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Journal of the Medical Library... Jul 2015Information professionals who train or instruct others can use Bloom's taxonomy to write learning objectives that describe the skills and abilities that they desire...
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.
Topics: Classification; Cognition; Humans; Learning; Models, Educational; Observer Variation; Teaching
PubMed: 26213509
DOI: 10.3163/1536-5050.103.3.010 -
Microbiology Spectrum Sep 2017The kingdom Fungi is one of the more diverse clades of eukaryotes in terrestrial ecosystems, where they provide numerous ecological services ranging from decomposition... (Review)
Review
The kingdom Fungi is one of the more diverse clades of eukaryotes in terrestrial ecosystems, where they provide numerous ecological services ranging from decomposition of organic matter and nutrient cycling to beneficial and antagonistic associations with plants and animals. The evolutionary relationships of the kingdom have represented some of the more recalcitrant problems in systematics and phylogenetics. The advent of molecular phylogenetics, and more recently phylogenomics, has greatly advanced our understanding of the patterns and processes associated with fungal evolution, however. In this article, we review the major phyla, subphyla, and classes of the kingdom Fungi and provide brief summaries of ecologies, morphologies, and exemplar taxa. We also provide examples of how molecular phylogenetics and evolutionary genomics have advanced our understanding of fungal evolution within each of the phyla and some of the major classes. In the current classification we recognize 8 phyla, 12 subphyla, and 46 classes within the kingdom. The ancestor of fungi is inferred to be zoosporic, and zoosporic fungi comprise three lineages that are paraphyletic to the remainder of fungi. Fungi historically classified as zygomycetes do not form a monophyletic group and are paraphyletic to Ascomycota and Basidiomycota. Ascomycota and Basidiomycota are each monophyletic and collectively form the subkingdom Dikarya.
Topics: Animals; Classification; Evolution, Molecular; Fungi; Genome, Fungal; Phylogeny; Plants
PubMed: 28917057
DOI: 10.1128/microbiolspec.FUNK-0053-2016 -
Applied and Environmental Microbiology Aug 2007The Ribosomal Database Project (RDP) Classifier, a naïve Bayesian classifier, can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order...
The Ribosomal Database Project (RDP) Classifier, a naïve Bayesian classifier, can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes (2nd ed., release 5.0, Springer-Verlag, New York, NY, 2004). It provides taxonomic assignments from domain to genus, with confidence estimates for each assignment. The majority of classifications (98%) were of high estimated confidence (> or = 95%) and high accuracy (98%). In addition to being tested with the corpus of 5,014 type strain sequences from Bergey's outline, the RDP Classifier was tested with a corpus of 23,095 rRNA sequences as assigned by the NCBI into their alternative higher-order taxonomy. The results from leave-one-out testing on both corpora show that the overall accuracies at all levels of confidence for near-full-length and 400-base segments were 89% or above down to the genus level, and the majority of the classification errors appear to be due to anomalies in the current taxonomies. For shorter rRNA segments, such as those that might be generated by pyrosequencing, the error rate varied greatly over the length of the 16S rRNA gene, with segments around the V2 and V4 variable regions giving the lowest error rates. The RDP Classifier is suitable both for the analysis of single rRNA sequences and for the analysis of libraries of thousands of sequences. Another related tool, RDP Library Compare, was developed to facilitate microbial-community comparison based on 16S rRNA gene sequence libraries. It combines the RDP Classifier with a statistical test to flag taxa differentially represented between samples. The RDP Classifier and RDP Library Compare are available online at http://rdp.cme.msu.edu/.
Topics: Algorithms; Bacteria; Bayes Theorem; Classification; Databases, Nucleic Acid; Phylogeny; RNA, Ribosomal; RNA, Ribosomal, 16S
PubMed: 17586664
DOI: 10.1128/AEM.00062-07 -
Health Technology Assessment... Nov 2015Meeting global health challenges requires effective behaviour change interventions (BCIs). This depends on advancing the science of behaviour change which, in turn,... (Randomized Controlled Trial)
Randomized Controlled Trial
Behaviour change techniques: the development and evaluation of a taxonomic method for reporting and describing behaviour change interventions (a suite of five studies involving consensus methods, randomised controlled trials and analysis of qualitative data).
BACKGROUND
Meeting global health challenges requires effective behaviour change interventions (BCIs). This depends on advancing the science of behaviour change which, in turn, depends on accurate intervention reporting. Current reporting often lacks detail, preventing accurate replication and implementation. Recent developments have specified intervention content into behaviour change techniques (BCTs) - the 'active ingredients', for example goal-setting, self-monitoring of behaviour. BCTs are 'the smallest components compatible with retaining the postulated active ingredients, i.e. the proposed mechanisms of change. They can be used alone or in combination with other BCTs' (Michie S, Johnston M. Theories and techniques of behaviour change: developing a cumulative science of behaviour change. Health Psychol Rev 2012;6:1-6). Domain-specific taxonomies of BCTs have been developed, for example healthy eating and physical activity, smoking cessation and alcohol consumption. We need to build on these to develop an internationally shared language for specifying and developing interventions. This technology can be used for synthesising evidence, implementing effective interventions and testing theory. It has enormous potential added value for science and global health.
