan N; Gordon, Keith C; Killeen, Daniel P

2016-01-01

Squalene is sourced predominantly from shark liver oils and to a lesser extent from plants such as olives. It is used for the production of surfactants, dyes, sunscreen, and cosmetics. The economic value of shark liver oil is directly related to the squalene content, which in turn is highly variable and species-dependent. Presented here is a validated gas chromatography-mass spectrometry analysis method for the quantitation of squalene in shark liver oils, with an accuracy of 99.0 %, precision of 0.23 % (standard deviation), and linearity of >0.999. The method has been used to measure the squalene concentration of 16 commercial shark liver oils. These reference squalene concentrations were related to infrared (IR) and Raman spectra of the same oils using partial least squares regression. The resultant models were suitable for the rapid quantitation of squalene in shark liver oils, with cross-validation r (2) values of >0.98 and root mean square errors of validation of ≤4.3 % w/w. Independent test set validation of these models found mean absolute deviations of the 4.9 and 1.0 % w/w for the IR and Raman models, respectively. Both techniques were more accurate than results obtained by an industrial refractive index analysis method, which is used for rapid, cheap quantitation of squalene in shark liver oils. In particular, the Raman partial least squares regression was suited to quantitative squalene analysis. The intense and highly characteristic Raman bands of squalene made quantitative analysis possible irrespective of the lipid matrix.

A hierarchical causal taxonomy of psychopathology across the life span.

PubMed

Lahey, Benjamin B; Krueger, Robert F; Rathouz, Paul J; Waldman, Irwin D; Zald, David H

2017-02-01

We propose a taxonomy of psychopathology based on patterns of shared causal influences identified in a review of multivariate behavior genetic studies that distinguish genetic and environmental influences that are either common to multiple dimensions of psychopathology or unique to each dimension. At the phenotypic level, first-order dimensions are defined by correlations among symptoms; correlations among first-order dimensions similarly define higher-order domains (e.g., internalizing or externalizing psychopathology). We hypothesize that the robust phenotypic correlations among first-order dimensions reflect a hierarchy of increasingly specific etiologic influences . Some nonspecific etiologic factors increase risk for all first-order dimensions of psychopathology to varying degrees through a general factor of psychopathology. Other nonspecific etiologic factors increase risk only for all first-order dimensions within a more specific higher-order domain. Furthermore, each first-order dimension has its own unique causal influences. Genetic and environmental influences common to family members tend to be nonspecific, whereas environmental influences unique to each individual are more dimension-specific. We posit that these causal influences on psychopathology are moderated by sex and developmental processes. This causal taxonomy also provides a novel framework for understanding the heterogeneity of each first-order dimension: Different persons exhibiting similar symptoms may be influenced by different combinations of etiologic influences from each of the 3 levels of the etiologic hierarchy. Furthermore, we relate the proposed causal taxonomy to transdimensional psychobiological processes, which also impact the heterogeneity of each psychopathology dimension. This causal taxonomy implies the need for changes in strategies for studying the etiology, psychobiology, prevention, and treatment of psychopathology. (PsycINFO Database Record (c) 2017 APA, all rights

Optical trapping and Raman spectroscopy of single nanostructures using standing-wave Raman tweezers

NASA Astrophysics Data System (ADS)

Wu, Mu-ying; He, Lin; Chen, Gui-hua; Yang, Guang; Li, Yong-qing

2017-08-01

Optical tweezers integrated with Raman spectroscopy allows analyzing a single trapped micro-particle, but is generally less effective for individual nano-sized objects in the 10-100 nm range. The main challenge is the weak gradient force on nanoparticles that is insufficient to overcome the destabilizing effect of scattering force and Brownian motion. Here, we present standing-wave Raman tweezers for stable trapping and sensitive characterization of single isolated nanostructures with a low laser power by combining a standing-wave optical trap (SWOT) with confocal Raman spectroscopy. This scheme has stronger intensity gradients and balanced scattering forces, and thus is more stable and sensitive in measuring nanoparticles in liquid with 4-8 fold increase in the Raman signals. It can be used to analyze many nanoparticles that cannot be measured with single-beam Raman tweezers, including individual single-walled carbon nanotubes (SWCNT), graphene flakes, biological particles, polystyrene beads (100 nm), SERS-active metal nanoparticles, and high-refractive semiconductor nanoparticles with a low laser power of a few milliwatts. This would enable sorting and characterization of specific SWCNTs and other nanoparticles based on their increased Raman fingerprints.

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.

Integrative taxonomy on the fast track - towards more sustainability in biodiversity research.

PubMed

Riedel, Alexander; Sagata, Katayo; Suhardjono, Yayuk R; Tänzler, Rene; Balke, Michael

2013-03-27

A so called "taxonomic impediment" has been recognized as a major obstacle to biodiversity research for the past two decades. Numerous remedies were then proposed. However, neither significant progress in terms of formal species descriptions, nor a minimum standard for descriptions have been achieved so far. Here, we analyze the problems of traditional taxonomy which often produces keys and descriptions of limited practical value. We suggest that phylogenetics and phenetics had a subtle and so far unnoticed effect on taxonomy leading to inflated species descriptions. The term "turbo-taxonomy" was recently coined for an approach combining cox1 sequences, concise morphological descriptions by an expert taxonomist, and high-resolution digital imaging to streamline the formal description of larger numbers of new species. We propose a further development of this approach which, together with open access web-publication and automated pushing of content from journal into a wiki, may create the most efficient and sustainable way to conduct taxonomy in the future. On demand, highly concise descriptions can be gradually updated or modified in the fully versioned wiki-framework we use. This means that the visibility of additional data is not compromised, while the original species description -the first version- remains preserved in the wiki, and of course in the journal version. A DNA sequence database with an identification engine replaces an identification key, helps to avoid synonyms and has the potential to detect grossly incorrect generic placements. We demonstrate the functionality of a species-description pipeline by naming 101 new species of hyperdiverse New Guinea Trigonopterus weevils in the open-access journal ZooKeys. Fast track taxonomy will not only increase speed, but also sustainability of global species inventories. It will be of great practical value to all the other disciplines that depend on a usable taxonomy and will change our perception of global

Raman Spectra of Glasses

DTIC Science & Technology

1986-11-30

Howard University , Department of Chemistry, Washington, DC Distribution Unlimited Per.. .Dr. Donald Polk, ONR/Code 1131M .IL. OFFICE OF NAVAL...the specific facilities to perform this extremely high temperature Raman work at Howard university . Of course, we do have very extensive facilities at... Howard University for CW laser-Raman spectroscopy of melts to about 1600 or 1800 OC. We have four complete laser-Raman instruments; Lhree holographic

76 FR 74050 - Measured Building Energy Performance Data Taxonomy

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-30

... data sources and taxonomies. Certain data fields have enumerated types that provide a discrete set of... Utility, Electric Rate Structure, and Electricity Summer Peak Power. The Priority 3 data fields include...

Quantitative micro-Raman analysis of volcanic glasses: influence and correction of matrix effects

NASA Astrophysics Data System (ADS)

Di Muro, Andrea

2014-05-01

. Geochimica et Cosmochimica Acta, 74, 5641-5656. Mercier, M., Di Muro, A., Giordano, D., Métrich, N.,Pichavant, M., Clocchiatti, R., Montagnac, G. (2009) The influence of glass polymerization and oxidation on micro-Raman water analysis in alumino-silicate glasses. Geochimica et Cosmochimica Acta, 73, 197-217 Di Muro, A., Métrich, N., Mercier, M., Giordano, D., Massare, D., Montagnac, G. (2009) Micro-Raman determination of iron redox state in dry natural glasses : application to peralkaline rhyolites and basalts. Chemical Geology (Special volume on experimental techniques for the study of hydrothermal fluids and silicate melts) 259:78-88. Di Muro A, Villemant B, Montagnac G, Scaillet B, Reynard B (2006) The influence of glass composition on the determination of water content and speciation by Raman spectrometry. Geochimica and Cosmochimica Acta, 70, 2868-2884 Di Muro A, Giordano D., Villemant B, Montagnac G, Romano C. (2006) Influence of composition and thermal history of volcanic glasses on water content determination by microRaman spectrometry. Applied Geochemistry (Special volume on developments in analytical geochemistry). 21, 802-812. Application Di Muro, A., Staudacher, T., Ferrazzini, V., Villemant, B., Besson, P., Garofalo, C. (2014) Tracking magma injection in the Piton de la Fournaise volcanic edifice after the 2007 Summit Caldera Collapse by Pele's Hair Composition. Chapman Special Volume on Hawaiian volcanoes, AGU Books. Ardia, P., Di Muro, A., Giordano, D., Massare, D., Sanchez-Valle, C., Schmidt, M.W. (2014) Densification mechanisms of haplogranite glasses as a function of water content and pressure based on density and Raman data. Under review, submitted to Geochimica et Cosmochimica Acta. Métrich, N, Allard, P., Aiuppa, A., Bani, P., Bertagnini, A., Belhadj, O., Di Muro, A., Garaebiti, E., Massare, D., Parello, F., Shinohara, H. (2011) Magma and volatile feeding of post-caldera Yasur volcanism and block resurgence in Tanna island (Vanuatu arc). Journal of

Micro-Raman spectroscopy in the identification of wulfenite and vanadinite in a Sasanian painted stucco fragment of the Ghaleh Guri in Ramavand, western Iran

NASA Astrophysics Data System (ADS)

Holakooei, Parviz; Karimy, Amir-Hossein; Hasanpour, Ata; Oudbashi, Omid

2016-12-01

This paper reports the results of studies performed on a painted stucco fragment excavated at the Ghaleh Guri in Ramavand, western Iran, and dated back to the late Sasanian period (224-651 AD). Analytical studies including micro-Raman spectroscopy (μ-Raman), micro-X-ray spectrometry (μ-XRF) and optical microscopy showed that red lead and vermilion were used as main pigments on this fragment. Moreover, carbon black was diagnosed to thinly cover some parts of the red lead. Peculiarly, wulfenite (PbMoO4) associated with vanadinite (Pb5(VO4)3Cl) was identified to compose a yellow stain sporadically dispersed on the other pigments.

Raman analysis of cobalt blue pigment in blue and white porcelain: A reassessment.

PubMed

Jiang, Xiaochenyang; Ma, Yanying; Chen, Yue; Li, Yuanqiu; Ma, Qinglin; Zhang, Zhaoxia; Wang, Changsui; Yang, Yimin

2018-02-05

Cobalt blue is a famous pigment in human history. In the past decade it is widely reported that the cobalt aluminate has been detected in ancient ceramics as blue colorant in glaze, yet the acquired Raman spectra are incredibly different from that of synthesised references, necessitating a reassessment of such contradictory scenario with more accurate analytic strategies. In this study, micro-Raman spectroscopy (MRS) and scanning electron microscopy (SEM) in association with energy dispersive spectrometry (EDS) were performed on under-glaze cobalt pigments from one submerged blue and white porcelain shard dated from Wanli reign (1573-1620CE) of Ming dynasty (1365-1644CE) excavated at Nan'ao I shipwreck off the southern coast of China. The micro-structural inspection reveals that the pigment particles have characteristics of small account, tiny size, heterogeneously distribution, and more importantly, been completely enwrapped by well-developed anorthite crystals in the glaze, indicating that the signals recorded in previous publications are probably not from cobalt pigments themselves but from outside thickset anorthite shell. The further spectromicroscopic analyses confirm this presumption when the accurate spectra of cobalt aluminate pigment and surrounding anorthite were obtained separately with precise optical positioning. Accordingly, we reassess and clarify the previous Raman studies dedicated to cobalt blue pigment in ancient ceramics, e.g. cobalt blue in celadon glaze, and in turn demonstrate the superiority and necessity of coupling spectroscopic analysis with corresponding structure observation, especially in the characterization of pigments from complicated physico-chemical environment like antiquities. Thus, this study promotes a better understanding of Raman spectroscopy study of cobalt blue pigments in art and archaeology field. Copyright © 2017 Elsevier B.V. All rights reserved.

Raman analysis of cobalt blue pigment in blue and white porcelain: A reassessment

NASA Astrophysics Data System (ADS)

Jiang, Xiaochenyang; Ma, Yanying; Chen, Yue; Li, Yuanqiu; Ma, Qinglin; Zhang, Zhaoxia; Wang, Changsui; Yang, Yimin

2018-02-01

Cobalt blue is a famous pigment in human history. In the past decade it is widely reported that the cobalt aluminate has been detected in ancient ceramics as blue colorant in glaze, yet the acquired Raman spectra are incredibly different from that of synthesised references, necessitating a reassessment of such contradictory scenario with more accurate analytic strategies. In this study, micro-Raman spectroscopy (MRS) and scanning electron microscopy (SEM) in association with energy dispersive spectrometry (EDS) were performed on under-glaze cobalt pigments from one submerged blue and white porcelain shard dated from Wanli reign (1573-1620 CE) of Ming dynasty (1365-1644 CE) excavated at Nan'ao I shipwreck off the southern coast of China. The micro-structural inspection reveals that the pigment particles have characteristics of small account, tiny size, heterogeneously distribution, and more importantly, been completely enwrapped by well-developed anorthite crystals in the glaze, indicating that the signals recorded in previous publications are probably not from cobalt pigments themselves but from outside thickset anorthite shell. The further spectromicroscopic analyses confirm this presumption when the accurate spectra of cobalt aluminate pigment and surrounding anorthite were obtained separately with precise optical positioning. Accordingly, we reassess and clarify the previous Raman studies dedicated to cobalt blue pigment in ancient ceramics, e.g. cobalt blue in celadon glaze, and in turn demonstrate the superiority and necessity of coupling spectroscopic analysis with corresponding structure observation, especially in the characterization of pigments from complicated physico-chemical environment like antiquities. Thus, this study promotes a better understanding of Raman spectroscopy study of cobalt blue pigments in art and archaeology field.

The structure of observed learning outcome (SOLO) taxonomy: a model to promote dental students' learning.

PubMed

Lucander, H; Bondemark, L; Brown, G; Knutsson, K

2010-08-01

Selective memorising of isolated facts or reproducing what is thought to be required - the surface approach to learning - is not the desired outcome for a dental student or a dentist in practice. The preferred outcome is a deep approach as defined by an intention to seek understanding, develop expertise and relate information and knowledge into a coherent whole. The aim of this study was to investigate whether the structure of observed learning outcome (SOLO) taxonomy could be used as a model to assist and promote the dental students to develop a deep approach to learning assessed as learning outcomes in a summative assessment. Thirty-two students, participating in course eight in 2007 at the Faculty of Odontology at Malmö University, were introduced to the SOLO taxonomy and constituted the test group. The control group consisted of 35 students participating in course eight in 2006. The effect of the introduction was measured by evaluating responses to a question in the summative assessment by using the SOLO taxonomy. The evaluators consisted of two teachers who performed the assessment of learning outcomes independently and separately on the coded material. The SOLO taxonomy as a model for learning was found to improve the quality of learning. Compared to the control group significantly more strings and structured relations between these strings were present in the test group after the SOLO taxonomy had been introduced (P < 0.01, one tailed test for both results). The SOLO taxonomy is recommended as a model for promoting and developing a deeper approach to learning in dentistry.

A Taxonomy of Interaction for Instructional Multimedia.

ERIC Educational Resources Information Center

Schwier, Richard A.

This paper rejects the hardware-based "levels of interaction" made popular in interactive video literature to describe human-machine interaction in favor of a new taxonomy of learner-media interaction based on the type of cognitive engagement experienced by learners. Interaction can be described on three levels, based on the quality of…

Detection of Prohibited Fish Drugs Using Silver Nanowires as Substrate for Surface-Enhanced Raman Scattering

PubMed Central

Song, Jia; Huang, Yiqun; Fan, Yuxia; Zhao, Zhihui; Yu, Wansong; Rasco, Barbara A.; Lai, Keqiang

2016-01-01

Surface-enhanced Raman scattering or surface-enhanced Raman spectroscopy (SERS) is a promising detection technology, and has captured increasing attention. Silver nanowires were synthesized using a rapid polyol method and optimized through adjustment of the molar ratio of poly(vinyl pyrrolidone) and silver nitrate in a glycerol system. Ultraviolet-visible spectrometry, X-ray diffraction, and transmission electron microscopy were used to characterize the silver nanowires. The optimal silver nanowires were used as a SERS substrate to detect prohibited fish drugs, including malachite green, crystal violet, furazolidone, and chloramphenicol. The SERS spectra of crystal violet could be clearly identified at concentrations as low as 0.01 ng/mL. The minimum detectable concentration for malachite green was 0.05 ng/mL, and for both furazolidone and chloramphenicol were 0.1 μg/mL. The results showed that the as-prepared Ag nanowires SERS substrate exhibits high sensitivity and activity. PMID:28335303

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

NASA Astrophysics Data System (ADS)

Skórnik-Pokarowska, Urszula; Orłowski, Arkadiusz

2004-12-01

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

Developing a Gap Taxonomy to Address Crew Health Risks in NASA's Human Research Program

NASA Technical Reports Server (NTRS)

Kundrot, Craig E.; Edwards, J. Michelle

2009-01-01

The mission of NASA's Human Research Program (HRP) is to understand and reduce the risk to crew health and performance in exploration missions. The HRP addresses 27 specific risks by identifying and then filling gaps in understanding the risks and in the ability to disposition the risks. The primary bases for identifying gaps have been past experience and requirements definition. This approach has been very effective in identifying some important, relevant gaps, but may be inadequate for identifying gaps outside the past experience base. We are exploring the use of a gap taxonomy as a comprehensive, underlying conceptual framework that allows a more systematic identification of gaps. The taxonomy is based on these stages in medical care: prediction, prevention, detection/diagnosis, treatment, monitoring, rehabilitation, and lifetime surveillance. This gap taxonomy approach identifies new gaps in HRP health risks. Many of the new gaps suggest risk reduction approaches that are more cost effective than present approaches. A major benefit of the gap taxonomy approach is to identify new, economical approaches that reduce the likelihood and/or consequence of a risk.

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

PubMed

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

2017-05-01

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

Towards a more molecular taxonomy of disease.

PubMed

Park, Jisoo; Hescott, Benjamin J; Slonim, Donna K

2017-07-27

Disease taxonomies have been designed for many applications, but they tend not to fully incorporate the growing amount of molecular-level knowledge of disease processes, inhibiting research efforts. Understanding the degree to which we can infer disease relationships from molecular data alone may yield insights into how to ultimately construct more modern taxonomies that integrate both physiological and molecular information. We introduce a new technique we call Parent Promotion to infer hierarchical relationships between disease terms using disease-gene data. We compare this technique with both an established ontology inference method (CliXO) and a minimum weight spanning tree approach. Because there is no gold standard molecular disease taxonomy available, we compare our inferred hierarchies to both the Medical Subject Headings (MeSH) category C forest of diseases and to subnetworks of the Disease Ontology (DO). This comparison provides insights about the inference algorithms, choices of evaluation metrics, and the existing molecular content of various subnetworks of MeSH and the DO. Our results suggest that the Parent Promotion method performs well in most cases. Performance across MeSH trees is also correlated between inference methods. Specifically, inferred relationships are more consistent with those in smaller MeSH disease trees than larger ones, but there are some notable exceptions that may correlate with higher molecular content in MeSH. Our experiments provide insights about learning relationships between diseases from disease genes alone. Future work should explore the prospect of disease term discovery from molecular data and how best to integrate molecular data with anatomical and clinical knowledge. This study nonetheless suggests that disease gene information has the potential to form an important part of the foundation for future representations of the disease landscape.

Novel micro-Raman setup with tunable laser excitation for time-efficient resonance Raman microscopy and imaging.

PubMed

Stürzl, Ninette; Lebedkin, Sergei; Klumpp, Stefanie; Hennrich, Frank; Kappes, Manfred M

2013-05-07

We describe a micro-Raman setup allowing for efficient resonance Raman spectroscopy (RRS), i.e., mapping of Raman spectra as a function of tunable laser excitation wavelength. The instrument employs angle-tunable bandpass optical filters which are integrated into software-controlled Raman and laser cleanup filter devices. These automatically follow the excitation laser wavelength and combine tunability with high bandpass transmission as well as high off-band blocking of light. Whereas the spectral intervals which can be simultaneously acquired are bandpass limited to ~350 cm(-1), they can be tuned across the spectrum of interest to access all characteristic Raman features. As an illustration of performance, we present Raman mapping of single-walled carbon nanotubes (SWNTs): (i) in a small volume of water-surfactant dispersion as well as (ii) after deposition onto a substrate. A significant improvement in the acquisition time (and efficiency) is demonstrated compared to previous RRS implementations. These results may help to establish (micro) Raman spectral mapping as a routine tool for characterization of SWNTs as well as other materials with a pronounced resonance Raman response in the visible-near-infrared spectral region.

A Taxonomy of Consumer Satisfaction/Dissatisfaction Measures

ERIC Educational Resources Information Center

Andreasen, Alan R.

1977-01-01

Government and business have become more concerned with measuring market performance in terms of consumer satisfactions and dissatisfactions (CS/D). This research is concerned with the question of how one ought to measure CS/D. Offers a taxonomy of alternative CS/D measures and presents data from a national urban study of consumer complaints to…

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

ERIC Educational Resources Information Center

Marshall, Jennings B.; Carson, Charles M.

2008-01-01

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

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

PubMed Central

2016-01-01

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

Micro-mirror arrays for Raman spectroscopy

NASA Astrophysics Data System (ADS)

Duncan, W. M.

2015-03-01

In this research we study Raman and fluorescence spectroscopies as non-destructive and noninvasive methods for probing biological material and "living systems." Particularly for a living material any probe need be non-destructive and non-invasive, as well as provide real time measurement information and be cost effective to be generally useful. Over the past few years the components needed to measure weak and complex processes such as Raman scattering have evolved substantially with the ready availability of lasers, dichroic filters, low noise and sensitive detectors, digitizers and signal processors. A Raman spectrum consists of a wavelength or frequency spectrum that corresponds to the inelastic (Raman) photon signal that results from irradiating a "Raman active" material. Raman irradiation of a material usually and generally uses a single frequency laser. The Raman fingerprint spectrum that results from a Raman interaction can be determined from the frequencies scattered and received by an appropriate detector. Spectra are usually "digitized" and numerically matched to a reference sample or reference material spectra in performing an analysis. Fortunately today with the many "commercial off-the-shelf" components that are available, weak intensity effects such as Raman and fluorescence spectroscopy can be used for a number of analysis applications. One of the experimental limitations in Raman measurement is the spectrometer itself. The spectrometer is the section of the system that either by interference plus detection or by dispersion plus detection that "signal" amplitude versus energy/frequency signals are measured. Particularly in Raman spectroscopy, optical signals carrying desired "information" about the analyte are extraordinarily weak and require special considerations when measuring. We will discuss here the use of compact spectrometers and a micro-mirror array system (used is the digital micro-mirror device (DMD) supplied by the DLP® Products group of

Taxonomic discrimination of higher plants by pyrolysis mass spectrometry.

PubMed

Kim, S W; Ban, S H; Chung, H J; Choi, D W; Choi, P S; Yoo, O J; Liu, J R

2004-02-01

Pyrolysis mass spectrometry (PyMS) is a rapid, simple, high-resolution analytical method based on thermal degradation of complex material in a vacuum and has been widely applied to the discrimination of closely related microbial strains. Leaf samples of six species and one variety of higher plants (Rosa multiflora, R. multiflora var. platyphylla, Sedum kamtschaticum, S. takesimense, S. sarmentosum, Hepatica insularis, and H. asiatica) were subjected to PyMS for spectral fingerprinting. Principal component analysis of PyMS data was not able to discriminate these plants in discrete clusters. However, canonical variate analysis of PyMS data separated these plants from one another. A hierarchical dendrogram based on canonical variate analysis was in agreement with the known taxonomy of the plants at the variety level. These results indicate that PyMS is able to discriminate higher plants based on taxonomic classification at the family, genus, species, and variety level.

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.

Raman scattering tensors of tyrosine.

PubMed

Tsuboi, M; Ezaki, Y; Aida, M; Suzuki, M; Yimit, A; Ushizawa, K; Ueda, T

1998-01-01

Polarized Raman scattering measurements have been made of a single crystal of L-tyrosine by the use of a Raman microscope with the 488.0-nm exciting beam from an argon ion laser. The L-tyrosine crystal belongs to the space group P2(1)2(1)2(1) (orthorhombic), and Raman scattering intensities corresponding to the aa, bb, cc, ab and ac components of the crystal Raman tensor have been determined for each prominent Raman band. A similar set of measurements has been made of L-tyrosine-d4, in which four hydrogen atoms on the benzene ring are replaced by deuterium atoms. The effects of NH3-->ND3 and OH-->OD on the Raman spectrum have also been examined. In addition, depolarization ratios of some bands of L-tyrosine in aqueous solutions of pH 13 and pH 1 were examined. For comparison with these experimental results, on the other hand, ab initio molecular orbital calculations have been made of the normal modes of vibration and their associated polarizability oscillations of the L-tyrosine molecule. On the basis of these experimental data and by referring to the results of the calculations, discussions have been presented on the Raman tensors associated to some Raman bands, including those at 829 cm-1 (benzene ring breathing), 642 cm-1 (benzene ring deformation), and 432 cm-1 (C alpha-C beta-C gamma bending).

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

Research into the development of a knowledge acquisition taxonomy

NASA Technical Reports Server (NTRS)

Fink, Pamela K.

1991-01-01

Monthly progress reports for September 1990 to January 1991 are given. Topics that are briefly covered include problem solving and learning taxonomies, knowledge acquisition techniques, software design, air traffic control, and space shuttle flight control.

Microcavity Enhanced Raman Scattering

NASA Astrophysics Data System (ADS)

Petrak, Benjamin J.

Raman scattering can accurately identify molecules by their intrinsic vibrational frequencies, but its notoriously weak scattering efficiency for gases presents a major obstacle to its practical application in gas sensing and analysis. This work explores the use of high finesse (≈50 000) Fabry-Perot microcavities as a means to enhance Raman scattering from gases. A recently demonstrated laser ablation method, which carves out a micromirror template on fused silica--either on a fiber tip or bulk substrates-- was implemented, characterized, and optimized to fabricate concave micromirror templates ˜10 mum diameter and radius of curvature. The fabricated templates were coated with a high-reflectivity dielectric coating by ion-beam sputtering and were assembled into microcavities ˜10 mum long and with a mode volume ˜100 mum 3. A novel gas sensing technique that we refer to as Purcell enhanced Raman scattering (PERS) was demonstrated using the assembled microcavities. PERS works by enhancing the pump laser's intensity through resonant recirculation at one longitudinal mode, while simultaneously, at a second mode at the Stokes frequency, the Purcell effect increases the rate of spontaneous Raman scattering by a change to the intra-cavity photon density of states. PERS was shown to enhance the rate of spontaneous Raman scattering by a factor of 107 compared to the same volume of sample gas in free space scattered into the same solid angle subtended by the cavity. PERS was also shown capable of resolving several Raman bands from different isotopes of CO2 gas for application to isotopic analysis. Finally, the use of the microcavity to enhance coherent anti-Stokes Raman scattering (CARS) from CO2 gas was demonstrated.

Is a rehabilitation treatment taxonomy the right answer to the rehabilitation black box?

PubMed

Cieza, Alarcos; Bickenbach, Jerome

2014-01-01

In this commentary on the development of an interventions taxonomy for medical rehabilitation, a rehabilitation treatment taxonomy (RTT), we acknowledge the authors' valuable contribution to rehabilitation science, and at the same time interrogate the assumption that a taxonomy has essential added value to address the challenge of rehabilitation's black box. The tripartite analytical structure of action of treatment, active ingredient, and mechanism of action, and not an RTT, is the key to addressing the rehabilitation black box. There is a need for clearly defined operationalized requirements of how the 3 components have to be expressed. We also recommend that this concerted effort be linked to all relevant stakeholders and all international endeavors that are pursuing a common goal of enhancing rehabilitation research. Copyright © 2014 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Multivariate Analysis of Combined Fourier Transform Near-Infrared Spectrometry (FT-NIR) and Raman Datasets for Improved Discrimination of Drying Oils.

PubMed

Carlesi, Serena; Ricci, Marilena; Cucci, Costanza; La Nasa, Jacopo; Lofrumento, Cristiana; Picollo, Marcello; Becucci, Maurizio

2015-07-01

This work explores the application of chemometric techniques to the analysis of lipidic paint binders (i.e., drying oils) by means of Raman and near-infrared spectroscopy. These binders have been widely used by artists throughout history, both individually and in mixtures. We prepared various model samples of the pure binders (linseed, poppy seed, and walnut oils) obtained from different manufacturers. These model samples were left to dry and then characterized by Raman and reflectance near-infrared spectroscopy. Multivariate analysis was performed by applying principal component analysis (PCA) on the first derivative of the corresponding Raman spectra (1800-750 cm(-1)), near-infrared spectra (6000-3900 cm(-1)), and their combination to test whether spectral differences could enable samples to be distinguished on the basis of their composition. The vibrational bands we found most useful to discriminate between the different products we studied are the fundamental ν(C=C) stretching and methylenic stretching and bending combination bands. The results of the multivariate analysis demonstrated the potential of chemometric approaches for characterizing and identifying drying oils, and also for gaining a deeper insight into the aging process. Comparison with high-performance liquid chromatography data was conducted to check the PCA results.

Raman technology for future planetary missions

NASA Astrophysics Data System (ADS)

Thiele, Hans; Hofer, Stefan; Stuffler, Timo; Glier, Markus; Popp, Jürgen; Sqalli, Omar; Wuttig, Andreas; Riesenberg, Rainer

2017-11-01

Scientific experiments on mineral and biological samples with Raman excitation below 300nm show a wealth of scientific information. The fluorescence, which typically decreases signal quality in the visual or near infrared wavelength regime can be avoided with deep ultraviolet excitation. This wavelength regime is therefore regarded as highly attractive for a compact high performance Raman spectrometer for in-situ planetary research. Main objective of the MIRAS II breadboard activity presented here (MIRAS: Mineral Investigation with Raman Spectroscopy) is to evaluate, design and build a compact fiber coupled deep-UV Raman system breadboard. Additionally, the Raman system is combined with an innovative scanning microscope system to allow effective auto-focusing and autonomous orientation on the sample surface for high precise positioning or high resolution Raman mapping.

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

A Taxonomy of Computer Media in Distance Education.

ERIC Educational Resources Information Center

Chacon, Fabio

1992-01-01

Describes a taxonomy of computer user modes in distance education and identifies three major learning and behavioral processes that are extended by computers: (1) information processing; (2) interaction; and (3) communication. Highlights for each process include the relationship to other media, pedagogical functions, hardware and software, and…

Wide-Field Raman Imaging of Dental Lesions

PubMed Central

Yang, Shan; Li, Bolan; Akkus, Anna; Akkus, Ozan; Lang, Lisa

2014-01-01

Detection of dental caries at the onset remains as a great challenge in dentistry. Raman spectroscopy could be successfully applied towards detecting caries since it is sensitive to the amount of the Raman active mineral crystals, the most abundant component of enamel. Effective diagnosis requires full examination of a tooth surface via a Raman mapping. Point-scan Raman mapping is not clinically relevant (feasible) due to lengthy data acquisition time. In this work, a wide-field Raman imaging system was assembled based on a high-sensitivity 2D CCD camera for imaging the mineralization status of teeth with lesions. Wide-field images indicated some lesions to be hypomineralized and others to be hypermineralized. The observations of wide-field Raman imaging were in agreement with point-scan Raman mapping. Therefore, sound enamel and lesions can be discriminated by Raman imaging of the mineral content. In conclusion, wide-field Raman imaging is a potentially useful tool for visualization of dental lesions in the clinic. PMID:24781363

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

"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

Integrated Raman spectroscopy and trimodal wide-field imaging techniques for real-time in vivo tissue Raman measurements at endoscopy.

PubMed

Huang, Zhiwei; Teh, Seng Khoon; Zheng, Wei; Mo, Jianhua; Lin, Kan; Shao, Xiaozhuo; Ho, Khek Yu; Teh, Ming; Yeoh, Khay Guan

2009-03-15

We report an integrated Raman spectroscopy and trimodal (white-light reflectance, autofluorescence, and narrow-band) imaging techniques for real-time in vivo tissue Raman measurements at endoscopy. A special 1.8 mm endoscopic Raman probe with filtering modules is developed, permitting effective elimination of interference of fluorescence background and silica Raman in fibers while maximizing tissue Raman collections. We demonstrate that high-quality in vivo Raman spectra of upper gastrointestinal tract can be acquired within 1 s or subseconds under the guidance of wide-field endoscopic imaging modalities, greatly facilitating the adoption of Raman spectroscopy into clinical research and practice during routine endoscopic inspections.

UV Raman imaging--a promising tool for astrobiology: comparative Raman studies with different excitation wavelengths on SNC Martian meteorites.

PubMed

Frosch, Torsten; Tarcea, Nicolae; Schmitt, Michael; Thiele, Hans; Langenhorst, Falko; Popp, Jürgen

2007-02-01

The great capabilities of UV Raman imaging have been demonstrated on the three Martian meteorites: Sayh al Uhaymir, Dar al Gani, and Zagami. Raman spectra without disturbing fluorescence and with high signal-to-noise-ratios and full of spectral features were derived. This result is of utmost importance for the development of powerful instruments for space missions. By point scanning the surfaces of the meteorite samples, it was possible for the first time to construct UV-Raman images out of the array of Raman spectra. Deep-UV Raman images are to the best of our knowledge presented for the first time. The images were used for a discussion of the chemical-mineralogical composition and texture of the meteorite surfaces. Comparative Raman studies applying visible and NIR Raman excitation wavelengths demonstrate a much better performance for UV Raman excitation. This comparative study of different Raman excitation wavelengths at the same sample spots was done by constructing a versatile, robust sample holder with a fixed micro-raster. The overall advantages of UV resonance Raman spectroscopy in terms of sensitivity and selectivity are demonstrated and discussed. Finally the application of this new technique for a UV Raman instrument for envisaged astrobiological focused space missions is suggested.

Spatially offset Raman spectroscopy based on a line-scan hyperspectral Raman system

USDA-ARS?s Scientific Manuscript database

Spatially offset Raman spectroscopy (SORS) is a technique that can obtain subsurface layered information by collecting Raman spectra from a series of surface positions laterally offset from the excitation laser. The current methods of SORS measurement are typically either slow due to mechanical move...