OBJECTIVE
(1) To develop a method of specifying content of BCIs in terms of component BCTs; (2) to lay a foundation for a comprehensive methodology applicable to different types of complex interventions; (3) to develop resources to support application of the taxonomy; and (4) to achieve multidisciplinary and international acceptance for future development.
DESIGN AND PARTICIPANTS
Four hundred participants (systematic reviewers, researchers, practitioners, policy-makers) from 12 countries engaged in investigating, designing and/or delivering BCIs. Development of the taxonomy involved a Delphi procedure, an iterative process of revisions and consultation with 41 international experts; hierarchical structure of the list was developed using inductive 'bottom-up' and theory-driven 'top-down' open-sort procedures (n = 36); training in use of the taxonomy (1-day workshops and distance group tutorials) (n = 161) was evaluated by changes in intercoder reliability and validity (agreement with expert consensus); evaluating the taxonomy for coding interventions was assessed by reliability (intercoder; test-retest) and validity (n = 40 trained coders); and evaluating the taxonomy for writing descriptions was assessed by reliability (intercoder; test-retest) and by experimentally testing its value (n = 190).
RESULTS
Ninety-three distinct, non-overlapping BCTs with clear labels and definitions formed Behaviour Change Technique Taxonomy version 1 (BCTTv1). BCTs clustered into 16 groupings using a 'bottom-up' open-sort procedure; there was overlap between these and groupings produced by a theory-driven, 'top-down' procedure. Both training methods improved validity (both p < 0.05), doubled the proportion of coders achieving competence and improved confidence in identifying BCTs in workshops (both p < 0.001) but did not improve intercoder reliability. Good intercoder reliability was observed for 80 of the 93 BCTs. Good within-coder agreement was observed after 1 month (p < 0.001). Validity was good for 14 of 15 BCTs in the descriptions. The usefulness of BCTTv1 to report descriptions of observed interventions had mixed results.
CONCLUSIONS
The developed taxonomy (BCTTv1) provides a methodology for identifying content of complex BCIs and a foundation for international cross-disciplinary collaboration for developing more effective interventions to improve health. Further work is needed to examine its usefulness for reporting interventions.
FUNDING
This project was funded by the Medical Research Council Ref: G0901474/1. Funding also came from the Peninsula Collaboration for Leadership in Applied Health Research and Care.
Topics: Behavior Therapy; Classification; Data Accuracy; Delphi Technique; Global Health; Health Behavior; Humans; Qualitative Research; Randomized Controlled Trials as Topic; Technology Assessment, Biomedical
PubMed: 26616119
DOI: 10.3310/hta19990 -
Proceedings of the National Academy of... Nov 1977A phylogenetic analysis based upon ribosomal RNA sequence characterization reveals that living systems represent one of three aboriginal lines of descent: (i) the...
A phylogenetic analysis based upon ribosomal RNA sequence characterization reveals that living systems represent one of three aboriginal lines of descent: (i) the eubacteria, comprising all typical bacteria; (ii) the archaebacteria, containing methanogenic bacteria; and (iii) the urkaryotes, now represented in the cytoplasmic component of eukaryotic cells.
Topics: Bacteria; Cells; Eukaryotic Cells; Phenotype; Phylogeny; Prokaryotic Cells
PubMed: 270744
DOI: 10.1073/pnas.74.11.5088 -
Scientific Reports Dec 2023There are 5 million fungal species. However, the discovery and classification of fungi are in high flux. Modern concepts indicate that the three kingdoms of “fungi”...
There are 5 million fungal species. However, the discovery and classification of fungi are in high flux. Modern concepts indicate that the three kingdoms of “fungi” are and . Strong support for the wrong phylogeny can occur without correct analytical methods. In the current Collection we envisaged fungi representing extremely diverse and ancient eukaryotic organisms, with familiar groups such as mushrooms, yeasts and “moulds”. We collected 6 fascinating papers in three areas of Diversity, Chemical Diversity and Evolution.
Topics: Phylogeny; Fungi
PubMed: 38052958
DOI: 10.1038/s41598-023-48471-0 -
Infection, Genetics and Evolution :... Dec 2016The International Committee for the Taxonomy and Nomenclature of Viruses does not rule on virus classifications below the species level. The definition of species for... (Review)
Review
The International Committee for the Taxonomy and Nomenclature of Viruses does not rule on virus classifications below the species level. The definition of species for viruses cannot be clearly defined for all types of viruses. The complex and interesting epidemiology of Human Immunodeficiency Viruses demands a detailed and informative nomenclature system, while at the same time it presents challenges such that many of the rules need to be flexibly applied or modified over time. This review outlines the nomenclature system for primate lentiviruses and provides an update on new findings since the last review was written in 2000.