Applying a Knowledge Management Taxonomy to Secondary Schools

ERIC Educational Resources Information Center

Thambi, Melinda; O'Toole, Paddy

2012-01-01

The purpose of this article is to examine the relevance of a corporate-based taxonomy of knowledge management to secondary schooling. Do the principles of knowledge management from the corporate world translate to the world of education; specifically, secondary schooling? This article examines categories of knowledge management articulated in…

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.

Development of a miRNA surface-enhanced Raman scattering assay using benchtop and handheld Raman systems

NASA Astrophysics Data System (ADS)

Schechinger, Monika; Marks, Haley; Locke, Andrea; Choudhury, Mahua; Cote, Gerard

2018-01-01

DNA-functionalized nanoparticles, when paired with surface-enhanced Raman spectroscopy (SERS), can rapidly detect microRNA. However, widespread use of this approach is hindered by drawbacks associated with large and expensive benchtop Raman microscopes. MicroRNA-17 (miRNA-17) has emerged as a potential epigenetic indicator of preeclampsia, a condition that occurs during pregnancy. Biomarker detection using an SERS point-of-care device could enable prompt diagnosis and prevention as early as the first trimester. Recently, strides have been made in developing portable Raman systems for field applications. An SERS assay for miRNA-17 was assessed and translated from traditional benchtop Raman microscopes to a handheld system. Three different photoactive molecules were compared as potential Raman reporter molecules: a chromophore, malachite green isothiocyanate (MGITC), a fluorophore, tetramethylrhodamine isothiocyanate, and a polarizable small molecule 5,5-dithio-bis-(2-nitrobenzoic acid) (DTNB). For the benchtop Raman microscope, the DTNB-labeled assay yielded the greatest sensitivity under 532-nm laser excitation, but the MGITC-labeled assay prevailed at 785 nm. Conversely, DTNB was preferable for the miniaturized 785-nm Raman system. This comparison showed significant SERS enhancement variation in response to 1-nM miRNA-17, implying that the sensitivity of the assay may be more heavily dependent on the excitation wavelength, instrumentation, and Raman reporter chosen than on the plasmonic coupling from DNA/miRNA-mediated nanoparticle assemblies.

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.

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.

Micro-Raman spectroscopy in the identification of wulfenite and vanadinite in a Sasanian painted stucco fragment of the Ghaleh Guri in Ramavand, western Iran.

PubMed

Holakooei, Parviz; Karimy, Amir-Hossein; Hasanpour, Ata; Oudbashi, Omid

2016-12-05

This paper reports the results of studies performed on a painted stucco fragment excavated at the Ghaleh Guri in Ramavand, western Iran, and dated back to the late Sasanian period (224-651AD). Analytical studies including micro-Raman spectroscopy (μ-Raman), micro-X-ray spectrometry (μ-XRF) and optical microscopy showed that red lead and vermilion were used as main pigments on this fragment. Moreover, carbon black was diagnosed to thinly cover some parts of the red lead. Peculiarly, wulfenite (PbMoO4) associated with vanadinite (Pb5(VO4)3Cl) was identified to compose a yellow stain sporadically dispersed on the other pigments. Copyright © 2016 Elsevier B.V. All rights reserved.

Patient complaints about hospital services: applying a complaint taxonomy to analyse and respond to complaints.

PubMed

Harrison, Reema; Walton, Merrilyn; Healy, Judith; Smith-Merry, Jennifer; Hobbs, Coletta

2016-04-01

To explore the applicability of a patient complaint taxonomy to data on serious complaint cases. Qualitative descriptive study. Complaints made to the New South Wales (NSW) Health Care Complaints Commission, Australia between 2005 and 2010. All 138 cases of serious complaints by patients about public hospitals and other health facilities investigated in the 5-year period. A thematic analysis of the complaints was conducted to identify particular complaint issues and the Reader et al. (Patient complaints in healthcare systems: a systematic review and coding taxonomy. BMJ Qual Saf 2014;23:678-89.) patient complaint taxonomy was then used to classify these issues into categories and sub-categories. The 138 investigated cases revealed 223 complaint issues. Complaint issues were distributed into the three domains of the patient complaint taxonomy: clinical, management and relationships. Complaint issue most commonly related to delayed diagnosis, misdiagnosis, medication errors, inadequate examinations, inadequate/nil treatment and quality of care including nursing care. The types of complaints from patients about their healthcare investigated by the NSW Commission were similar to those received by other patient complaint entities in Australia and worldwide. The application of a standard taxonomy to large numbers of complaints cases from different sources would enable the creation of aggregated data. Such data would have better statistical capacity to identify common safety and quality healthcare problems and so point to important areas for improvement. Some conceptual challenges in devising and using a taxonomy must be addressed, such as inherent problems in ensuring coding consistency, and giving greater weight to patient concerns about their treatment. © The Author 2016. Published by Oxford University Press in association with the International Society for Quality in Health Care; all rights reserved.

Scientific teaching: defining a taxonomy of observable practices.

PubMed

Couch, Brian A; Brown, Tanya L; Schelpat, Tyler J; Graham, Mark J; Knight, Jennifer K

2015-03-02

Over the past several decades, numerous reports have been published advocating for changes to undergraduate science education. These national calls inspired the formation of the National Academies Summer Institutes on Undergraduate Education in Biology (SI), a group of regional workshops to help faculty members learn and implement interactive teaching methods. The SI curriculum promotes a pedagogical framework called Scientific Teaching (ST), which aims to bring the vitality of modern research into the classroom by engaging students in the scientific discovery process and using student data to inform the ongoing development of teaching methods. With the spread of ST, the need emerges to systematically define its components in order to establish a common description for education researchers and practitioners. We describe the development of a taxonomy detailing ST's core elements and provide data from classroom observations and faculty surveys in support of its applicability within undergraduate science courses. The final taxonomy consists of 15 pedagogical goals and 37 supporting practices, specifying observable behaviors, artifacts, and features associated with ST. This taxonomy will support future educational efforts by providing a framework for researchers studying the processes and outcomes of ST-based course transformations as well as a concise guide for faculty members developing classes. © 2015 B. A. Couch et al. CBE—Life Sciences Education © 2015 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

[Laser Raman spectrum analysis of carbendazim pesticide].

PubMed

Wang, Xiao-bin; Wu, Rui-mei; Liu, Mu-hua; Zhang, Lu-ling; Lin, Lei; Yan, Lin-yuan

2014-06-01

Raman signal of solid and liquid carbendazim pesticide was collected by laser Raman spectrometer. The acquired Raman spectrum signal of solid carbendazim was preprocessed by wavelet analysis method, and the optimal combination of wavelet denoising parameter was selected through mixed orthogonal test. The results showed that the best effect was got with signal to noise ratio (SNR) being 62.483 when db2 wavelet function was used, decomposition level was 2, the threshold option scheme was 'rigisure' and reset mode was 'sln'. According to the vibration mode of different functional groups, the de-noised Raman bands could be divided into 3 areas: 1 400-2 000, 700-1 400 and 200-700 cm(-1). And the de-noised Raman bands were assigned with and analyzed. The characteristic vibrational modes were gained in different ranges of wavenumbers. Strong Raman signals were observed in the Raman spectrum at 619, 725, 964, 1 022, 1 265, 1 274 and 1 478 cm(-1), respectively. These characteristic vibrational modes are characteristic Raman peaks of solid carbendazim pesticide. Find characteristic Raman peaks at 629, 727, 1 001, 1 219, 1 258 and 1 365 cm(-1) in Raman spectrum signal of liquid carbendazim. These characteristic peaks were basically tallies with the solid carbendazim. The results can provide basis for the rapid screening of pesticide residue in food and agricultural products based on Raman spectrum.

A Taxonomy of Attacks on the DNP3 Protocol

NASA Astrophysics Data System (ADS)

East, Samuel; Butts, Jonathan; Papa, Mauricio; Shenoi, Sujeet

Distributed Network Protocol (DNP3) is the predominant SCADA protocol in the energy sector - more than 75% of North American electric utilities currently use DNP3 for industrial control applications. This paper presents a taxonomy of attacks on the protocol. The attacks are classified based on targets (control center, outstation devices and network/communication paths) and threat categories (interception, interruption, modification and fabrication). To facilitate risk analysis and mitigation strategies, the attacks are associated with the specific DNP3 protocol layers they exploit. Also, the operational impact of the attacks is categorized in terms of three key SCADA objectives: process confi- dentiality, process awareness and process control. The attack taxonomy clarifies the nature and scope of the threats to DNP3 systems, and can provide insights into the relative costs and benefits of implementing mitigation strategies.

Driver distraction and driver inattention: definition, relationship and taxonomy.

PubMed

Regan, Michael A; Hallett, Charlene; Gordon, Craig P

2011-09-01

There is accumulating evidence that driver distraction and driver inattention are leading causes of vehicle crashes and incidents. However, as applied psychological constructs, they have been inconsistently defined and the relationship between them remains unclear. In this paper, driver distraction and driver inattention are defined and a taxonomy is presented in which driver distraction is distinguished from other forms of driver inattention. The taxonomy and the definitions provided are intended (a) to provide a common framework for coding different forms of driver inattention as contributing factors in crashes and incidents, so that comparable estimates of their role as contributing factors can be made across different studies, and (b) to make it possible to more accurately interpret and compare, across studies, the research findings for a given form of driver inattention. Copyright © 2011 Elsevier Ltd. All rights reserved.

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

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

PubMed

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

2018-06-07

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

Raman spectroscopy of oral bacteria

NASA Astrophysics Data System (ADS)

Berger, Andrew J.; Zhu, Qingyuan; Quivey, Robert G.

2003-10-01

Raman spectroscopy has been employed to measure the varying concentrations of two oral bacteria in simple mixtures. Evaporated droplets of centrifuged mixtures of Streptococcus sanguis and Streptococcus mutans were analyzed via Raman microspectroscopy. The concentration of s. sanguis was determined based upon the measured Raman spectrum, using partial least squares cross-validation, with an r2 value of 0.98.

Polarized micro Raman spectroscopy of bilayer graphene

NASA Astrophysics Data System (ADS)

Moon, Hyerim; Yoon, Duhee; Son, Young-Woo; Cheong, Hyeonsik

2009-03-01

The frequency of Raman 2D band of the graphite depends on the excitation laser energy. This phenomenon is explained with double resonance Raman process. In polarized micro-Raman spectroscopy of single layer graphene, Raman G band (˜1586 cm-1) is isotropic, and 2D band (˜2686 cm-1) strongly depends on relative polarizations of the incident and scattered photons. This strong polarization dependence originates from inhomogeneous optical absorption and emission mediated by resonant electron-phonon interaction. In bi-layer graphene, Raman 2D band can be decomposed into four Lorenztian peaks which can be interpreted in terms of the four transition paths in the double resonance Raman process. We investigated the polarization dependence of each Lorenztian peak in the Raman 2D band of bi-layer graphene for different excitation laser energies. Strong polarization dependence of the Raman 2D band, similar to the case of single layer graphene, is observed. The excitation energy dependence of the polarized Raman scattering is analyzed in terms of the band structure of bi-layer graphene.

Raman and surface enhanced Raman spectroscopy of amino acids and peptide

NASA Astrophysics Data System (ADS)

Yuan, Xiaojuan; Gu, Huaimin; Wu, Jiwei; Kang, Jian; Dong, Xiao

2009-08-01

Surface enhanced Raman scattering (SERS) is potentially tool in the characterization of biomolecules such as amino acids, complicated peptides and proteins, and even tissues or living cells. Amino acids and short peptides contain different functional groups. Therefore, they are suitable for the investigations of the competitive-interactions of these functional groups with colloidal silver surfaces. In this paper, Normal Raman and SERS of amino acids Leucine and Isoleucine and short peptide Leu-Leu were measured on the silver colloidal substrate. Raman shifts that stem from different vibrational mode in the molecular inner structure, and the variations of SERS of the samples were analyzed in this study. The results show that different connection of one methyl to the main chains of the isomer amino acids resulted in different vibration modes in the Normal Raman spectra of Leucine and Isoleucine. In the SERS spectra of the isomer amino acids, all frequency shifts are expressed more differently than those in Normal Raman spectra of solid state. Orientation of this isomer amino acids, as well as specific-competitive interactions of their functional groups with the colloidal silver surface, were speculated by detailed spectral analysis of the obtained SERS spectra. In addition, the dipeptide Leu-Leu, as the corresponding homodipeptide of Leucine, was also measured adsorbed on the colloidal silver surface. The SERS spectrum of Leu-Leu is different from its corresponding amino acid Leucine but both of them are adsorbed on the silver surface through the carboxylate moiety.

Optimizing laser crater enhanced Raman spectroscopy.

PubMed

Lednev, V N; Sdvizhenskii, P A; Grishin, M Ya; Filichkina, V A; Shchegolikhin, A N; Pershin, S M

2018-03-20

Raman signal enhancement by laser crater production was systematically studied for 785 nm continuous wave laser pumping. Laser craters were produced in L-aspartic acid powder by a nanosecond pulsed solid state neodymium-doped yttrium aluminum garnet laser (532 nm, 8 ns, 1 mJ/pulse), while Raman spectra were then acquired by using a commercial spectrometer with 785 nm laser beam pumping. The Raman signal enhancement effect was studied in terms of the number of ablating pulses used, the lens-to-sample distance, and the crater-center-laser-spot offset. The influence of the experiment parameters on Raman signal enhancement was studied for different powder materials. Maximum Raman signal enhancement reached 11 fold for loose powders but decreased twice for pressed tablets. Raman signal enhancement was demonstrated for several diverse powder materials like gypsum or ammonium nitrate with better results achieved for the samples tending to give narrow and deep craters upon the laser ablation stage. Alternative ways of cavity production (steel needle tapping and hole drilling) were compared with the laser cratering technique in terms of Raman signal enhancement. Drilling was found to give the poorest enhancement of the Raman signal, while both laser ablation and steel needle tapping provided comparable results. Here, we have demonstrated for the first time, to the best of our knowledge, that a Raman signal can be enhanced 10 fold with the aid of simple cavity production by steel needle tapping in rough highly reflective materials. Though laser crater enhancement Raman spectroscopy requires an additional pulsed laser, this technique is more appropriate for automatization compared to the needle tapping approach.

Algal taxonomy: a road to nowhere?

PubMed

De Clerck, Olivier; Guiry, Michael D; Leliaert, Frederik; Samyn, Yves; Verbruggen, Heroen

2013-04-01

The widespread view of taxonomy as an essentially retrogressive and outmoded science unable to cope with the current biodiversity crisis stimulated us to analyze the current status of cataloguing global algal diversity. Contrary to this largely pessimistic belief, species description rates of algae through time and trends in the number of active taxonomists, as revealed by the web resource AlgaeBase, show a much more positive picture. More species than ever before are being described by a large community of algal taxonomists. The lack of any decline in the rate at which new species and genera are described, however, is indicative of the large proportion of undiscovered diversity and bears heavily on any prediction of global algal species diversity and the time needed to catalogue it. The saturation of accumulation curves of higher taxa (family, order, and classes) on the other hand suggest that at these taxonomic levels most diversity has been discovered. This reasonably positive picture does not imply that algal taxonomy does not face serious challenges in the near future. The observed levels of cryptic diversity in algae, combined with the shift in methods used to characterize them, have resulted in a rampant uncertainty about the status of many older species. As a consequence, there is a tendency in phycology to move gradually away from traditional names to a more informal system whereby clade-, specimen- or strain-based identifiers are used to communicate biological information. Whether these informal names for species-level clades represent a temporary situation stimulated by the lag between species discovery and formal description, or an incipient alternative or parallel taxonomy, will be largely determined by how well we manage to integrate historical collections into modern taxonomic research. Additionally, there is a pressing need for a consensus about the organizational framework to manage the information about algal species names. An eventual strategy

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

Raman microspectrometer combined with scattering microscopy and lensless imaging for bacteria identification

NASA Astrophysics Data System (ADS)

Strola, S. A.; Schultz, E.; Allier, C. P.; DesRoches, B.; Lemmonier, J.; Dinten, J.-M.

2013-03-01

In this paper, we report on a compact prototype capable both of lensfree imaging, Raman spectrometry and scattering microscopy from bacteria samples. This instrument allows high-throughput real-time characterization without the need of markers, making it potentially suitable to field label-free biomedical and environmental applications. Samples are illuminated from above with a focused-collimated 532nm laser beam and can be x-y-z scanned. The bacteria detection is based on emerging lensfree imaging technology able to localize cells of interest over a large field-of-view of 24mm2. Raman signal and scattered light are then collected by separate measurement arms simultaneously. In the first arm the emission light is fed by a fiber into a prototype spectrometer, developed by Tornado Spectral System based on Tornado's High Throughput Virtual Slit (HTVS) novel technology. The enhanced light throughput in the spectral region of interest (500-1800 cm-1) reduces Raman acquisition time down to few seconds, thus facilitating experimental protocols and avoiding the bacteria deterioration induced by laser thermal heating. Scattered light impinging in the second arm is collected onto a charge-coupled-device. The reconstructed image allows studying the single bacteria diffraction pattern and their specific structural features. The characterization and identification of different bacteria have been performed to validate and optimize the acquisition system and the component setup. The results obtained demonstrate the benefits of these three techniques combination by providing the precise bacteria localization, their chemical composition and a morphology description. The procedure for a rapid identification of particular pathogen bacteria in a sample is illustrated.

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

The comprehensive 'Communicate to Vaccinate' taxonomy of communication interventions for childhood vaccination in routine and campaign contexts.

PubMed

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

2017-05-10

Communication can be used to generate demand for vaccination or address vaccine hesitancy, and is crucial to successful childhood vaccination programmes. Research efforts have primarily focused on communication for routine vaccination. However, vaccination campaigns, particularly in low- or middle-income countries (LMICs), also use communication in diverse ways. Without a comprehensive framework integrating communication interventions from routine and campaign contexts, it is not possible to conceptualise the full range of possible vaccination communication interventions. Therefore, vaccine programme managers may be unaware of potential communication options and researchers may not focus on building evidence for interventions used in practice. In this paper, we broaden the scope of our existing taxonomy of communication interventions for routine vaccination to include communication used in campaigns, and integrate these into a comprehensive taxonomy of vaccination communication interventions. Building on our taxonomy of communication for routine vaccination, we identified communication interventions used in vaccination campaigns through a targeted literature search; observation of vaccination activities in Cameroon, Mozambique and Nigeria; and stakeholder consultations. We added these interventions to descriptions of routine vaccination communication and categorised the interventions according to their intended purposes, building from an earlier taxonomy of communication related to routine vaccination. The comprehensive taxonomy groups communication used in campaigns and routine childhood vaccination into seven purpose categories: 'Inform or Educate'; 'Remind or Recall'; 'Enhance Community Ownership'; 'Teach Skills'; 'Provide Support'; 'Facilitate Decision Making' and 'Enable Communication'. Consultations with LMIC stakeholders and experts informed the taxonomy's definitions and structure and established its potential uses. This taxonomy provides a standardised way

Blood analysis by Raman spectroscopy.

PubMed

Enejder, Annika M K; Koo, Tae-Woong; Oh, Jeankun; Hunter, Martin; Sasic, Slobodan; Feld, Michael S; Horowitz, Gary L

2002-11-15

Concentrations of multiple analytes were simultaneously measured in whole blood with clinical accuracy, without sample processing, using near-infrared Raman spectroscopy. Spectra were acquired with an instrument employing nonimaging optics, designed using Monte Carlo simulations of the influence of light-scattering-absorbing blood cells on the excitation and emission of Raman light in turbid medium. Raman spectra were collected from whole blood drawn from 31 individuals. Quantitative predictions of glucose, urea, total protein, albumin, triglycerides, hematocrit, and hemoglobin were made by means of partial least-squares (PLS) analysis with clinically relevant precision (r(2) values >0.93). The similarity of the features of the PLS calibration spectra to those of the respective analyte spectra illustrates that the predictions are based on molecular information carried by the Raman light. This demonstrates the feasibility of using Raman spectroscopy for quantitative measurements of biomolecular contents in highly light-scattering and absorbing media.

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

PubMed Central

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

2002-01-01

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

Raman water vapor lidar calibration

NASA Astrophysics Data System (ADS)

Landulfo, E.; Da Costa, R. F.; Torres, A. S.; Lopes, F. J. S.; Whiteman, D. N.; Venable, D. D.

2009-09-01

We show here new results of a Raman LIDAR calibration methodology effort putting emphasis in the assessment of the cross-section ratio between water vapor and nitrogen by the use of a calibrated NIST traceable tungsten lamp. Therein we give a step by step procedure of how to employ such equipment by means of a mapping/scanning procedure over the receiving optics of a water vapor Raman LIDAR. This methodology has been independently used at Howard University Raman LIDAR and at IPEN Raman LIDAR what strongly supports its reproducibility and points towards an independently calibration methodology to be carried on within an experiment routine.

Novel Raman Techniques for Imaging and Sensing

NASA Astrophysics Data System (ADS)

Edwards, Perry S.

Raman scattering spectroscopy is extensively demonstrated as a label-free, chemically selective sensing and imaging technique for a multitude of chemical and biological applications. The ability to detect "fingerprint" spectral signatures of individual molecules, without the need to introduce chemical labelers, makes Raman scattering a powerful sensing technique. However, spectroscopy based on spontaneous Raman scattering traditionally suffers from inherently weak signals due to small Raman scattering cross-sections. Thus, considerable efforts have been put forth to find pathways towards enhancing Raman signals to bolster sensitivity for detecting small concentrations of molecules or particles. The development of coherent Raman techniques that can offer orders of magnitude increase in signal have garnered significant interest in recent years for their application in imaging; such techniques include coherent anti-Stokes Raman scattering and stimulated Raman scattering. Additionally, methods to enhance the local field of either the pump or generated Raman signal, such as through surface enhanced Raman scattering, have been investigated for their orders of magnitude improvement in sensitivity and single molecule sensing capability. The work presented in this dissertation describes novel techniques for performing high speed and highly sensitive Raman imaging as well as sensing applications towards bioimaging and biosensing. Coherent anti-Stokes Raman scattering (CARS) is combined with holography to enable recording of high-speed (single laser shot), wide field CARS holograms which can be used to reconstruct the both the amplitude and the phase of the anti-Stokes field therefore allowing 3D imaging. This dissertation explores CARS holography as a viable label-free bio-imaging technique. A Raman scattering particle sensing system is also developed that utilizes wave guide properties of optical fibers and ring-resonators to perform enhanced particle sensing. Resonator

Quantitative Analysis of Microbicide Concentrations in Fluids, Gels and Tissues Using Confocal Raman Spectroscopy

PubMed Central

Chuchuen, Oranat; Henderson, Marcus H.; Sykes, Craig; Kim, Min Sung; Kashuba, Angela D. M.; Katz, David F.

2013-01-01

Topical vaginal anti-HIV microbicides are an important focus in female-based strategies to prevent the sexual transmission of HIV. Understanding microbicide pharmacokinetics is essential to development, characterization and implementation of efficacious microbicide drug delivery formulations. Current methods to measure drug concentrations in tissue (e.g., LC-MS/MS, liquid chromatography coupled with tandem mass spectrometry) are highly sensitive, but destructive and complex. This project explored the use of confocal Raman spectroscopy to detect microbicide drugs and to measure their local concentrations in fluids, drug delivery gels, and tissues. We evaluated three candidate microbicide drugs: tenofovir, Dapivirine and IQP-0528. Measurements were performed in freshly excised porcine buccal tissue specimens, gel vehicles and fluids using two Horiba Raman microscopes, one of which is confocal. Characteristic spectral peak calibrations for each drug were obtained using serial dilutions in the three matrices. These specific Raman bands demonstrated strong linear concentration dependences in the matrices and were characterized with respect to their unique vibrational signatures. At least one specific Raman feature was identified for each drug as a marker band for detection in tissue. Sensitivity of detection was evaluated in the three matrices. A specific peak was also identified for tenofovir diphosphate, the anti-HIV bioactive product of tenofovir after phosphorylation in host cells. Z-scans of drug concentrations vs. depth in excised tissue specimens, incubated under layers of tenofovir solution in a Transwell assay, showed decreasing concentration with depth from the surface into the tissue. Time-dependent concentration profiles were obtained from tissue samples incubated in the Transwell assay, for times ranging 30 minutes - 6 hours. Calibrations and measurements from tissue permeation studies for tenofovir showed good correlation with gold standard LC-MS/MS data

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

ERIC Educational Resources Information Center

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

1995-01-01

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

Kerr-gated picosecond Raman spectroscopy and Raman photon migration of equine bone tissue with 400-nm excitation

NASA Astrophysics Data System (ADS)

Morris, Michael D.; Goodship, Allen E.; Draper, Edward R. C.; Matousek, Pavel; Towrie, Michael; Parker, Anthony W.

2004-07-01

We show that Raman spectroscopy with visible lasers, even in the deep blue is possible with time-gated Raman spectroscopy. A 4 picosec time gate allows efficient fluorescence rejection, up to 1000X, and provides almost background-free Raman spectra with low incident laser power. The technology enables spectroscopy with better than 10X higher scattering efficiency than is possible with the NIR (785 nm and 830 nm) lasers that are conventionally used. Raman photon migration is shown to allow depth penetration. We show for the first time that Kerr-gated Raman spectra of bone tissue with blue laser excitation enables both fluorescence rejection and depth penetration.

Development of a miRNA surface-enhanced Raman scattering assay using benchtop and handheld Raman systems.

PubMed

Schechinger, Monika; Marks, Haley; Locke, Andrea; Choudhury, Mahua; Cote, Gerard

2018-01-01

DNA-functionalized nanoparticles, when paired with surface-enhanced Raman spectroscopy (SERS), can rapidly detect microRNA. However, widespread use of this approach is hindered by drawbacks associated with large and expensive benchtop Raman microscopes. MicroRNA-17 (miRNA-17) has emerged as a potential epigenetic indicator of preeclampsia, a condition that occurs during pregnancy. Biomarker detection using an SERS point-of-care device could enable prompt diagnosis and prevention as early as the first trimester. Recently, strides have been made in developing portable Raman systems for field applications. An SERS assay for miRNA-17 was assessed and translated from traditional benchtop Raman microscopes to a handheld system. Three different photoactive molecules were compared as potential Raman reporter molecules: a chromophore, malachite green isothiocyanate (MGITC), a fluorophore, tetramethylrhodamine isothiocyanate, and a polarizable small molecule 5,5-dithio-bis-(2-nitrobenzoic acid) (DTNB). For the benchtop Raman microscope, the DTNB-labeled assay yielded the greatest sensitivity under 532-nm laser excitation, but the MGITC-labeled assay prevailed at 785 nm. Conversely, DTNB was preferable for the miniaturized 785-nm Raman system. This comparison showed significant SERS enhancement variation in response to 1-nM miRNA-17, implying that the sensitivity of the assay may be more heavily dependent on the excitation wavelength, instrumentation, and Raman reporter chosen than on the plasmonic coupling from DNA/miRNA-mediated nanoparticle assemblies. (2018) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

Introduction to Raman chemical imaging technology

USDA-ARS?s Scientific Manuscript database

New developments in computer and imaging hardware have significantly advanced Raman spectroscopy and spectral imaging technologies, and have led to the recent emergence of new Raman detection techniques for rapid and online applications. This book chapter presents Raman chemical imaging technology a...

Rapid detection and identification of energetic materials with surface enhanced raman spectrometry (SERS)

DOEpatents

Han, Thomas Yong-Jin; Valdez, Carlos A; Olson, Tammy Y; Kim, Sung Ho; Satcher, Jr., Joe H

2015-04-21

In one embodiment, a system includes a plurality of metal nanoparticles functionalized with a plurality of organic molecules tethered thereto, wherein the plurality of organic molecules preferentially interact with one or more analytes when placed in proximity therewith. According to another embodiment, a method for detecting analytes includes contacting a fluid having one or more analytes of interest therein with a plurality of metal nanoparticles, each metal nanoparticle having a plurality of organic molecules tethered thereto, and detecting Raman scattering from an analyte of interest from the fluid, the analyte interacting with one or more of the plurality of organic molecules. In another embodiment, a method includes chemically modifying a plurality of cyclodextrin molecules at a primary hydroxyl moiety to create a chemical handle, and tethering the plurality of cyclodextrin molecules to a metal nanoparticle using the chemical handle. Other systems and methods for detecting analytes are also described.

Pigment identification in artwork using graphite furnace atomic absorption spectrometry.

PubMed

Goltz, D M; Coombs, J; Marion, C; Cloutis, E; Gibson, J; Attas, M; Choo-Smith, L-P; Collins, C

2004-06-17

The use of a sampling technique is described for the identification of metals from inorganic pigments in paint. The sampling technique involves gently contacting a cotton swab with the painted surface to physically remove a minute quantity ( approximately 1-2mug) of pigment. The amount of material removed from the painted surface is invisible to the unaided eye and does not cause any visible effect to the painted surface. The cotton swab was then placed in a 1.5ml polystyrene beaker containing HNO(3) to extract pigment metals prior to analysis using graphite furnace atomic absorption spectrometry (GFAAS). GFAAS is well suited for identifying pigment metals since it requires small samples and many pigments consist of main group elements (e.g. Al) as well as transition metals (e.g. Zn, Fe and Cd). Using Cd (cadmium red) as the test element, the reproducibility of sampling a paint surface with the cotton swab was approximately 13% in either a water or oil medium. To test the feasibility of cotton sampling for pigment identification, samples were obtained from paintings (watercolour and oil) of a local collection. Raman spectra provided complementary information to the GFAAS, which together are essential for positive identification of some pigments. For example, GFAAS indicated the presence of Cu, but the Raman spectra positively identified the modern copper pigment phthalocyanine green (Cu(C(32)Cl(16)N(8)). Both Raman spectroscopy and GFAAS were useful for identifying ZnO as a white pigment.

Taxonomy of oxalotrophic Methylobacterium strains.

PubMed

Sahin, Nurettin; Kato, Yuko; Yilmaz, Ferah

2008-10-01

Most of the oxalotrophic bacteria are facultative methylotrophs and play important ecological roles in soil fertility and cycling of elements. This study gives a detailed picture of the taxonomy and diversity of these bacteria and provides new information about the taxonomical variability within the genus Methylobacterium. Twelve mesophilic, pink-pigmented, and facultatively methylotrophic oxalate-oxidizing strains were included in this work that had been previously isolated from the soil and some plant tissues by the potassium oxalate enrichment method. The isolates were characterized using biochemical tests, cellular lipid profiles, spectral characteristics of carotenoid pigments, G+C content of the DNA, and 16S rDNA sequencing. The taxonomic similarities among the strains were analyzed using the simple matching (S (SM)) and Jaccard (S (J)) coefficients, and the UPGMA clustering algorithm. The phylogenetic position of the strains was inferred by the neighbor-joining method on the basis of the 16S rDNA sequences. All isolates were Gram-negative, facultatively methylotrophic, oxidase and catalase positive, and required no growth factors. Based on the results of numerical taxonomy, the strains formed four closely related clusters sharing > or =85% similarity. Analysis of the 16S rDNA sequences demonstrated that oxalotrophic, pink-pigmented, and facultatively methylotrophic strains could be identified as members of the genus Methylobacterium. Except for M. variabile and M. aquaticum, all of the Methylobacterium type strains tested had the ability of oxalate utilization. Our results indicate that the capability of oxalate utilization seems to be an uncommon trait and could be used as a valuable taxonomic criterion for differentiation of Methylobacterium species.

Taxonomy of oxalotrophic Methylobacterium strains

NASA Astrophysics Data System (ADS)

Sahin, Nurettin; Kato, Yuko; Yilmaz, Ferah

2008-10-01

Most of the oxalotrophic bacteria are facultative methylotrophs and play important ecological roles in soil fertility and cycling of elements. This study gives a detailed picture of the taxonomy and diversity of these bacteria and provides new information about the taxonomical variability within the genus Methylobacterium. Twelve mesophilic, pink-pigmented, and facultatively methylotrophic oxalate-oxidizing strains were included in this work that had been previously isolated from the soil and some plant tissues by the potassium oxalate enrichment method. The isolates were characterized using biochemical tests, cellular lipid profiles, spectral characteristics of carotenoid pigments, G+C content of the DNA, and 16S rDNA sequencing. The taxonomic similarities among the strains were analyzed using the simple matching ( S SM) and Jaccard ( S J) coefficients, and the UPGMA clustering algorithm. The phylogenetic position of the strains was inferred by the neighbor-joining method on the basis of the 16S rDNA sequences. All isolates were Gram-negative, facultatively methylotrophic, oxidase and catalase positive, and required no growth factors. Based on the results of numerical taxonomy, the strains formed four closely related clusters sharing ≥85% similarity. Analysis of the 16S rDNA sequences demonstrated that oxalotrophic, pink-pigmented, and facultatively methylotrophic strains could be identified as members of the genus Methylobacterium. Except for M. variabile and M. aquaticum, all of the Methylobacterium type strains tested had the ability of oxalate utilization. Our results indicate that the capability of oxalate utilization seems to be an uncommon trait and could be used as a valuable taxonomic criterion for differentiation of Methylobacterium species.

A Taxonomy of Virtual Worlds Usage in Education

ERIC Educational Resources Information Center

Duncan, Ishbel; Miller, Alan; Jiang, Shangyi

2012-01-01

Virtual worlds are an important tool in modern education practices as well as providing socialisation, entertainment and a laboratory for collaborative work. This paper focuses on the uses of virtual worlds for education and synthesises over 100 published academic papers, reports and educational websites from around the world. A taxonomy is then…

A Novel Technique for Raman Analysis of Highly Radioactive Samples Using Any Standard Micro-Raman Spectrometer

PubMed Central

Colle, Jean-Yves; Naji, Mohamed; Sierig, Mark; Manara, Dario

2017-01-01

A novel approach for the Raman measurement of nuclear materials is reported in this paper. It consists of the enclosure of the radioactive sample in a tight capsule that isolates the material from the atmosphere. The capsule can optionally be filled with a chosen gas pressurized up to 20 bars. The micro-Raman measurement is performed through an optical-grade quartz window. This technique permits accurate Raman measurements with no need for the spectrometer to be enclosed in an alpha-tight containment. It therefore allows the use of all options of the Raman spectrometer, like multi-wavelength laser excitation, different polarizations, and single or triple spectrometer modes. Some examples of measurements are shown and discussed. First, some spectral features of a highly radioactive americium oxide sample (AmO2) are presented. Then, we report the Raman spectra of neptunium oxide (NpO2) samples, the interpretation of which is greatly improved by employing three different excitation wavelengths, 17O doping, and a triple mode configuration to measure the anti-stokes Raman lines. This last feature also allows the estimation of the sample surface temperature. Finally, data that were measured on a sample from Chernobyl lava, where phases are identified by Raman mapping, are shown. PMID:28448046

Taxonomies of Higher Educational Institutions Predicted from Organizational Climate.