Topics: Animals; Humans; Lentivirus Infections; Lentiviruses, Primate; Phylogeny; Primates
PubMed: 27789390
DOI: 10.1016/j.meegid.2016.10.018 -
Systematic Biology May 2018Phylogenetic comparative methods explore the relationships between quantitative traits adjusting for shared evolutionary history. This adjustment often occurs through a...
Phylogenetic comparative methods explore the relationships between quantitative traits adjusting for shared evolutionary history. This adjustment often occurs through a Brownian diffusion process along the branches of the phylogeny that generates model residuals or the traits themselves. For high-dimensional traits, inferring all pair-wise correlations within the multivariate diffusion is limiting. To circumvent this problem, we propose phylogenetic factor analysis (PFA) that assumes a small unknown number of independent evolutionary factors arise along the phylogeny and these factors generate clusters of dependent traits. Set in a Bayesian framework, PFA provides measures of uncertainty on the factor number and groupings, combines both continuous and discrete traits, integrates over missing measurements and incorporates phylogenetic uncertainty with the help of molecular sequences. We develop Gibbs samplers based on dynamic programming to estimate the PFA posterior distribution, over 3-fold faster than for multivariate diffusion and a further order-of-magnitude more efficiently in the presence of latent traits. We further propose a novel marginal likelihood estimator for previously impractical models with discrete data and find that PFA also provides a better fit than multivariate diffusion in evolutionary questions in columbine flower development, placental reproduction transitions and triggerfish fin morphometry.
Topics: Animals; Classification; Computer Simulation; Factor Analysis, Statistical; Models, Genetic; Phylogeny
PubMed: 28950376
DOI: 10.1093/sysbio/syx066 -
Bioinformatics (Oxford, England) May 2015Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally...
MOTIVATION
Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed in many bacterial and viral genomes. Here, we propose a classification model that exploits the complementary nature of alignment-based and alignment-free similarity measures with the aim to improve the accuracy with which DNA and protein sequences are characterized.
RESULTS
Our model classifies sequences using a combined sequence similarity score calculated by adaptively weighting the contribution of different sequence similarity measures. Weights are determined independently for each sequence in the test set and reflect the discriminatory ability of individual similarity measures in the training set. Because the similarity between some sequences is determined more accurately with one type of measure rather than another, our classifier allows different sets of weights to be associated with different sequences. Using five different similarity measures, we show that our model significantly improves the classification accuracy over the current composition- and alignment-based models, when predicting the taxonomic lineage for both short viral sequence fragments and complete viral sequences. We also show that our model can be used effectively for the classification of reads from a real metagenome dataset as well as protein sequences.
AVAILABILITY AND IMPLEMENTATION
All the datasets and the code used in this study are freely available at https://collaborators.oicr.on.ca/vferretti/borozan_csss/csss.html.
CONTACT
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Topics: Algorithms; Classification; DNA, Viral; Metagenomics; Models, Theoretical; Sequence Alignment; Sequence Analysis, DNA; Sequence Analysis, Protein; Viruses
PubMed: 25573913
DOI: 10.1093/bioinformatics/btv006 -
Advances in Therapy Jun 2020During the last 60 years numerous significant attempts have been made to achieve a widely acceptable terminology and histological grading for laryngeal squamous... (Review)
Review
During the last 60 years numerous significant attempts have been made to achieve a widely acceptable terminology and histological grading for laryngeal squamous intraepithelial lesions. While dysplasia was included in the pathology of the uterine cervix already in 1953, the term dysplasia was accepted in laryngeal pathology first after the Toronto Centennial Conference on Laryngeal Cancer in 1974. In 1963 Kleinsasser proposed a three-tier classification, and in 1971 Kambic and Lenart proposed a four-tier classification. Since then, four editions of the World Health Organisation (WHO) classification have been proposed (1978, 1991, 2005 and 2017). Several terms such as squamous intraepithelial neoplasia (SIN) and laryngeal intraepithelial neoplasia (LIN) are now being abandoned and replaced by squamous intraepithelial lesions (SIL). The essential change between the 2005 and 2017 WHO classifications is the attempt to induce a simplification from a four- to a two-tier system. The current WHO classification (2017) thus recommends the use of a two-tier system with reasonably clear histopathological criteria for the two groups: low-grade and high-grade dysplasia. Problems with interobserver variability apart, subjectivities and uncertainties remain, but to a lesser degree. Ongoing and additional molecular studies may help to clarify underlying events that will increase our understanding and possibly can facilitate our attempts to obtain an even better classification. The classification needs to be easier for the general pathologist to perform and easier for the clinician to interpret. These two objectives are equally important to provide each patient the best personalised treatment available for squamous intraepithelial lesions.
Topics: Carcinoma in Situ; Classification; History; Humans; Laryngeal Diseases; Laryngeal Neoplasms; Precancerous Conditions
PubMed: 32329013
DOI: 10.1007/s12325-020-01348-4