ERIC Educational Resources Information Center

Lysons, Art

1990-01-01

Application of the Perceived Climate Questionnaire involving senior-level staff from Australian institutions used climate factors as the basis for testing hypothesized taxonomies of the institutions. Results reinforce the relevance of contemporary management theories and demonstrate the importance of leadership styles in organizational…

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

PubMed

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

2016-02-01

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

Development and evaluation of a specialized task taxonomy for spatial planning - A map literacy experiment with topographic maps

NASA Astrophysics Data System (ADS)

Rautenbach, Victoria; Coetzee, Serena; Çöltekin, Arzu

2017-05-01

Topographic maps are among the most commonly used map types, however, their complex and information-rich designs depicting natural, human-made and cultural features make them difficult to read. Regardless of their complexity, spatial planners make extensive use of topographic maps in their work. On the other hand, various studies suggest that map literacy among the development planning professionals in South Africa is not very high. The widespread use of topographic maps combined with the low levels of map literacy presents challenges for effective development planning. In this paper we address some of these challenges by developing a specialized task taxonomy based on systematically assessed map literacy levels; and conducting an empirical experiment with topographic maps to evaluate our task taxonomy. In such empirical studies if non-realistic tasks are used, the results of map literacy tests may be skewed. Furthermore, experience and familiarity with the studied map type play a role in map literacy. There is thus a need to develop map literacy tests aimed at planners specifically. We developed a taxonomy of realistic map reading tasks typically executed during the planning process. The taxonomy defines six levels tasks of increasing difficulty and complexity, ranging from recognising symbols to extracting knowledge. We hypothesized that competence in the first four levels indicates functional map literacy. In this paper, we present results from an empirical experiment with 49 map literate participants solving a subset of tasks from the first four levels of the taxonomy with a topographic map. Our findings suggest that the proposed taxonomy is a good reference for evaluating topographic map literacy. Participants solved the tasks on all four levels as expected and we therefore conclude that the experiment based on the first four levels of the taxonomy successfully determined the functional map literacy of the participants. We plan to continue the study for the

“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

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).

Optimization of surface enhanced Raman scattering (SERS) assay for the transition from benchtop to handheld Raman systems

NASA Astrophysics Data System (ADS)

Schechinger, Monika; Marks, Haley; Locke, Andrea; Choudhury, Mahua; Coté, Gerard

2017-02-01

Human biomarkers are indicative of the body's relative state prior to the onset of disease, and sometimes before symptoms present. While blood biomarker detection has achieved considerable success in laboratory settings, its clinical application is lagging and commercial point-of-care devices are rare. A physician's ability to detect biomarkers such as microRNA-17, a potential epigenetic indicator of preeclampsia in pregnant woman, could enable early diagnosis and preventive intervention as early as the 1st trimester. One detection approach employing DNA-functionalized nanoparticles to detect microRNA-17, in conjunction with surface-enhanced Raman spectroscopy (SERS), has shown promise but is hindered, in part, by the use of large and expensive benchtop Raman microscopes. However, recent strides have been made in developing portable Raman systems for field applications. Characteristics of the SERS assay responsible for strengthening the assay's plasmonic response were explored, whilst comparing the results from both benchtop and portable Raman systems. The Raman spectra and intensity of three different types of photoactive molecules were compared as potential Raman reporter molecules: chromophores, fluorophores, and highly polarizable small molecules. Furthermore, the plasmonic characteristics governing the formation of SERS colloidal nanoparticle assemblies in response to DNA/miRNA hybridization were investigated. There were significant variations in the SERS enhancement in response to microRNA-17 using our assay depending on the excitation lasers at wavelengths of 532 nm and 785 nm, depending on which of the three different Raman systems were used (benchtop, portable, and handheld), and depending on which of the three different Raman reporters (chromophore, fluorophore, or Raman active molecule) were used. Analysis of data obtained did indicate that signal enhancement was better for the chromophore (MGITC) and Raman active molecule (DTNB) than it was for the

Quantitative determinations using portable Raman spectroscopy.

PubMed

Navin, Chelliah V; Tondepu, Chaitanya; Toth, Roxana; Lawson, Latevi S; Rodriguez, Jason D

2017-03-20

A portable Raman spectrometer was used to develop chemometric models to determine percent (%) drug release and potency for 500mg ciprofloxacin HCl tablets. Parallel dissolution and chromatographic experiments were conducted alongside Raman experiments to assess and compare the performance and capabilities of portable Raman instruments in determining critical drug attributes. All batches tested passed the 30min dissolution specification and the Raman model for drug release was able to essentially reproduce the dissolution profiles obtained by ultraviolet spectroscopy at 276nm for all five batches of the 500mg ciprofloxacin tablets. The five batches of 500mg ciprofloxacin tablets also passed the potency (assay) specification and the % label claim for the entire set of tablets run were nearly identical, 99.4±5.1 for the portable Raman method and 99.2±1.2 for the chromatographic method. The results indicate that portable Raman spectrometers can be used to perform quantitative analysis of critical product attributes of finished drug products. The findings of this study indicate that portable Raman may have applications in the areas of process analytical technology and rapid pharmaceutical surveillance. Published by Elsevier B.V.

Circularly polarized Raman study on diamond structure crystals

NASA Astrophysics Data System (ADS)

Lee, Je-Ho; Kim, Sera; Seong, Maeng-Je

2018-01-01

Circularly polarized Raman and/or photoluminescence (PL) analyses have recently been very important in studying physical properties of many layered materials that were either mechanically exfoliated or grown by chemical-vapor-deposition (CVD) on silicon substrates. Since silicon Raman signal is always accompanied by the circularly polarized Raman and/or PL signal from the layered materials, observation of proper circularly polarized Raman selection rules on silicon substrates would be extremely good indicator that the circularly polarized Raman and/or PL measurements on the layered materials were done properly. We have performed circularly polarized Raman measurements on silicon substrates and compared the results with the Raman intensities calculated by using Raman tensors of the diamond crystal structure. Our experimental results were in excellent agreement with the calculation. Similar circularly polarized Raman analysis done on germanium substrate also showed good agreement.

Charge Transfer Effect on Raman and Surface Enhanced Raman Spectroscopy of Furfural Molecules.

PubMed

Wan, Fu; Shi, Haiyang; Chen, Weigen; Gu, Zhaoliang; Du, Lingling; Wang, Pinyi; Wang, Jianxin; Huang, Yingzhou

2017-08-02

The detection of furfural in transformer oil through surface enhanced Raman spectroscopy (SERS) is one of the most promising online monitoring techniques in the process of transformer aging. In this work, the Raman of individual furfural molecules and SERS of furfural-M x (M = Ag, Au, Cu) complexes are investigated through density functional theory (DFT). In the Raman spectrum of individual furfural molecules, the vibration mode of each Raman peak is figured out, and the deviation from experimental data is analyzed by surface charge distribution. In the SERS of furfural-M x complexes, the influence of atom number and species on SERS chemical enhancement factors (EFs) are studied, and are further analyzed by charge transfer effect. Our studies strengthen the understanding of charge transfer effect in the SERS of furfural molecules, which is important in the online monitoring of the transformer aging process through SERS.

Charge Transfer Effect on Raman and Surface Enhanced Raman Spectroscopy of Furfural Molecules

PubMed Central

Wan, Fu; Shi, Haiyang; Chen, Weigen; Gu, Zhaoliang; Du, Lingling; Wang, Pinyi; Wang, Jianxin

2017-01-01

The detection of furfural in transformer oil through surface enhanced Raman spectroscopy (SERS) is one of the most promising online monitoring techniques in the process of transformer aging. In this work, the Raman of individual furfural molecules and SERS of furfural-Mx (M = Ag, Au, Cu) complexes are investigated through density functional theory (DFT). In the Raman spectrum of individual furfural molecules, the vibration mode of each Raman peak is figured out, and the deviation from experimental data is analyzed by surface charge distribution. In the SERS of furfural-Mx complexes, the influence of atom number and species on SERS chemical enhancement factors (EFs) are studied, and are further analyzed by charge transfer effect. Our studies strengthen the understanding of charge transfer effect in the SERS of furfural molecules, which is important in the online monitoring of the transformer aging process through SERS. PMID:28767053

ICTV Virus Taxonomy Profile: Avsunviroidae.

PubMed

Di Serio, Francesco; Li, Shi-Fang; Matoušek, Jaroslav; Owens, Robert A; Pallás, Vicente; Randles, John W; Sano, Teruo; Verhoeven, Jacobus Th J; Vidalakis, Georgios; Flores, Ricardo; Ictv Report Consortium

2018-05-01

Members of the family Avsunviroidae have a single-stranded circular RNA genome that adopts a rod-like or branched conformation and can form, in the strands of either polarity, hammerhead ribozymes involved in their replication in plastids through a symmetrical RNA-RNA rolling-circle mechanism. These viroids lack the central conserved region typical of members of the family Pospiviroidae. The family Avsunviroidae includes three genera, Avsunviroid, Pelamoviroid and Elaviroid, with a total of four species. This is a summary of the ICTV Report on the taxonomy of the family Avsunviroidae, which is available at http://www.ictv.global/report/avsunviroidae.

Using the COMMVAC taxonomy to map vaccination communication interventions in Mozambique

PubMed Central

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

2017-01-01

ABSTRACT Background: Improved communication about childhood vaccination is fundamental to increasing vaccine uptake in low-income countries. Mozambique, with 64% of children fully vaccinated, uses a range of communication interventions to promote uptake of childhood immunisation. Objectives: Using a taxonomy developed by the ‘Communicate to Vaccinate’ (COMMVAC) project, the study aims to identify and classify the existing communication interventions for vaccination in Mozambique and to find the gaps. Methods: We used a qualitative research approach to identify the range of communication interventions used in Mozambique. In-depth semi-structured interviews were carried out with key purposively selected personnel at national level and relevant documents were collected and analysed. These data were complemented with observations of communication during routine vaccination and campaigns in Nampula province. We used the COMMVAC taxonomy, which organises vaccination communication intervention according to its intended purpose and the population targeted, to map both routine and campaign interventions. Results: We identified interventions used in campaign and routine vaccination, or in both, fitting five of the seven taxonomy purposes, with informing or educating community members predominating. We did not identify any interventions that aimed to provide support or facilitate decision-making. There were interventions for all main target groups, although fewer for health providers. Overlap occurred: for example, interventions often targeted both parents and community members. Conclusions: We consider that the predominant focus on informing and educating community members is appropriate in the Mozambican context, where there is a high level of illiteracy and poor knowledge of the reasons for vaccination. We recommend increasing interventions for health providers, in particular training them in better communication for vaccination. The taxonomy was useful for identifying

Near infrared Raman spectra of Rhizoma dioscoreae

NASA Astrophysics Data System (ADS)

Lin, Wenshuo; Chen, Rong; Chen, Guannan; Feng, Sangyuan; Li, Yongzeng; Huang, Zufang; Li, Yongsen

2008-03-01

A novel and compact near-infrared (NIR) Raman system is developed using 785-nm diode laser, volume-phase technology holographic system, and NIR intensified charge-coupled device (CCD). Raman spectra and first derivative spectra of Rhizoma Dioscoreae are obtained. Raman spectra of Rhizoma Dioscoreae showed three strong characteristic peaks at 477.4cm -1, 863.9cm -1, and 936.0cm -1. The major ingredients are protein, amino acid, starch, polysaccharides and so on, matched with the known basic biochemical composition of Rhizoma Dioscoreae. In the first derivative spectra of Rhizoma Dioscoreae, distinguishing characteristic peaks appeared at 467.674cm -1, 484.603cm -1, 870.37cm -1, 943.368cm -1. Contrasted with Rhizoma Dioscoreae Raman spectra, in 600cm -1 to 800cm -1, 1000cm -1 to 1400cm -1 regions, changes in Rhizoma Dioscoreae Raman first derivative spectra are represented more clearly than Rhizoma Dioscoreae Raman spectra. So Rhizoma Dioscoreae raman first derivative spectra can be an accurate supplementary analysis method to Rhizoma Dioscoreae Raman spectra.

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…

Detection of latent prints by Raman imaging

DOEpatents

Lewis, Linda Anne [Andersonville, TN; Connatser, Raynella Magdalene [Knoxville, TN; Lewis, Sr., Samuel Arthur

2011-01-11

The present invention relates to a method for detecting a print on a surface, the method comprising: (a) contacting the print with a Raman surface-enhancing agent to produce a Raman-enhanced print; and (b) detecting the Raman-enhanced print using a Raman spectroscopic method. The invention is particularly directed to the imaging of latent fingerprints.

Miniature standoff Raman probe for neurosurgical applications

NASA Astrophysics Data System (ADS)

Stevens, Oliver A. C.; Hutchings, Joanne; Gray, William; Vincent, Rosa Louise; Day, John C.

2016-08-01

Removal of intrinsic brain tumors is a delicate process, where a high degree of specificity is required to remove all of the tumor tissue without damaging healthy brain. The accuracy of this process can be greatly enhanced by intraoperative guidance. Optical biopsies using Raman spectroscopy are a minimally invasive and lower-cost alternative to current guidance methods. A miniature Raman probe for performing optical biopsies of human brain tissue is presented. The probe allows sampling inside a conventional stereotactic brain biopsy system: a needle of length 200 mm and inner diameter of 1.8 mm. By employing a miniature stand-off Raman design, the probe removes the need for any additional components to be inserted into the brain. Additionally, the probe achieves a very low internal silica background while maintaining good collection of Raman signal. To illustrate this, the probe is compared with a Raman probe that uses a pair of optical fibers for collection. The miniature stand-off Raman probe is shown to collect a comparable number of Raman scattered photons, but the Raman signal to background ratio is improved by a factor of five at Raman shifts below ˜500 cm-1. The probe's suitability for use on tissue is demonstrated by discriminating between different types of healthy porcine brain tissue.

High Fidelity Raman Chemical Imaging of Materials

NASA Astrophysics Data System (ADS)

Bobba, Venkata Nagamalli Koteswara Rao

The development of high fidelity Raman imaging systems is important for a number of application areas including material science, bio-imaging, bioscience and healthcare, pharmaceutical analysis, and semiconductor characterization. The use of Raman imaging as a characterization tool for detecting the amorphous and crystalline regions in the biopolymer poly-L-lactic acid (PLLA) is the precis of my thesis. In the first chapter, a brief insight about the basics of Raman spectroscopy, Raman chemical imaging, Raman mapping, and Raman imaging techniques has been provided. The second chapter contains details about the successful development of tailored sample of PLLA. Biodegradable polymers are used in areas of tissue engineering, agriculture, packaging, and in medical field for drug delivery, implant devices, and surgical sutures. Detailed information about the sample preparation and characterization of these cold-drawn PLLA polymer substrates has been provided. Wide-field Raman hyperspectral imaging using an acousto-optic tunable filter (AOTF) was demonstrated in the early 1990s. The AOTF contributed challenges such as image walk, distortion, and image blur. A wide-field AOTF Raman imaging system has been developed as part of my research and methods to overcome some of the challenges in performing AOTF wide-field Raman imaging are discussed in the third chapter. This imaging system has been used for studying the crystalline and amorphous regions on the cold-drawn sample of PLLA. Of all the different modalities that are available for performing Raman imaging, Raman point-mapping is the most extensively used method. The ease of obtaining the Raman hyperspectral cube dataset with a high spectral and spatial resolution is the main motive of performing this technique. As a part of my research, I have constructed a Raman point-mapping system and used it for obtaining Raman hyperspectral image data of various minerals, pharmaceuticals, and polymers. Chapter four offers

Are Patient and Carer Experiences Mirrored in the Practice Reviews of Self-management Support (Prisms) Provider Taxonomy?

PubMed Central

Kenealy, Timothy; Kuluski, Kerry; McKillop, Ann; Parsons, John; Wong-Cornall, Cecilia

2017-01-01

Introduction: Patient self-management support is central to care for long term conditions and for integrated care. Patients and their carers are the final arbiter of whether support for self-management has been effective. A new taxonomy lists 14 categories of provider activities that support patient self-management (Practical Reviews in Self-Management Support, PRISMS). We asked whether we could recognise these provider activities in narratives from patients and carers. We sought to extend the theoretical framework of the taxonomy to include the view from patient and carers. Methods: We interviewed 28 patients and family carers in a case study of primary health care in New Zealand in 2015 to determine which components of the taxonomy were visible. We drew on interviews with clinicians and organisation persons to explain case study context. Results: We found, within patient and carer data, evidence of all 14 components of provider self-management support. The overarching dimensions of the taxonomy helped reveal an intensity and consistency of provider behaviour that was not apparent considering the individual components. Conclusions: Patient and carer data mapped to provider activities. The taxonomy was not explicit on provider relationships and engagement with, or separate support needs of, patients and carers. PMID:28970749

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.

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

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.

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

ERIC Educational Resources Information Center

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

2010-01-01

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

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.

Raman scattering in crystals

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

Edwards, D.F.

1988-09-30

A tutorial presentation is given of Raman scattering in crystals. The physical concepts are emphasized rather than the detailed mathematical formalism. Starting with an introduction to the concepts of phonons and conservation laws, the effects of photon-phonon interactions are presented. This interaction concept is shown for a simple cubic crystal and is extended to a uniaxial crystal. The correlation table method is used for determining the number and symmetry of the Raman active modes. Finally, examples are given to illustrate the relative ease of using this group theoretical method and the predictions are compared with measured Raman spectra. 37 refs.,more » 17 figs., 6 tabs.« less

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...

The Unfortunate Consequences of Bloom's Taxonomy

ERIC Educational Resources Information Center

Case, Roland

2013-01-01

The sequenced levels of thinking articulated in Bloom's original taxonomy (or in the multitude of subsequent variations) is the most widely known list in education. In addition to enduring popularity, it is arguably one of the most destructive theories in education. In this article, the author explains what makes it so damaging and how…

Issues in the Taxonomy of Psychopathology in Mental Retardation.

ERIC Educational Resources Information Center

Einfeld, Stewart L.; Aman, Michael

1995-01-01

Factors affecting the development of a taxonomy of psychopathology for children with mental retardation are considered, along with the following diagnostic areas to address: stereotypic behavior and self-injury, autism, organic brain syndromes, and pervasive developmental disorders. Using data from multivariate studies and findings related to…

Improving Access to and Understanding of Regulations through Taxonomies

ERIC Educational Resources Information Center

Cheng, Chin Pang; Lau. Gloria T.; Law, Kincho H.; Pan, Jiayi; Jones, Albert

2009-01-01

Industrial taxonomies have the potential to automate information retrieval, facilitate interoperability and, most importantly, improve decision making - decisions that must comply with existing government regulations and codes of practice. However, it is difficult to find those regulations and codes most relevant to a particular decision, even…

50 years of formal virus taxonomy: overview and prospects

USDA-ARS?s Scientific Manuscript database

To mark the 50th anniversary of the origins of the International Committee on Taxonomy of Viruses (ICTV), we present a brief history of the foundation, consolidation, establishment and growth of this organisation. We also outline recent developments, supported by a grant from the Wellcome Trust, tha...

Applications of Raman spectroscopy to gemology.

PubMed

Bersani, Danilo; Lottici, Pier Paolo

2010-08-01

Being nondestructive and requiring short measurement times, a low amount of material, and no sample preparation, Raman spectroscopy is used for routine investigation in the study of gemstone inclusions and treatments and for the characterization of mounted gems. In this work, a review of the use of laboratory Raman and micro-Raman spectrometers and of portable Raman systems in the gemology field is given, focusing on gem identification and on the evaluation of the composition, provenance, and genesis of gems. Many examples are shown of the use of Raman spectroscopy as a tool for the identification of imitations, synthetic gems, and enhancement treatments in natural gemstones. Some recent developments are described, with particular attention being given to the semiprecious stone jade and to two important organic materials used in jewelry, i.e., pearls and corals.

Tephritid Integrative Taxonomy: Where We Are Now, with a Focus on the Resolution of Three Tropical Fruit Fly Species Complexes.

PubMed

Schutze, Mark K; Virgilio, Massimiliano; Norrbom, Allen; Clarke, Anthony R

2017-01-31

Accurate species delimitation underpins good taxonomy. Formalization of integrative taxonomy in the past decade has provided a framework for using multidisciplinary data to make species delimitation hypotheses more rigorous. We address the current state of integrative taxonomy by using as a case study an international project targeted at resolving three important tephritid species complexes: Bactrocera dorsalis complex, Anastrepha fraterculus complex, and Ceratitis FAR (C. fasciventris, C. anonae, C. rosa) complex. The integrative taxonomic approach has helped deliver significant advances in resolving these complexes: It has been used to identify some taxa as belonging to the same biological species as well as to confirm hidden cryptic diversity under a single taxonomic name. Nevertheless, the general application of integrative taxonomy has not been without issue, revealing challenges that must be considered when undertaking an integrative taxonomy project. Scrutiny of this international case study provides a unique opportunity to document lessons learned for the benefit of not only tephritid taxonomists, but also the wider taxonomic community.

Biology in Bloom: Implementing Bloom's Taxonomy to Enhance Student Learning in Biology

PubMed Central

Dirks, Clarissa; Wenderoth, Mary Pat

2008-01-01

We developed the Blooming Biology Tool (BBT), an assessment tool based on Bloom's Taxonomy, to assist science faculty in better aligning their assessments with their teaching activities and to help students enhance their study skills and metacognition. The work presented here shows how assessment tools, such as the BBT, can be used to guide and enhance teaching and student learning in a discipline-specific manner in postsecondary education. The BBT was first designed and extensively tested for a study in which we ranked almost 600 science questions from college life science exams and standardized tests. The BBT was then implemented in three different collegiate settings. Implementation of the BBT helped us to adjust our teaching to better enhance our students' current mastery of the material, design questions at higher cognitive skills levels, and assist students in studying for college-level exams and in writing study questions at higher levels of Bloom's Taxonomy. From this work we also created a suite of complementary tools that can assist biology faculty in creating classroom materials and exams at the appropriate level of Bloom's Taxonomy and students to successfully develop and answer questions that require higher-order cognitive skills. PMID:19047424

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

PubMed

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

2007-01-01

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

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

PubMed

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

2016-02-17

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

Cascaded-cladding-pumped cascaded Raman fiber amplifier.

PubMed

Jiang, Huawei; Zhang, Lei; Feng, Yan

2015-06-01

The conversion efficiency of double-clad Raman fiber laser is limited by the cladding-to-core area ratio. To get high conversion efficiency, the inner-cladding-to-core area ratio has to be less than about 8, which limits the brightness enhancement. To overcome the problem, a cascaded-cladding-pumped cascaded Raman fiber laser with multiple-clad fiber as the Raman gain medium is proposed. A theoretical model of Raman fiber amplifier with multiple-clad fiber is developed, and numerical simulation proves that the proposed scheme can improve the conversion efficiency and brightness enhancement of cladding pumped Raman fiber laser.

Raman spectra of lignin model compounds

Treesearch

Umesh P. Agarwal; Richard S. Reiner; Ashok K. Pandey; Sally A. Ralph; Kolby C. Hirth; Rajai H. Atalla

2005-01-01

To fully exploit the value of Raman spectroscopy for analyzing lignins and lignin containing materials, a detailed understanding of lignins’ Raman spectra needs to be achieved. Although advances made thus far have led to significant growth in application of Raman techniques, further developments are needed to improve upon the existing knowledge. Considering that lignin...

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

PubMed

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

2015-01-01

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

Raman spectroscopy of white wines.

PubMed

Martin, Coralie; Bruneel, Jean-Luc; Guyon, François; Médina, Bernard; Jourdes, Michael; Teissedre, Pierre-Louis; Guillaume, François

2015-08-15

The feasibility of exploiting Raman scattering to analyze white wines has been investigated using 3 different wavelengths of the incoming laser radiation in the near-UV (325 nm), visible (532 nm) and near infrared (785 nm). To help in the interpretation of the Raman spectra, the absorption properties in the UV-visible range of two wine samples as well as their laser induced fluorescence have also been investigated. Thanks to the strong intensity enhancement of the Raman scattered light due to electronic resonance with 325 nm laser excitation, hydroxycinnamic acids may be detected and analyzed selectively. Fructose and glucose may also be easily detected below ca. 1000 cm(-1). This feasibility study demonstrates the potential of the Raman spectroscopic technique for the analysis of white wines. Copyright © 2015 Elsevier Ltd. All rights reserved.

Raman accumulator as a fusion laser driver

DOEpatents

George, E. Victor; Swingle, James C.

1985-01-01

Apparatus for simultaneous laser pulse amplification and compression, using multiple pass Raman scattering in one Raman cell and pulse switchout from the optical cavity through use of a dichroic device associated with the Raman cell.

Raman accumulator as a fusion laser driver

DOEpatents

George, E.V.; Swingle, J.C.

1982-03-31

Apparatus for simultaneous laser pulse amplification and compression, using multiple pass Raman scattering in one Raman cell and pulse switchout from the optical cavity through use of a dichroic device associated with the Raman cell.

"Bringing Taxonomy to the Service of Genetics": Edgar Anderson and Introgressive Hybridization.

PubMed

Kleinman, Kim

2016-12-01

In introgressive hybridization (the repeated backcrossing of hybrids with parental populations), Edgar Anderson found a source for variation upon which natural selection could work. In his 1953 review article "Introgressive Hybridization," he asserted that he was "bringing taxonomy to the service of genetics" whereas distinguished colleagues such as Theodosius Dobzhansky and Ernst Mayr did the precise opposite. His work as a geneticist particularly focused on linkage and recombination and was enriched by collaborations with Missouri Botanical Garden colleagues interested in taxonomy as well as with cytologists C.D. Darlington and Karl Sax. As the culmination of a biosystemtatic research program, Anderson's views challenged the mainstream of the Evolutionary Synthesis.

An Evidence-Based Forensic Taxonomy of Windows Phone Communication Apps.

PubMed

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

2018-05-01

Communication apps can be an important source of evidence in a forensic investigation (e.g., in the investigation of a drug trafficking or terrorism case where the communications apps were used by the accused persons during the transactions or planning activities). This study presents the first evidence-based forensic taxonomy of Windows Phone communication apps, using an existing two-dimensional Android forensic taxonomy as a baseline. Specifically, 30 Windows Phone communication apps, including Instant Messaging (IM) and Voice over IP (VoIP) apps, are examined. Artifacts extracted using physical acquisition are analyzed, and seven digital evidence objects of forensic interest are identified, namely: Call Log, Chats, Contacts, Locations, Installed Applications, SMSs and User Accounts. Findings from this study would help to facilitate timely and effective forensic investigations involving Windows Phone communication apps. © 2017 American Academy of Forensic Sciences.

Taxonomy of Behavioral Objectives for Vocational Programs. Vol. I.

ERIC Educational Resources Information Center

Gloucester County Vocational-Technical School, Sewell, NJ.

Developed from courses of study in two-year vocational technical programs at the Gloucester County Vocational Technical School, these taxonomies present behavioral objectives for 12 subjects. They are intended for use by vocational teachers in the preparation of the vocational component of the individualized educational plan (IEP) for special…

Developing Learning Objectives for Accounting Ethics Using Bloom's Taxonomy

ERIC Educational Resources Information Center

Kidwell, Linda A.; Fisher, Dann G.; Braun, Robert L.; Swanson, Diane L.

2013-01-01

The purpose of our article is to offer a set of core knowledge learning objectives for accounting ethics education. Using Bloom's taxonomy of educational objectives, we develop learning objectives in six content areas: codes of ethical conduct, corporate governance, the accounting profession, moral development, classical ethics theories, and…

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.

Laser wavelength selection for Raman spectroscopy of microbial pigments in situ in Antarctic desert ecosystem analogues of former habitats on Mars

NASA Astrophysics Data System (ADS)

Edwards, Howell G. M.; Newton, Emma M.; Wynn-Williams, David D.; Dickensheets, David; Schoen, Chris; Crowder, Chelle

2002-10-01

The vital ultraviolet- (UV-) protective and photosynthetic pigments of cyanobacteria and lichens (microbial symbioses) that dominate primary production in Antarctic desert ecosystems auto-fluoresce at short wavelengths. We therefore use a long-wavelength (1064 nm) infrared laser for non-intrusive in situ Raman spectrometry of their ecologically significant compounds (especially pigments). To confirm that the power loss at this longer wavelength is justified to avoid swamping by background fluorescence, we compared Raman spectra obtained with excitation at 1064, 852, 830, 785, 633 and 515 nm. These are typical of lasers used for Raman spectroscopy. We analysed communities of the cyanobacterium Nostoc commune and the highly pigmented lichens Acarospora chlorophana and Caloplaca saxicola. These require screening compounds (e.g. pigments such as scytonemin in cyanobacteria and rhizocarpic acid in the fungal symbiont of lichens). They are augmented by quenching pigments (e.g. carotenoids) to dissipate the energy of free radicals generated by penetrating UV. We also analysed organisms having avoidance strategies (e.g. endolithic communities within translucent rocks, including the common cyanobacterium Chroococcidiopsis). These require accessory pigments for photosynthesis at very low light intensities. Although some organisms gave useable Raman spectra with short-wavelength lasers, 1064 nm was the only excitation that was consistently excellent for all organisms. We conclude that a 1064 nm Raman spectrometer, miniaturized using an InGaAs detector, is the optimal instrument for in situ studies of pigmented microbial communities at the limits of life on Earth. This has practical potential for the quest for biomolecules residual from any former surface life on Mars.

Mapping the Diagnosis Axis of an Interface Terminology to the NANDA International Taxonomy

PubMed Central

Juvé Udina, Maria-Eulàlia; Gonzalez Samartino, Maribel; Matud Calvo, Cristina

2012-01-01

Background. Nursing terminologies are designed to support nursing practice but, as with any other clinical tool, they should be evaluated. Cross-mapping is a formal method for examining the validity of the existing controlled vocabularies. Objectives. The study aims to assess the inclusiveness and expressiveness of the nursing diagnosis axis of a newly implemented interface terminology by cross-mapping with the NANDA-I taxonomy. Design/Methods. The study applied a descriptive design, using a cross-sectional, bidirectional mapping strategy. The sample included 728 concepts from both vocabularies. Concept cross-mapping was carried out to identify one-to-one, negative, and hierarchical connections. The analysis was conducted using descriptive statistics. Results. Agreement of the raters' mapping achieved 97%. More than 60% of the nursing diagnosis concepts in the NANDA-I taxonomy were mapped to concepts in the diagnosis axis of the new interface terminology; 71.1% were reversely mapped. Conclusions. Main results for outcome measures suggest that the diagnosis axis of this interface terminology meets the validity criterion of cross-mapping when mapped from and to the NANDA-I taxonomy. PMID:22830046

Mapping the Diagnosis Axis of an Interface Terminology to the NANDA International Taxonomy.

PubMed

Juvé Udina, Maria-Eulàlia; Gonzalez Samartino, Maribel; Matud Calvo, Cristina

2012-01-01

Background. Nursing terminologies are designed to support nursing practice but, as with any other clinical tool, they should be evaluated. Cross-mapping is a formal method for examining the validity of the existing controlled vocabularies. Objectives. The study aims to assess the inclusiveness and expressiveness of the nursing diagnosis axis of a newly implemented interface terminology by cross-mapping with the NANDA-I taxonomy. Design/Methods. The study applied a descriptive design, using a cross-sectional, bidirectional mapping strategy. The sample included 728 concepts from both vocabularies. Concept cross-mapping was carried out to identify one-to-one, negative, and hierarchical connections. The analysis was conducted using descriptive statistics. Results. Agreement of the raters' mapping achieved 97%. More than 60% of the nursing diagnosis concepts in the NANDA-I taxonomy were mapped to concepts in the diagnosis axis of the new interface terminology; 71.1% were reversely mapped. Conclusions. Main results for outcome measures suggest that the diagnosis axis of this interface terminology meets the validity criterion of cross-mapping when mapped from and to the NANDA-I taxonomy.

Taxonomy of Lecture Note-Taking Skills and Subskills

ERIC Educational Resources Information Center

Al-Musalli, Alaa M.

2015-01-01

Note taking (NT) in lectures is as active a skill as listening, which stimulates it, and as challenging as writing, which is the end product. Literature on lecture NT misses an integration of the processes involved in listening with those in NT. In this article, a taxonomy is proposed of lecture NT skills and subskills based on a similar list…

Applications of Raman spectroscopy in life science

NASA Astrophysics Data System (ADS)

Martin, Airton A.; T. Soto, Cláudio A.; Ali, Syed M.; Neto, Lázaro P. M.; Canevari, Renata A.; Pereira, Liliane; Fávero, Priscila P.

2015-06-01

Raman spectroscopy has been applied to the analysis of biological samples for the last 12 years providing detection of changes occurring at the molecular level during the pathological transformation of the tissue. The potential use of this technology in cancer diagnosis has shown encouraging results for the in vivo, real-time and minimally invasive diagnosis. Confocal Raman technics has also been successfully applied in the analysis of skin aging process providing new insights in this field. In this paper it is presented the latest biomedical applications of Raman spectroscopy in our laboratory. It is shown that Raman spectroscopy (RS) has been used for biochemical and molecular characterization of thyroid tissue by micro-Raman spectroscopy and gene expression analysis. This study aimed to improve the discrimination between different thyroid pathologies by Raman analysis. A total of 35 thyroid tissues samples including normal tissue (n=10), goiter (n=10), papillary (n=10) and follicular carcinomas (n=5) were analyzed. The confocal Raman spectroscopy allowed a maximum discrimination of 91.1% between normal and tumor tissues, 84.8% between benign and malignant pathologies and 84.6% among carcinomas analyzed. It will be also report the application of in vivo confocal Raman spectroscopy as an important sensor for detecting advanced glycation products (AGEs) on human skin.

Metabarcoding of marine nematodes - evaluation of reference datasets used in tree-based taxonomy assignment approach.

PubMed

Holovachov, Oleksandr

2016-01-01

Metabarcoding is becoming a common tool used to assess and compare diversity of organisms in environmental samples. Identification of OTUs is one of the critical steps in the process and several taxonomy assignment methods were proposed to accomplish this task. This publication evaluates the quality of reference datasets, alongside with several alignment and phylogeny inference methods used in one of the taxonomy assignment methods, called tree-based approach. This approach assigns anonymous OTUs to taxonomic categories based on relative placements of OTUs and reference sequences on the cladogram and support that these placements receive. In tree-based taxonomy assignment approach, reliable identification of anonymous OTUs is based on their placement in monophyletic and highly supported clades together with identified reference taxa. Therefore, it requires high quality reference dataset to be used. Resolution of phylogenetic trees is strongly affected by the presence of erroneous sequences as well as alignment and phylogeny inference methods used in the process. Two preparation steps are essential for the successful application of tree-based taxonomy assignment approach. Curated collections of genetic information do include erroneous sequences. These sequences have detrimental effect on the resolution of cladograms used in tree-based approach. They must be identified and excluded from the reference dataset beforehand.Various combinations of multiple sequence alignment and phylogeny inference methods provide cladograms with different topology and bootstrap support. These combinations of methods need to be tested in order to determine the one that gives highest resolution for the particular reference dataset.Completing the above mentioned preparation steps is expected to decrease the number of unassigned OTUs and thus improve the results of the tree-based taxonomy assignment approach.

Enhanced Raman scattering in porous silicon grating.

PubMed

Wang, Jiajia; Jia, Zhenhong; Lv, Changwu

2018-03-19

The enhancement of Raman signal on monocrystalline silicon gratings with varying groove depths and on porous silicon grating were studied for a highly sensitive surface enhanced Raman scattering (SERS) response. In the experiment conducted, porous silicon gratings were fabricated. Silver nanoparticles (Ag NPs) were then deposited on the porous silicon grating to enhance the Raman signal of the detective objects. Results show that the enhancement of Raman signal on silicon grating improved when groove depth increased. The enhanced performance of Raman signal on porous silicon grating was also further improved. The Rhodamine SERS response based on Ag NPs/ porous silicon grating substrates was enhanced relative to the SERS response on Ag NPs/ porous silicon substrates. Ag NPs / porous silicon grating SERS substrate system achieved a highly sensitive SERS response due to the coupling of various Raman enhancement factors.

Gain suppression involving both stimulated Raman and hyper-Raman photons in two-step stimulated emissions

NASA Astrophysics Data System (ADS)

Deng, Lu; Garrett, W. R.; Payne, M. G.; Moore, M. A.

1997-05-01

We show that multiphoton destructive interference leading to gain suppression can be produced even when two different step-wise stimulated emissions, such as stimulated Raman and hyper-Raman emissions, are included in the interference loop.

Towards a unified taxonomy of health indicators: academic health centers and communities working together to improve population health.

PubMed

Aguilar-Gaxiola, Sergio; Ahmed, Syed; Franco, Zeno; Kissack, Anne; Gabriel, Davera; Hurd, Thelma; Ziegahn, Linda; Bates, Nancy J; Calhoun, Karen; Carter-Edwards, Lori; Corbie-Smith, Giselle; Eder, Milton Mickey; Ferrans, Carol; Hacker, Karen; Rumala, Bernice B; Strelnick, A Hal; Wallerstein, Nina

2014-04-01

The Clinical and Translational Science Awards (CTSA) program represents a significant public investment. To realize its major goal of improving the public's health and reducing health disparities, the CTSA Consortium's Community Engagement Key Function Committee has undertaken the challenge of developing a taxonomy of community health indicators. The objective is to initiate a unified approach for monitoring progress in improving population health outcomes. Such outcomes include, importantly, the interests and priorities of community stakeholders, plus the multiple, overlapping interests of universities and of the public health and health care professions involved in the development and use of local health care indicators.The emerging taxonomy of community health indicators that the authors propose supports alignment of CTSA activities and facilitates comparative effectiveness research across CTSAs, thereby improving the health of communities and reducing health disparities. The proposed taxonomy starts at the broadest level, determinants of health; subsequently moves to more finite categories of community health indicators; and, finally, addresses specific quantifiable measures. To illustrate the taxonomy's application, the authors have synthesized 21 health indicator projects from the literature and categorized them into international, national, or local/special jurisdictions. They furthered categorized the projects within the taxonomy by ranking indicators with the greatest representation among projects and by ranking the frequency of specific measures. They intend for the taxonomy to provide common metrics for measuring changes to population health and, thus, extend the utility of the CTSA Community Engagement Logic Model. The input of community partners will ultimately improve population health.

Improved multiple-pass Raman spectrometer

NASA Astrophysics Data System (ADS)

Kc, Utsav; Silver, Joel A.; Hovde, David C.; Varghese, Philip L.

2011-08-01

An improved Raman gain spectrometer for flame measurements of gas temperature and species concentrations is described. This instrument uses a multiple-pass optical cell to enhance the incident light intensity in the measurement volume. The Raman signal is 83 times larger than from a single pass, and the Raman signal-to-noise ratio (SNR) in room-temperature air of 153 is an improvement over that from a single-pass cell by a factor of 9.3 when the cell is operated with 100 passes and the signal is integrated over 20 laser shots. The SNR improvement with the multipass cell is even higher for flame measurements at atmospheric pressure, because detector readout noise is more significant for single-pass measurements when the gas density is lower. Raman scattering is collected and dispersed in a spectrograph with a transmission grating and recorded with a fast gated CCD array detector to help eliminate flame interferences. The instrument is used to record spontaneous Raman spectra from N2, CO2, O2, and CO in a methane--air flame. Curve fits of the recorded Raman spectra to detailed simulations of nitrogen spectra are used to determine the flame temperature from the shapes of the spectral signatures and from the ratio of the total intensities of the Stokes and anti-Stokes signals. The temperatures measured are in good agreement with radiation-corrected thermocouple measurements for a range of equivalence ratios.

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…

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

PubMed Central

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

2006-01-01

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

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.

Emerging technology: applications of Raman spectroscopy for prostate cancer.

PubMed

Kast, Rachel E; Tucker, Stephanie C; Killian, Kevin; Trexler, Micaela; Honn, Kenneth V; Auner, Gregory W

2014-09-01

There is a need in prostate cancer diagnostics and research for a label-free imaging methodology that is nondestructive, rapid, objective, and uninfluenced by water. Raman spectroscopy provides a molecular signature, which can be scaled from micron-level regions of interest in cells to macroscopic areas of tissue. It can be used for applications ranging from in vivo or in vitro diagnostics to basic science laboratory testing. This work describes the fundamentals of Raman spectroscopy and complementary techniques including surface enhanced Raman scattering, resonance Raman spectroscopy, coherent anti-Stokes Raman spectroscopy, confocal Raman spectroscopy, stimulated Raman scattering, and spatially offset Raman spectroscopy. Clinical applications of Raman spectroscopy to prostate cancer will be discussed, including screening, biopsy, margin assessment, and monitoring of treatment efficacy. Laboratory applications including cell identification, culture monitoring, therapeutics development, and live imaging of cellular processes are discussed. Potential future avenues of research are described, with emphasis on multiplexing Raman spectroscopy with other modalities.

Preventing Raman Lasing in High-Q WGM Resonators

NASA Technical Reports Server (NTRS)

Savchenkov, Anatoliy; Matsko, Andrey; Strekalov, Dmitry; Maleki, Lute

2007-01-01

A generic design has been conceived to suppress the Raman effect in whispering- gallery-mode (WGM) optical resonators that have high values of the resonance quality factor (Q). Although it is possible to exploit the Raman effect (even striving to maximize the Raman gain to obtain Raman lasing), the present innovation is intended to satisfy a need that arises in applications in which the Raman effect inhibits the realization of the full potential of WGM resonators as frequency-selection components. Heretofore, in such applications, it has been necessary to operate high-Q WGM resonators at unattractively low power levels to prevent Raman lasing. (The Raman-lasing thresholds of WGM optical resonators are very low and are approximately proportional to Q(sup -2)). Heretofore, two ways of preventing Raman lasting at high power levels have been known, but both entail significant disadvantages: A resonator can be designed so that the optical field is spread over a relatively large mode volume to bring the power density below the threshold. For any given combination of Q and power level, there is certain mode volume wherein Raman lasing does not start. Unfortunately, a resonator that has a large mode volume also has a high spectral density, which is undesirable in a typical photonic application. A resonator can be cooled to the temperature of liquid helium, where the Raman spectrum is narrower and, therefore, the Raman gain is lower. However, liquid-helium cooling is inconvenient. The present design overcomes these disadvantages, making it possible to operate a low-spectral-density (even a single-mode) WGM resonator at a relatively high power level at room temperature, without risk of Raman lasing.

A tunable single-monochromator Raman system based on the supercontinuum laser and tunable filters for resonant Raman profile measurements.

PubMed

Liu, X-L; Liu, H-N; Tan, P-H

2017-08-01

Resonant Raman spectroscopy requires that the wavelength of the laser used is close to that of an electronic transition. A tunable laser source and a triple spectrometer are usually necessary for resonant Raman profile measurements. However, such a system is complex with low signal throughput, which limits its wide application by scientific community. Here, a tunable micro-Raman spectroscopy system based on the supercontinuum laser, transmission grating, tunable filters, and single-stage spectrometer is introduced to measure the resonant Raman profile. The supercontinuum laser in combination with transmission grating makes a tunable excitation source with a bandwidth of sub-nanometer. Such a system exhibits continuous excitation tunability and high signal throughput. Its good performance and flexible tunability are verified by resonant Raman profile measurement of twisted bilayer graphene, which demonstrates its potential application prospect for resonant Raman spectroscopy.

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.

A New Genomics-Driven Taxonomy of Bacteria and Archaea: Are We There Yet?

PubMed Central

2016-01-01

Taxonomy is often criticized for being too conservative and too slow and having limited relevance because it has not taken into consideration the latest methods and findings. Yet the cumulative work product of its practitioners underpins contemporary microbiology and serves as a principal means of shaping and referencing knowledge. Using methods drawn from the field of exploratory data analysis, this minireview examines the current state of the field as it transitions from a taxonomy based on 16S rRNA gene sequences to one based on whole-genome sequences and tests the validity of some commonly held beliefs. PMID:27194687

The ACTTION-American Pain Society Pain Taxonomy (AAPT): an evidence-based and multidimensional approach to classifying chronic pain conditions.

PubMed

Fillingim, Roger B; Bruehl, Stephen; Dworkin, Robert H; Dworkin, Samuel F; Loeser, John D; Turk, Dennis C; Widerstrom-Noga, Eva; Arnold, Lesley; Bennett, Robert; Edwards, Robert R; Freeman, Roy; Gewandter, Jennifer; Hertz, Sharon; Hochberg, Marc; Krane, Elliot; Mantyh, Patrick W; Markman, John; Neogi, Tuhina; Ohrbach, Richard; Paice, Judith A; Porreca, Frank; Rappaport, Bob A; Smith, Shannon M; Smith, Thomas J; Sullivan, Mark D; Verne, G Nicholas; Wasan, Ajay D; Wesselmann, Ursula

2014-03-01

Current approaches to classification of chronic pain conditions suffer from the absence of a systematically implemented and evidence-based taxonomy. Moreover, existing diagnostic approaches typically fail to incorporate available knowledge regarding the biopsychosocial mechanisms contributing to pain conditions. To address these gaps, the Analgesic, Anesthetic, and Addiction Clinical Trial Translations Innovations Opportunities and Networks (ACTTION) public-private partnership with the U.S. Food and Drug Administration and the American Pain Society (APS) have joined together to develop an evidence-based chronic pain classification system called the ACTTION-APS Pain Taxonomy. This paper describes the outcome of an ACTTION-APS consensus meeting, at which experts agreed on a structure for this new taxonomy of chronic pain conditions. Several major issues around which discussion revolved are presented and summarized, and the structure of the taxonomy is presented. ACTTION-APS Pain Taxonomy will include the following dimensions: 1) core diagnostic criteria; 2) common features; 3) common medical comorbidities; 4) neurobiological, psychosocial, and functional consequences; and 5) putative neurobiological and psychosocial mechanisms, risk factors, and protective factors. In coming months, expert working groups will apply this taxonomy to clusters of chronic pain conditions, thereby developing a set of diagnostic criteria that have been consistently and systematically implemented across nearly all common chronic pain conditions. It is anticipated that the availability of this evidence-based and mechanistic approach to pain classification will be of substantial benefit to chronic pain research and treatment. The ACTTION-APS Pain Taxonomy is an evidence-based chronic pain classification system designed to classify chronic pain along the following dimensions: 1) core diagnostic criteria; 2) common features; 3) common medical comorbidities; 4) neurobiological, psychosocial

The necessity of DNA taxonomy to reveal cryptic diversity and spatial distribution of meiofauna, with a focus on Nemertea.

PubMed

Leasi, Francesca; Norenburg, Jon L

2014-01-01

Meiofauna represent one of the most abundant and diverse communities in marine benthic ecosystems. However, an accurate assessment of diversity at the level of species has been and remains challenging for these microscopic organisms. Therefore, for many taxa, especially the soft body forms such as nemerteans, which often lack clear diagnostic morphological traits, DNA taxonomy is an effective means to assess species diversity. Morphological taxonomy of Nemertea is well documented as complicated by scarcity of unambiguous character states and compromised by diagnoses of a majority of species (and higher clades) being inadequate or based on ambiguous characters and character states. Therefore, recent studies have advocated for the primacy of molecular tools to solve the taxonomy of this group. DNA taxonomy uncovers possible hidden cryptic species, provides a coherent means to systematize taxa in definite clades, and also reveals possible biogeographic patterns. Here, we analyze diversity of nemertean species by considering the barcode region of the mitochondrial gene Cytochrome Oxidase subunit I (COI) and different species delineation approaches in order to infer evolutionarily significant units. In the aim to uncover actual diversity of meiofaunal nemerteans across different sites in Central America, COI sequences were obtained for specimens assigned here to the genera Cephalothrix, Ototyphlonemertes, and Tetrastemma-like worms, each commonly encountered in our sampling. Additional genetic, taxonomic, and geographic data of other specimens belonging to these genera were added from GenBank. Results are consistent across different DNA taxonomy approaches, and revealed (i) the presence of several hidden cryptic species and (ii) numerous potential misidentifications due to traditional taxonomy. (iii) We additionally test a possible biogeographic pattern of taxonomic units revealed by this study, and, except for a few cases, the putative species seem not to be widely

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

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.

[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

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.

Collector Size or Range Independence of SNR in Fixed-Focus Remote Raman Spectrometry.

PubMed

Hirschfeld, T

1974-07-01

When sensitivity allows, remote Raman spectrometers can be operated at a fixed focus with purely electronic (easily multiplexable) range gating. To keep the background small, the system etendue must be minimized. For a maximum range larger than the hyperfocal one, this is done by focusing the system at roughly twice the minimum range at which etendue matching is still required. Under these conditions the etendue varies as the fourth power of the collector diameter, causing the background shot noise to vary as its square. As the signal also varies with the same power, and background noise is usually limiting in this type instrument, the SNR becomes independent of the collector size. Below this minimum etendue-matched range, the transmission at the limiting aperture grows with the square of the range, canceling the inverse square loss of signal with range. The SNR is thus range independent below the minimum etendue matched range and collector size independent above it, with the location of transition being determined by the system etendue and collector diameter. The range of validity of these outrageousstatements is discussed.

Raman active components of skin cancer.

PubMed

Feng, Xu; Moy, Austin J; Nguyen, Hieu T M; Zhang, Jason; Fox, Matthew C; Sebastian, Katherine R; Reichenberg, Jason S; Markey, Mia K; Tunnell, James W

2017-06-01

Raman spectroscopy (RS) has shown great potential in noninvasive cancer screening. Statistically based algorithms, such as principal component analysis, are commonly employed to provide tissue classification; however, they are difficult to relate to the chemical and morphological basis of the spectroscopic features and underlying disease. As a result, we propose the first Raman biophysical model applied to in vivo skin cancer screening data. We expand upon previous models by utilizing in situ skin constituents as the building blocks, and validate the model using previous clinical screening data collected from a Raman optical fiber probe. We built an 830nm confocal Raman microscope integrated with a confocal laser-scanning microscope. Raman imaging was performed on skin sections spanning various disease states, and multivariate curve resolution (MCR) analysis was used to resolve the Raman spectra of individual in situ skin constituents. The basis spectra of the most relevant skin constituents were combined linearly to fit in vivo human skin spectra. Our results suggest collagen, elastin, keratin, cell nucleus, triolein, ceramide, melanin and water are the most important model components. We make available for download (see supplemental information) a database of Raman spectra for these eight components for others to use as a reference. Our model reveals the biochemical and structural makeup of normal, nonmelanoma and melanoma skin cancers, and precancers and paves the way for future development of this approach to noninvasive skin cancer diagnosis.

Raman active components of skin cancer

PubMed Central

Feng, Xu; Moy, Austin J; Nguyen, Hieu T. M.; Zhang, Jason; Fox, Matthew C.; Sebastian, Katherine R.; Reichenberg, Jason S.; Markey, Mia K.; Tunnell, James W.

2017-01-01

Raman spectroscopy (RS) has shown great potential in noninvasive cancer screening. Statistically based algorithms, such as principal component analysis, are commonly employed to provide tissue classification; however, they are difficult to relate to the chemical and morphological basis of the spectroscopic features and underlying disease. As a result, we propose the first Raman biophysical model applied to in vivo skin cancer screening data. We expand upon previous models by utilizing in situ skin constituents as the building blocks, and validate the model using previous clinical screening data collected from a Raman optical fiber probe. We built an 830nm confocal Raman microscope integrated with a confocal laser-scanning microscope. Raman imaging was performed on skin sections spanning various disease states, and multivariate curve resolution (MCR) analysis was used to resolve the Raman spectra of individual in situ skin constituents. The basis spectra of the most relevant skin constituents were combined linearly to fit in vivo human skin spectra. Our results suggest collagen, elastin, keratin, cell nucleus, triolein, ceramide, melanin and water are the most important model components. We make available for download (see supplemental information) a database of Raman spectra for these eight components for others to use as a reference. Our model reveals the biochemical and structural makeup of normal, nonmelanoma and melanoma skin cancers, and precancers and paves the way for future development of this approach to noninvasive skin cancer diagnosis. PMID:28663910

Raman scattering of Cisplatin near silver nanoparticles

NASA Astrophysics Data System (ADS)

Mirsaleh-Kohan, Nasrin; Duplanty, Michael; Torres, Marjorie; Moazzezi, Mojtaba; Rostovtsev, Yuri V.

2018-03-01

The Raman scattering of Cisplatin (the first generation of anticancer drugs) has been studied. In the presence of silver nanoparticles, strong modifications of Raman spectra have been observed. The Raman frequencies have been shifted and the line profiles are broadened. We develop a theoretical model to explain the observed features of the Raman scattering. The model takes into account self-consistently the interaction of molecules with surface plasmonic waves excited in the silver nanoparticles, and it provides a qualitative agreement with the observed Raman spectra. We have demonstrated that the using silver nanoparticles can increase sensitivity of the technique, and potentially it has a broader range of applications to both spectroscopy and microscopy.

Use of Bloom's Taxonomy in Developing Reading Comprehension Specifications

ERIC Educational Resources Information Center

Luebke, Stephen; Lorie, James

2013-01-01

This article is a brief account of the use of Bloom's Taxonomy of Educational Objectives (Bloom, Engelhart, Furst, Hill, & Krathwohl, 1956) by staff of the Law School Admission Council in the 1990 development of redesigned specifications for the Reading Comprehension section of the Law School Admission Test. Summary item statistics for the…

Merlin C. Wittrock and the Revision of Bloom's Taxonomy

ERIC Educational Resources Information Center

Krathwohl, David R.; Anderson, Lorin W.

2010-01-01

Merl Wittrock, a cognitive psychologist who had proposed a generative model of learning, was an essential member of the group that over a period of 5 years revised the "Taxonomy of Educational Objectives," originally published in 1956. This article describes the development of that 2001 revision (Anderson and Krathwohl, Editors) and Merl's…

Fail Better: Toward a Taxonomy of E-Learning Error

ERIC Educational Resources Information Center

Priem, Jason

2010-01-01

The study of student error, important across many fields of educational research, has begun to attract interest in the field of e-learning, particularly in relation to usability. However, it remains unclear when errors should be avoided (as usability failures) or embraced (as learning opportunities). Many domains have benefited from taxonomies of…

Learning Assessment in Tertiary Business Education with Revised Taxonomy

ERIC Educational Resources Information Center

Hossain, Md. Shajjad

2017-01-01

The goal of this study was to evaluate the assessment criteria of learning in tertiary education of Bangladesh. The study was aimed at identifying percentage of questions during learning assessment of business graduates following cognitive levels of Bloom's in revised Taxonomy and to test whether there was any significant difference in the…

Taxonomy development and knowledge representation of nurses' personal cognitive artifacts.

PubMed

McLane, Sharon; Turley, James P

2009-11-14

Nurses prepare knowledge representations, or summaries of patient clinical data, each shift. These knowledge representations serve multiple purposes, including support of working memory, workload organization and prioritization, critical thinking, and reflection. This summary is integral to internal knowledge representations, working memory, and decision-making. Study of this nurse knowledge representation resulted in development of a taxonomy of knowledge representations necessary to nursing practice.This paper describes the methods used to elicit the knowledge representations and structures necessary for the work of clinical nurses, described the development of a taxonomy of this knowledge representation, and discusses translation of this methodology to the cognitive artifacts of other disciplines. Understanding the development and purpose of practitioner's knowledge representations provides important direction to informaticists seeking to create information technology alternatives. The outcome of this paper is to suggest a process template for transition of cognitive artifacts to an information system.

Raman imaging of lipid bilayer membrane by surface enhanced Raman scattering

NASA Astrophysics Data System (ADS)

Mori, Motoaki; Abe, Shunsuke; Kondo, Takahiro; Saito, Yuika

2018-04-01

We investigated two-dimensional lipid bilayers by spectroscopic imaging with surface enhanced Raman spectroscopy (SERS). A DSPC lipid bilayer incubated on a glass substrate was coated with a thin layer of silver. Due to the strong electromagnetic enhancement of the silver film and the affinity to lipid molecules, the Raman spectrum of a single bilayer was obtained in a 1 s exposure time with 0.1 mW of incident laser power. In the C-H vibrational region of the spectra, which is sensitive to bilayer configurations, a randomly stacked area was dominated by the CH3 asymmetric-stretch mode, whereas flat areas including double bilayers showed typical SERS spectra. The spectral features of the randomly stacked area are explained by the existence of many free lipid molecules, which is supported by DFT calculations of paired DSPC molecules. Our method can be applied to reveal the local crystallinity of single lipid bilayers, which is difficult to assess by conventional Raman imaging.

Developing the FARSEEING Taxonomy of Technologies: Classification and description of technology use (including ICT) in falls prevention studies.

PubMed

Boulton, Elisabeth; Hawley-Hague, Helen; Vereijken, Beatrix; Clifford, Amanda; Guldemond, Nick; Pfeiffer, Klaus; Hall, Alex; Chesani, Federico; Mellone, Sabato; Bourke, Alan; Todd, Chris

2016-06-01

Recent Cochrane reviews on falls and fall prevention have shown that it is possible to prevent falls in older adults living in the community and in care facilities. Technologies aimed at fall detection, assessment, prediction and prevention are emerging, yet there has been no consistency in describing or reporting on interventions using technologies. With the growth of eHealth and data driven interventions, a common language and classification is required. The FARSEEING Taxonomy of Technologies was developed as a tool for those in the field of biomedical informatics to classify and characterise components of studies and interventions. The Taxonomy Development Group (TDG) comprised experts from across Europe. Through face-to-face meetings and contributions via email, five domains were developed, modified and agreed: Approach; Base; Components of outcome measures; Descriptors of technologies; and Evaluation. Each domain included sub-domains and categories with accompanying definitions. The classification system was tested against published papers and further amendments undertaken, including development of an online tool. Six papers were classified by the TDG with levels of consensus recorded. Testing the taxonomy with papers highlighted difficulties in definitions across international healthcare systems, together with differences of TDG members' backgrounds. Definitions were clarified and amended accordingly, but some difficulties remained. The taxonomy and manual were large documents leading to a lengthy classification process. The development of the online application enabled a much simpler classification process, as categories and definitions appeared only when relevant. Overall consensus for the classified papers was 70.66%. Consensus scores increased as modifications were made to the taxonomy. The FARSEEING Taxonomy of Technologies presents a common language, which should now be adopted in the field of biomedical informatics. In developing the taxonomy as an

Raman Hyperspectral Imaging of Microfossils: Potential Pitfalls

PubMed Central

Olcott Marshall, Alison

2013-01-01

Abstract Initially, Raman spectroscopy was a specialized technique used by vibrational spectroscopists; however, due to rapid advancements in instrumentation and imaging techniques over the last few decades, Raman spectrometers are widely available at many institutions, allowing Raman spectroscopy to become a widespread analytical tool in mineralogy and other geological sciences. Hyperspectral imaging, in particular, has become popular due to the fact that Raman spectroscopy can quickly delineate crystallographic and compositional differences in 2-D and 3-D at the micron scale. Although this rapid growth of applications to the Earth sciences has provided great insight across the geological sciences, the ease of application as the instruments become increasingly automated combined with nonspecialists using this techique has resulted in the propagation of errors and misunderstandings throughout the field. For example, the literature now includes misassigned vibration modes, inappropriate spectral processing techniques, confocal depth of laser penetration incorrectly estimated into opaque crystalline solids, and a misconstrued understanding of the anisotropic nature of sp2 carbons. Key Words: Raman spectroscopy—Raman imaging—Confocal Raman spectroscopy—Disordered sp2 carbons—Hematite—Microfossils. Astrobiology 13, 920–931. PMID:24088070

Evaluation of Shifted Excitation Raman Difference Spectroscopy and Comparison to Computational Background Correction Methods Applied to Biochemical Raman Spectra.

PubMed

Cordero, Eliana; Korinth, Florian; Stiebing, Clara; Krafft, Christoph; Schie, Iwan W; Popp, Jürgen

2017-07-27

Raman spectroscopy provides label-free biochemical information from tissue samples without complicated sample preparation. The clinical capability of Raman spectroscopy has been demonstrated in a wide range of in vitro and in vivo applications. However, a challenge for in vivo applications is the simultaneous excitation of auto-fluorescence in the majority of tissues of interest, such as liver, bladder, brain, and others. Raman bands are then superimposed on a fluorescence background, which can be several orders of magnitude larger than the Raman signal. To eliminate the disturbing fluorescence background, several approaches are available. Among instrumentational methods shifted excitation Raman difference spectroscopy (SERDS) has been widely applied and studied. Similarly, computational techniques, for instance extended multiplicative scatter correction (EMSC), have also been employed to remove undesired background contributions. Here, we present a theoretical and experimental evaluation and comparison of fluorescence background removal approaches for Raman spectra based on SERDS and EMSC.

Role of Raman spectroscopy and surface enhanced Raman spectroscopy in colorectal cancer

PubMed Central

Jenkins, Cerys A; Lewis, Paul D; Dunstan, Peter R; Harris, Dean A

2016-01-01

Colorectal cancer (CRC) is the fourth most common cancer in the United Kingdom and is the second largest cause of cancer related death in the United Kingdom after lung cancer. Currently in the United Kingdom there is not a diagnostic test that has sufficient differentiation between patients with cancer and those without cancer so the current referral system relies on symptomatic presentation in a primary care setting. Raman spectroscopy and surface enhanced Raman spectroscopy (SERS) are forms of vibrational spectroscopy that offer a non-destructive method to gain molecular information about biological samples. The techniques offer a wide range of applications from in vivo or in vitro diagnostics using endoscopic probes, to the use of micro-spectrometers for analysis of biofluids. The techniques have the potential to detect molecular changes prior to any morphological changes occurring in the tissue and therefore could offer many possibilities to aid the detection of CRC. The purpose of this review is to look at the current state of diagnostic technology in the United Kingdom. The development of Raman spectroscopy and SERS in clinical applications relation for CRC will then be discussed. Finally, future areas of research of Raman/SERS as a clinical tool for the diagnosis of CRC are also discussed. PMID:27190582

Taxonomies of Organizational Change: Literature Review and Analysis

DTIC Science & Technology

1978-09-01

operational terms presented a sig- nificant problem. The redundancy and circularity in discussions of variable groups reflects this dilemma . -34...Behavioral event and structured inteview protocols to be used to collect data from internal Army OE change agent and client subjects are presented with a...TABLE 22: Data Collection Method Proposed for Each Intervention Variable 168 *1 ABSTRACT This report presents a taxonomy and data collection method

The evolution of trypanosomatid taxonomy.

PubMed

Kaufer, Alexa; Ellis, John; Stark, Damien; Barratt, Joel

2017-06-08

Trypanosomatids are protozoan parasites of the class Kinetoplastida predominately restricted to invertebrate hosts (i.e. possess a monoxenous life-cycle). However, several genera are pathogenic to humans, animals and plants, and have an invertebrate vector that facilitates their transmission (i.e. possess a dixenous life-cycle). Phytomonas is one dixenous genus that includes several plant pathogens transmitted by phytophagous insects. Trypanosoma and Leishmania are dixenous genera that infect vertebrates, including humans, and are transmitted by hematophagous invertebrates. Traditionally, monoxenous trypanosomatids such as Leptomonas were distinguished from morphologically similar dixenous species based on their restriction to an invertebrate host. Nonetheless, this criterion is somewhat flawed as exemplified by Leptomonas seymouri which reportedly infects vertebrates opportunistically. Similarly, Novymonas and Zelonia are presumably monoxenous genera yet sit comfortably in the dixenous clade occupied by Leishmania. The isolation of Leishmania macropodum from a biting midge (Forcipomyia spp.) rather than a phlebotomine sand fly calls into question the exclusivity of the Leishmania-sand fly relationship, and its suitability for defining the Leishmania genus. It is now accepted that classic genus-defining characteristics based on parasite morphology and host range are insufficient to form the sole basis of trypanosomatid taxonomy as this has led to several instances of paraphyly. While improvements have been made, resolution of evolutionary relationships within the Trypanosomatidae is confounded by our incomplete knowledge of its true diversity. The known trypanosomatids probably represent a fraction of those that exist and isolation of new species will help resolve relationships in this group with greater accuracy. This review incites a dialogue on how our understanding of the relationships between certain trypanosomatids has shifted, and discusses new knowledge

The Athena Raman Spectrometer

NASA Technical Reports Server (NTRS)

Wang, Alian; Haskin, Larry A.; Jolliff, Bradley; Wdowiak, Tom; Agresti, David; Lane, Arthur L.

2000-01-01

Raman spectroscopy provides a powerful tool for in situ mineralogy, petrology, and detection of water and carbon. The Athena Raman spectrometer is a microbeam instrument intended for close-up analyses of targets (rock or soils) selected by the Athena Pancam and Mini-TES. It will take 100 Raman spectra along a linear traverse of approximately one centimeter (point-counting procedure) in one to four hours during the Mars' night. From these spectra, the following information about the target will extracted: (1) the identities of major, minor, and trace mineral phases, organic species (e.g., PAH or kerogen-like polymers), reduced inorganic carbon, and water-bearing phases; (2) chemical features (e.g. Mg/Fe ratio) of major minerals; and (3) rock textural features (e.g., mineral clusters, amygdular filling and veins). Part of the Athena payload, the miniaturized Raman spectrometer has been under development in a highly interactive collaboration of a science team at Washington University and the University of Alabama at Birmingham, and an engineering team at the Jet Propulsion Laboratory. The development has completed the brassboard stage and has produced the design for the engineering model.

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…

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.

Clinical decision support alert malfunctions: analysis and empirically derived taxonomy.

PubMed

Wright, Adam; Ai, Angela; Ash, Joan; Wiesen, Jane F; Hickman, Thu-Trang T; Aaron, Skye; McEvoy, Dustin; Borkowsky, Shane; Dissanayake, Pavithra I; Embi, Peter; Galanter, William; Harper, Jeremy; Kassakian, Steve Z; Ramoni, Rachel; Schreiber, Richard; Sirajuddin, Anwar; Bates, David W; Sittig, Dean F

2018-05-01

To develop an empirically derived taxonomy of clinical decision support (CDS) alert malfunctions. We identified CDS alert malfunctions using a mix of qualitative and quantitative methods: (1) site visits with interviews of chief medical informatics officers, CDS developers, clinical leaders, and CDS end users; (2) surveys of chief medical informatics officers; (3) analysis of CDS firing rates; and (4) analysis of CDS overrides. We used a multi-round, manual, iterative card sort to develop a multi-axial, empirically derived taxonomy of CDS malfunctions. We analyzed 68 CDS alert malfunction cases from 14 sites across the United States with diverse electronic health record systems. Four primary axes emerged: the cause of the malfunction, its mode of discovery, when it began, and how it affected rule firing. Build errors, conceptualization errors, and the introduction of new concepts or terms were the most frequent causes. User reports were the predominant mode of discovery. Many malfunctions within our database caused rules to fire for patients for whom they should not have (false positives), but the reverse (false negatives) was also common. Across organizations and electronic health record systems, similar malfunction patterns recurred. Challenges included updates to code sets and values, software issues at the time of system upgrades, difficulties with migration of CDS content between computing environments, and the challenge of correctly conceptualizing and building CDS. CDS alert malfunctions are frequent. The empirically derived taxonomy formalizes the common recurring issues that cause these malfunctions, helping CDS developers anticipate and prevent CDS malfunctions before they occur or detect and resolve them expediently.

Resolved discrepancies between visible spontaneous Raman cross-section and direct near-infrared Raman gain measurements in TeO2-based glasses.

PubMed

Rivero, Clara; Stegeman, Robert; Couzi, Michel; Talaga, David; Cardinal, Thierry; Richardson, Kathleen; Stegeman, George

2005-06-13

Disagreements on the Raman gain response of different tellurite-based glasses, measured at different wavelengths, have been recently reported in the literature. In order to resolve this controversy, a multi-wavelength Raman cross-section experiment was conducted on two different TeO2-based glass samples. The estimated Raman gain response of the material shows good agreement with the directly-measured Raman gain data at 1064 nm, after correction for the dispersion and wavelength-dependence of the Raman gain process.

Development of 873 nm Raman Seed Pulse for Raman-seeded Laser Wakefield Acceleration

NASA Astrophysics Data System (ADS)

Grigsby, F.; Peng, D.; Downer, M. C.

2004-12-01

By using a Raman-shifted seed pulse coincident with a main driving pulse, laser wakefields can be generated with sub-relativistic intensity, coherent control and high repetition rate in the self-modulated regime. Experimentally, the generation of a chirped Stokes laser pulse by inserting a solid state Raman shifter, Ba(NO3)2, into a CPA system before the compressor (to suppress self-phase modulation) will be described. We will also report on design, modeling and experimental demonstration of a novel compressor for the Stokes pulse that uses a mismatched grating pair to achieve a near transform-limited seed pulse. Finally, we will describe the design, simulation and current status of Raman-seeded LWFA experiments that use this novel source.

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

PubMed Central

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

2007-01-01

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

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

PubMed

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

2007-08-01

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

From cognition to the system: developing a multilevel taxonomy of patient safety in general practice.